diff --git a/README.Rmd b/README.Rmd index 6f0b78a..c5e8305 100644 --- a/README.Rmd +++ b/README.Rmd @@ -57,6 +57,8 @@ devtools::install_github("diazrenata/birdsize") library(birdsize) ``` +Note that, while the package itself depends only on R>= 2.10, the vignettes use the base R pipe (`|>`), which was introduced in R 4.1.0. + ## Core functions ## Estimating body masses for a population diff --git a/README.md b/README.md index 074541c..59edf6b 100644 --- a/README.md +++ b/README.md @@ -90,6 +90,9 @@ devtools::install_github("diazrenata/birdsize") library(birdsize) ``` +Note that, while the package itself depends only on R\>= 2.10, the +vignettes use the base R pipe (`|>`), which was introduced in R 4.1.0. + ## Core functions ## Estimating body masses for a population diff --git a/docs/404.html b/docs/404.html index 7b54ff4..cd8b01b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -61,6 +61,9 @@ <a href="articles/species.html">species</a> </li> </ul> +</li> +<li> + <a href="news/index.html">Changelog</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index eda3851..393e380 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -44,6 +44,9 @@ <a href="articles/species.html">species</a> </li> </ul></li> +<li> + <a href="news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 81972be..f0d3b8b 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -44,6 +44,9 @@ <a href="articles/species.html">species</a> </li> </ul></li> +<li> + <a href="news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/LICENSE.html b/docs/LICENSE.html index a6ee98a..a82ecfe 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -44,6 +44,9 @@ <a href="articles/species.html">species</a> </li> </ul></li> +<li> + <a href="news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/articles/bbs-data.html b/docs/articles/bbs-data.html index 72b8174..7c2a020 100644 --- a/docs/articles/bbs-data.html +++ b/docs/articles/bbs-data.html @@ -62,6 +62,9 @@ <a href="../articles/species.html">species</a> </li> </ul> +</li> +<li> + <a href="../news/index.html">Changelog</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -119,8 +122,7 @@ <h3 id="obtaining-data">Obtaining data<a class="anchor" aria-label="anchor" href the column names, see the Help page for <a href="../reference/demo_route_raw.html">demo_route_raw</a> or the metadata available on ScienceBase.</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">demo_raw_data</span> <span class="op"><-</span> <span class="fu">birdsize</span><span class="fu">::</span><span class="va"><a href="../reference/demo_route_raw.html">demo_route_raw</a></span></span> +<code class="sourceCode R"><span><span class="va">demo_raw_data</span> <span class="op"><-</span> <span class="fu">birdsize</span><span class="fu">::</span><span class="va"><a href="../reference/demo_route_raw.html">demo_route_raw</a></span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">demo_raw_data</span><span class="op">)</span></span> <span><span class="co">#> record_id routedataid countrynum statenum route rpid year AOU count10</span></span> @@ -146,8 +148,7 @@ <h3 id="cleaning-data">Cleaning data<a class="anchor" aria-label="anchor" href=" (e.g. nightbirds, waterbirds) and to remove unidenitifed taxa. The <code>filter_bbs_survey</code> function performs this cleaning:</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">demo_clean_data</span> <span class="op"><-</span> <span class="fu">birdsize</span><span class="fu">::</span><span class="fu"><a href="../reference/filter_bbs_survey.html">filter_bbs_survey</a></span><span class="op">(</span><span class="va">demo_raw_data</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="va">demo_clean_data</span> <span class="op"><-</span> <span class="fu">birdsize</span><span class="fu">::</span><span class="fu"><a href="../reference/filter_bbs_survey.html">filter_bbs_survey</a></span><span class="op">(</span><span class="va">demo_raw_data</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">demo_clean_data</span><span class="op">)</span></span> <span><span class="co">#> record_id routedataid countrynum statenum route rpid year AOU count10</span></span> @@ -173,8 +174,7 @@ <h3 id="simulating-individual-level-measurements">Simulating individual-level me a community data frame of the type available from ScienceBase, the Retriever, or the included demo data:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">2022</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">2022</span><span class="op">)</span></span> <span></span> <span><span class="va">demo_community</span> <span class="op"><-</span> <span class="fu">birdsize</span><span class="fu">::</span><span class="fu"><a href="../reference/community_generate.html">community_generate</a></span><span class="op">(</span><span class="va">demo_clean_data</span><span class="op">)</span></span> <span></span> diff --git a/docs/articles/birdsize.html b/docs/articles/birdsize.html index e4d0550..025ddba 100644 --- a/docs/articles/birdsize.html +++ b/docs/articles/birdsize.html @@ -62,6 +62,9 @@ <a href="../articles/species.html">species</a> </li> </ul> +</li> +<li> + <a href="../news/index.html">Changelog</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -94,6 +97,20 @@ <h1 data-toc-skip>birdsize</h1> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/diazrenata/birdsize" class="external-link">birdsize</a></span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span> +<span><span class="co">#> Warning: package 'dplyr' was built under R version 4.3.2</span></span> +<span><span class="co">#> </span></span> +<span><span class="co">#> Attaching package: 'dplyr'</span></span> +<span><span class="co">#> The following objects are masked from 'package:stats':</span></span> +<span><span class="co">#> </span></span> +<span><span class="co">#> filter, lag</span></span> +<span><span class="co">#> The following objects are masked from 'package:base':</span></span> +<span><span class="co">#> </span></span> +<span><span class="co">#> intersect, setdiff, setequal, union</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme_get.html" class="external-link">theme_set</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <div class="section level2"> <h2 id="overview">Overview<a class="anchor" aria-label="anchor" href="#overview"></a> </h2> @@ -153,9 +170,8 @@ <h3 id="using-species-identity">Using species identity<a class="anchor" aria-lab <p>For the birds known to <code>birdsize</code> you can use the species’ code (AOU) to simulate a population directly. For the hummingbird <em>Selasphorus calliope</em>:</p> -<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">a_hundred_hummingbirds</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>, AOU <span class="op">=</span> <span class="fl">4360</span><span class="op">)</span></span> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">a_hundred_hummingbirds</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>, AOU <span class="op">=</span> <span class="fl">4360</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">a_hundred_hummingbirds</span><span class="op">)</span></span> <span><span class="co">#> AOU sim_species_id individual_mass individual_bmr mean_size sd_size</span></span> @@ -173,12 +189,12 @@ <h3 id="using-species-identity">Using species identity<a class="anchor" aria-lab <span><span class="co">#> 5 100 AOU lookup Selasphorus calliope</span></span> <span><span class="co">#> 6 100 AOU lookup Selasphorus calliope</span></span> <span></span> -<span><span class="fu">ggplot</span><span class="op">(</span><span class="va">a_hundred_hummingbirds</span>, <span class="fu">aes</span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> </span> -<span> <span class="fu">geom_histogram</span><span class="op">(</span>bins <span class="op">=</span> <span class="fl">25</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">xlab</span><span class="op">(</span><span class="st">"Mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ylab</span><span class="op">(</span><span class="st">"Count"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ggtitle</span><span class="op">(</span><span class="st">"A population of hummingbirds"</span><span class="op">)</span> </span></code></pre></div> -<p><img src="birdsize_files/figure-html/unnamed-chunk-2-1.png" width="336"></p> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">a_hundred_hummingbirds</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html" class="external-link">geom_histogram</a></span><span class="op">(</span>bins <span class="op">=</span> <span class="fl">25</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Count"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"A population of hummingbirds"</span><span class="op">)</span></span></code></pre></div> +<p><img src="birdsize_files/figure-html/unnamed-chunk-3-1.png" width="336"></p> </div> <div class="section level3"> <h3 id="using-a-known-mean-and-standard-deviation">Using a known mean and standard deviation<a class="anchor" aria-label="anchor" href="#using-a-known-mean-and-standard-deviation"></a> @@ -191,9 +207,8 @@ <h3 id="using-a-known-mean-and-standard-deviation">Using a known mean and standa <p><strong>Note that, if both mean mass and a species code are provided, the species code will be used and the mean mass provided will be ignored!</strong></p> -<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">a_hundred_hypotheticals</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>, mean_size <span class="op">=</span> <span class="fl">25</span>, sd_size <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">a_hundred_hypotheticals</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>, mean_size <span class="op">=</span> <span class="fl">25</span>, sd_size <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">a_hundred_hypotheticals</span><span class="op">)</span></span> <span><span class="co">#> AOU sim_species_id individual_mass individual_bmr mean_size sd_size abundance</span></span> @@ -211,12 +226,12 @@ <h3 id="using-a-known-mean-and-standard-deviation">Using a known mean and standa <span><span class="co">#> 5 Mean and SD provided <NA></span></span> <span><span class="co">#> 6 Mean and SD provided <NA></span></span> <span></span> -<span><span class="fu">ggplot</span><span class="op">(</span><span class="va">a_hundred_hypotheticals</span>, <span class="fu">aes</span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> </span> -<span> <span class="fu">geom_histogram</span><span class="op">(</span>bins <span class="op">=</span> <span class="fl">25</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">xlab</span><span class="op">(</span><span class="st">"Mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ylab</span><span class="op">(</span><span class="st">"Count"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ggtitle</span><span class="op">(</span><span class="st">"A population of hypothetical birds"</span>, subtitle <span class="op">=</span><span class="st">"Mean mass = 25 g\nStandard deviation = 3"</span><span class="op">)</span> </span></code></pre></div> -<p><img src="birdsize_files/figure-html/unnamed-chunk-3-1.png" width="336"></p> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">a_hundred_hypotheticals</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html" class="external-link">geom_histogram</a></span><span class="op">(</span>bins <span class="op">=</span> <span class="fl">25</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Count"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"A population of hypothetical birds"</span>, subtitle <span class="op">=</span> <span class="st">"Mean mass = 25 g\nStandard deviation = 3"</span><span class="op">)</span></span></code></pre></div> +<p><img src="birdsize_files/figure-html/unnamed-chunk-4-1.png" width="336"></p> </div> <div class="section level3"> <h3 id="using-a-known-mean-but-no-standard-deviation">Using a known mean, but no standard deviation<a class="anchor" aria-label="anchor" href="#using-a-known-mean-but-no-standard-deviation"></a> @@ -224,10 +239,8 @@ <h3 id="using-a-known-mean-but-no-standard-deviation">Using a known mean, but no <p>If the mean mass is not known or not provided, <code>pop_generate</code> will estimate the standard deviation based on scaling between the mean and standard deviation of body mass:</p> -<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span></span> -<span><span class="va">another_hundred_hypotheticals</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>, mean_size <span class="op">=</span> <span class="fl">25</span><span class="op">)</span></span> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">another_hundred_hypotheticals</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>, mean_size <span class="op">=</span> <span class="fl">25</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">another_hundred_hypotheticals</span><span class="op">)</span></span> <span><span class="co">#> AOU sim_species_id individual_mass individual_bmr mean_size sd_size</span></span> @@ -245,12 +258,12 @@ <h3 id="using-a-known-mean-but-no-standard-deviation">Using a known mean, but no <span><span class="co">#> 5 100 SD estimated from mean <NA></span></span> <span><span class="co">#> 6 100 SD estimated from mean <NA></span></span> <span></span> -<span><span class="fu">ggplot</span><span class="op">(</span><span class="va">another_hundred_hypotheticals</span>, <span class="fu">aes</span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> </span> -<span> <span class="fu">geom_histogram</span><span class="op">(</span>bins <span class="op">=</span> <span class="fl">25</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">xlab</span><span class="op">(</span><span class="st">"Mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ylab</span><span class="op">(</span><span class="st">"Count"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ggtitle</span><span class="op">(</span><span class="st">"A population of hypothetical birds"</span>, subtitle <span class="op">=</span><span class="st">"Mean mass = 25 g\nStandard deviation = 1.74"</span><span class="op">)</span> </span></code></pre></div> -<p><img src="birdsize_files/figure-html/unnamed-chunk-4-1.png" width="336"></p> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">another_hundred_hypotheticals</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html" class="external-link">geom_histogram</a></span><span class="op">(</span>bins <span class="op">=</span> <span class="fl">25</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Count"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"A population of hypothetical birds"</span>, subtitle <span class="op">=</span> <span class="st">"Mean mass = 25 g\nStandard deviation = 1.74"</span><span class="op">)</span></span></code></pre></div> +<p><img src="birdsize_files/figure-html/unnamed-chunk-5-1.png" width="336"></p> </div> </div> <div class="section level2"> @@ -266,7 +279,7 @@ <h3 id="simulations-using-aou">Simulations using AOU<a class="anchor" aria-label </h3> <p>Here, we use a synthetic dataset with records of <code>AOU</code> and <code>abundance</code> for 5 species, to make up a community:</p> -<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"toy_aou_community"</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">toy_aou_community</span><span class="op">)</span></span> @@ -284,9 +297,8 @@ <h3 id="simulations-using-aou">Simulations using AOU<a class="anchor" aria-label <code>toy_aou_community</code> to look up species’ mean and standard deviation body masses based on their AOU and then draw individual size measurements from a normal distribution with those parameters.</p> -<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">toy_aou_sims</span> <span class="op"><-</span> <span class="fu"><a href="../reference/community_generate.html">community_generate</a></span><span class="op">(</span>community_data_table <span class="op">=</span> <span class="va">toy_aou_community</span>, abundance_column_name <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">toy_aou_sims</span> <span class="op"><-</span> <span class="fu"><a href="../reference/community_generate.html">community_generate</a></span><span class="op">(</span>community_data_table <span class="op">=</span> <span class="va">toy_aou_community</span>, abundance_column_name <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">toy_aou_sims</span><span class="op">)</span></span> <span><span class="co">#> AOU sim_species_id individual_mass individual_bmr mean_size sd_size</span></span> @@ -308,20 +320,20 @@ <h3 id="simulations-using-aou">Simulations using AOU<a class="anchor" aria-label for that individual.</p> <p>We can then plot the individual size distribution for the community, colored by species ID:</p> -<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span></span> -<span><span class="va">toy_aou_sims</span><span class="op">$</span><span class="va">AOU</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="va">toy_aou_sims</span><span class="op">$</span><span class="va">AOU</span><span class="op">)</span></span> +<span><span class="va">toy_aou_sims</span><span class="op">$</span><span class="va">`Scientific name`</span> <span class="op">=</span> <span class="va">toy_aou_sims</span><span class="op">$</span><span class="va">scientific_name</span></span> <span></span> -<span><span class="fu">ggplot</span><span class="op">(</span><span class="va">toy_aou_sims</span>, <span class="fu">aes</span><span class="op">(</span><span class="va">individual_mass</span>, fill <span class="op">=</span> <span class="va">AOU</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">geom_histogram</span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">scale_fill_viridis_d</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">scale_x_log10</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ggtitle</span><span class="op">(</span><span class="st">"Community simulated via AOU"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">xlab</span><span class="op">(</span><span class="st">"Body mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ylab</span><span class="op">(</span><span class="st">"Number of individuals"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">theme</span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"right"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">toy_aou_sims</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">individual_mass</span>, fill <span class="op">=</span> <span class="va">`Scientific name`</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html" class="external-link">geom_histogram</a></span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_fill_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_x_log10</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"Community simulated via AOU"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Body mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Number of individuals"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"bottom"</span>, legend.direction <span class="op">=</span> <span class="st">"vertical"</span><span class="op">)</span></span> <span><span class="co">#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</span></span></code></pre></div> -<p><img src="birdsize_files/figure-html/unnamed-chunk-7-1.png" width="480"></p> +<p><img src="birdsize_files/figure-html/unnamed-chunk-8-1.png" width="480"></p> </div> <div class="section level3"> <h3 id="simulation-given-species-names">Simulation given species’ names<a class="anchor" aria-label="anchor" href="#simulation-given-species-names"></a> @@ -329,9 +341,8 @@ <h3 id="simulation-given-species-names">Simulation given species’ names<a clas <p>If the AOU is not known or not provided, <code>community_generate</code> will attempt to look up species’ size parameters based on their scientific name.</p> -<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"toy_species_name_community"</span><span class="op">)</span></span> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"toy_species_name_community"</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">toy_species_name_community</span><span class="op">)</span></span> <span><span class="co">#> <span style="color: #949494;"># A tibble: 5 × 2</span></span></span> @@ -346,10 +357,8 @@ <h3 id="simulation-given-species-names">Simulation given species’ names<a clas <code>sd_method</code> here is listed as <code>Scientific name lookup</code> rather than <code>AOU lookup</code> (above).</p> -<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span></span> -<span><span class="va">toy_species_name_sims</span> <span class="op"><-</span> <span class="fu"><a href="../reference/community_generate.html">community_generate</a></span><span class="op">(</span><span class="va">toy_species_name_community</span>, abundance_column_name <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">toy_species_name_sims</span> <span class="op"><-</span> <span class="fu"><a href="../reference/community_generate.html">community_generate</a></span><span class="op">(</span><span class="va">toy_species_name_community</span>, abundance_column_name <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">toy_species_name_sims</span><span class="op">)</span></span> <span><span class="co">#> AOU sim_species_id individual_mass individual_bmr mean_size sd_size</span></span> @@ -366,20 +375,19 @@ <h3 id="simulation-given-species-names">Simulation given species’ names<a clas <span><span class="co">#> 4 95 Scientific name lookup Alauda arvensis</span></span> <span><span class="co">#> 5 95 Scientific name lookup Alauda arvensis</span></span> <span><span class="co">#> 6 95 Scientific name lookup Alauda arvensis</span></span></code></pre></div> -<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">toy_species_name_sims</span><span class="op">$</span><span class="va">scientific_name</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="va">toy_species_name_sims</span><span class="op">$</span><span class="va">scientific_name</span><span class="op">)</span></span> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">toy_species_name_sims</span><span class="op">$</span><span class="va">`Scientific name`</span> <span class="op">=</span> <span class="va">toy_species_name_sims</span><span class="op">$</span><span class="va">scientific_name</span></span> <span></span> -<span><span class="fu">ggplot</span><span class="op">(</span><span class="va">toy_species_name_sims</span>, <span class="fu">aes</span><span class="op">(</span><span class="va">individual_mass</span>, fill <span class="op">=</span> <span class="va">scientific_name</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">geom_histogram</span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">scale_fill_viridis_d</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">scale_x_log10</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ggtitle</span><span class="op">(</span><span class="st">"Community simulated via scientific name"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">xlab</span><span class="op">(</span><span class="st">"Body mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ylab</span><span class="op">(</span><span class="st">"Number of individuals"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">theme</span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"right"</span>, legend.direction <span class="op">=</span> <span class="st">"vertical"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">toy_species_name_sims</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">individual_mass</span>, fill <span class="op">=</span> <span class="va">scientific_name</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html" class="external-link">geom_histogram</a></span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_fill_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_x_log10</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"Community simulated via scientific name"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Body mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Number of individuals"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"bottom"</span>, legend.direction <span class="op">=</span> <span class="st">"vertical"</span><span class="op">)</span></span> <span><span class="co">#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</span></span></code></pre></div> -<p><img src="birdsize_files/figure-html/unnamed-chunk-10-1.png" width="576"></p> +<p><img src="birdsize_files/figure-html/unnamed-chunk-11-1.png" width="480"></p> </div> <div class="section level3"> <h3 id="simulation-given-mean-size-measurements">Simulation given mean size measurements<a class="anchor" aria-label="anchor" href="#simulation-given-mean-size-measurements"></a> @@ -401,7 +409,7 @@ <h3 id="simulation-given-mean-size-measurements">Simulation given mean size meas named <code>mean_size</code> and 2) the <code>sim_species_id</code> column acts as a species identifier in the absence of other taxonomic information:</p> -<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">toy_size_community</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">toy_size_community</span><span class="op">)</span></span> @@ -413,10 +421,8 @@ <h3 id="simulation-given-mean-size-measurements">Simulation given mean size meas <span><span class="co">#> <span style="color: #BCBCBC;">3</span> 63 346 3</span></span> <span><span class="co">#> <span style="color: #BCBCBC;">4</span> 69 63.9 4</span></span> <span><span class="co">#> <span style="color: #BCBCBC;">5</span> 53 37.4 5</span></span></code></pre></div> -<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span></span> -<span><span class="va">toy_size_sims</span> <span class="op"><-</span> <span class="fu"><a href="../reference/community_generate.html">community_generate</a></span><span class="op">(</span><span class="va">toy_size_community</span>, abundance_column_name <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span> +<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">toy_size_sims</span> <span class="op"><-</span> <span class="fu"><a href="../reference/community_generate.html">community_generate</a></span><span class="op">(</span><span class="va">toy_size_community</span>, abundance_column_name <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">toy_size_sims</span><span class="op">)</span></span> <span><span class="co">#> AOU sim_species_id individual_mass individual_bmr mean_size sd_size</span></span> @@ -433,20 +439,19 @@ <h3 id="simulation-given-mean-size-measurements">Simulation given mean size meas <span><span class="co">#> 4 95 SD estimated from mean <NA></span></span> <span><span class="co">#> 5 95 SD estimated from mean <NA></span></span> <span><span class="co">#> 6 95 SD estimated from mean <NA></span></span></code></pre></div> -<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">toy_size_sims</span><span class="op">$</span><span class="va">sim_species_id</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="va">toy_size_sims</span><span class="op">$</span><span class="va">sim_species_id</span><span class="op">)</span></span> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">toy_size_sims</span><span class="op">$</span><span class="va">`Sim species ID`</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="va">toy_size_sims</span><span class="op">$</span><span class="va">sim_species_id</span><span class="op">)</span></span> <span></span> -<span><span class="fu">ggplot</span><span class="op">(</span><span class="va">toy_size_sims</span>, <span class="fu">aes</span><span class="op">(</span><span class="va">individual_mass</span>, fill <span class="op">=</span> <span class="va">sim_species_id</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">geom_histogram</span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">scale_fill_viridis_d</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">scale_x_log10</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ggtitle</span><span class="op">(</span><span class="st">"Community simulated via mean body size"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">xlab</span><span class="op">(</span><span class="st">"Body mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">ylab</span><span class="op">(</span><span class="st">"Number of individuals"</span><span class="op">)</span> <span class="op">+</span></span> -<span> <span class="fu">theme</span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"right"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">toy_size_sims</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">individual_mass</span>, fill <span class="op">=</span> <span class="va">`Sim species ID`</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html" class="external-link">geom_histogram</a></span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_fill_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_x_log10</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"Community simulated via mean body size"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Body mass (g)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Number of individuals"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"bottom"</span><span class="op">)</span></span> <span><span class="co">#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</span></span></code></pre></div> -<p><img src="birdsize_files/figure-html/unnamed-chunk-13-1.png" width="480"></p> +<p><img src="birdsize_files/figure-html/unnamed-chunk-14-1.png" width="480"></p> </div> <div class="section level3"> <h3 id="community-wide-summary-statistics">Community-wide summary statistics<a class="anchor" aria-label="anchor" href="#community-wide-summary-statistics"></a> @@ -459,14 +464,15 @@ <h3 id="community-wide-summary-statistics">Community-wide summary statistics<a c <div class="section level4"> <h4 id="biomass-total-by-species">Biomass total by species<a class="anchor" aria-label="anchor" href="#biomass-total-by-species"></a> </h4> -<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">toy_species_name_sims_summary</span> <span class="op"><-</span></span> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">toy_species_name_sims_summary</span> <span class="op"><-</span></span> <span> <span class="va">toy_species_name_sims</span> <span class="op">|></span></span> -<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">scientific_name</span><span class="op">)</span> <span class="op">|></span></span> -<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>total_mass <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span>,</span> -<span> total_n_individuals <span class="op">=</span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span> </span> +<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">scientific_name</span><span class="op">)</span> <span class="op">|></span></span> +<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span></span> +<span> total_mass <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span>,</span> +<span> total_n_individuals <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span></span> +<span> <span class="op">)</span></span> +<span></span> <span><span class="va">toy_species_name_sims_summary</span></span> <span><span class="co">#> <span style="color: #949494;"># A tibble: 5 × 3</span></span></span> <span><span class="co">#> scientific_name total_mass total_n_individuals</span></span> @@ -480,13 +486,12 @@ <h4 id="biomass-total-by-species">Biomass total by species<a class="anchor" aria <div class="section level4"> <h4 id="community-total-biomass">Community total biomass<a class="anchor" aria-label="anchor" href="#community-total-biomass"></a> </h4> -<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">toy_species_name_sims_totals</span> <span class="op"><-</span> </span> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">toy_species_name_sims_totals</span> <span class="op"><-</span></span> <span> <span class="va">toy_species_name_sims</span> <span class="op">|></span></span> -<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span></span> +<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span></span> <span> total_mass <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">individual_mass</span><span class="op">)</span>,</span> -<span> total_n_individuals <span class="op">=</span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> total_n_individuals <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> total_species_richness <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">scientific_name</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="op">)</span></span> <span></span> diff --git a/docs/articles/birdsize_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/birdsize_files/figure-html/unnamed-chunk-11-1.png new file mode 100644 index 0000000..34d8ed4 Binary files /dev/null and b/docs/articles/birdsize_files/figure-html/unnamed-chunk-11-1.png differ diff --git a/docs/articles/birdsize_files/figure-html/unnamed-chunk-14-1.png b/docs/articles/birdsize_files/figure-html/unnamed-chunk-14-1.png new file mode 100644 index 0000000..935b810 Binary files /dev/null and b/docs/articles/birdsize_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/docs/articles/birdsize_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/birdsize_files/figure-html/unnamed-chunk-3-1.png index f8fbb9a..b4dd283 100644 Binary files a/docs/articles/birdsize_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/birdsize_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/birdsize_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/birdsize_files/figure-html/unnamed-chunk-4-1.png index 76349a0..f8fbb9a 100644 Binary files a/docs/articles/birdsize_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/birdsize_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/birdsize_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/birdsize_files/figure-html/unnamed-chunk-5-1.png new file mode 100644 index 0000000..76349a0 Binary files /dev/null and b/docs/articles/birdsize_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/birdsize_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/birdsize_files/figure-html/unnamed-chunk-8-1.png new file mode 100644 index 0000000..d642f1f Binary files /dev/null and b/docs/articles/birdsize_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index a913424..eba5e0f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/articles/scaling.html b/docs/articles/scaling.html index e83a552..d7d817a 100644 --- a/docs/articles/scaling.html +++ b/docs/articles/scaling.html @@ -62,6 +62,9 @@ <a href="../articles/species.html">species</a> </li> </ul> +</li> +<li> + <a href="../news/index.html">Changelog</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -106,42 +109,103 @@ <h1 data-toc-skip>scaling</h1> uses this scaling relationship to estimate the standard deviation of body mass from the mean. This vignette illustrates the scaling relationship and how it is used in the package.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/diazrenata/birdsize" class="external-link">birdsize</a></span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span> +<span><span class="co">#> Warning: package 'dplyr' was built under R version 4.3.2</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme_get.html" class="external-link">theme_set</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p>The <code>raw_masses</code> dataset (included in <code>bbssize</code>) includes all records from the CRC Handbook (Dunning 2008) available for species in this subset of the Breeding Bird Survey.</p> -<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">raw_masses</span> <span class="op"><-</span> <span class="va">raw_masses</span></span></code></pre></div> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">raw_masses</span><span class="op">)</span></span></code></pre></div> <p>Of the 928 records in <code>raw_masses</code>, 353 are missing the standard deviation (affecting 204 species).</p> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">sp_for_sd</span> <span class="op"><-</span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span> +<span> <span class="va">raw_masses</span>,</span> +<span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">sd</span><span class="op">)</span></span> +<span><span class="op">)</span> <span class="op">|></span></span> +<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span> +<span> mass <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric</a></span><span class="op">(</span><span class="va">mass</span><span class="op">)</span>,</span> +<span> sd <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric</a></span><span class="op">(</span><span class="va">sd</span><span class="op">)</span></span> +<span> <span class="op">)</span> <span class="op">|></span></span> +<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>var <span class="op">=</span> <span class="va">sd</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span> <span class="op">|></span></span> +<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span> +<span> log_m <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="va">mass</span><span class="op">)</span>,</span> +<span> log_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="va">var</span><span class="op">)</span></span> +<span> <span class="op">)</span></span> +<span></span> +<span><span class="va">sd_fit</span> <span class="op"><-</span> <span class="fu">stats</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">sp_for_sd</span>, formula <span class="op">=</span> <span class="va">log_var</span> <span class="op">~</span> <span class="va">log_m</span><span class="op">)</span></span> +<span></span> +<span><span class="va">sd_fit_summary</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">sd_fit</span><span class="op">)</span></span> +<span></span> +<span><span class="va">sp_for_sd</span> <span class="op"><-</span> <span class="va">sp_for_sd</span> <span class="op">|></span></span> +<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>est_sd <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">sd_fit</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p>For records <em>with</em> reports of standard deviation, there is a close scaling relationship between mean and variance of body mass. A linear model of the form <code>log(variance(body_mass)) ~ log(mean(body_mass))</code> has a model R2 of 0.89.</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">sp_for_sd</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="va">log_m</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="va">log_var</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="va">est_sd</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_x_log10</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_y_log10</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"Scaling of variance with mean body mass"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Mean body mass\n(note log scale)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Variance of body mass\n(note log scale)"</span><span class="op">)</span></span></code></pre></div> <p><img src="scaling_files/figure-html/unnamed-chunk-4-1.png" width="480"></p> <p>The model parameters are:</p> -<pre><code><span><span class="co">#> (Intercept) log_m </span></span> -<span><span class="co">#> -5.373838 2.015833</span></span></code></pre> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/coef.html" class="external-link">coefficients</a></span><span class="op">(</span><span class="va">sd_fit</span><span class="op">)</span></span> +<span><span class="co">#> (Intercept) log_m </span></span> +<span><span class="co">#> -5.373838 2.015833</span></span></code></pre></div> <p>Which translate into a scaling relationship of:</p> <p><span class="math inline">\(var(m) = 0.0047\bar{m}^{2.01}\)</span></p> <p>We use this scaling relationship to estimate the standard deviations for records that have mass, but no reported standard deviation (353 records), shown in green in this plot:</p> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">raw_masses_with_estimated_sd</span> <span class="op"><-</span> <span class="va">raw_masses</span> <span class="op">|></span></span> +<span> <span class="fu">birdsize</span><span class="fu">:::</span><span class="fu"><a href="../reference/clean_sp_size_data.html">clean_sp_size_data</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|></span></span> +<span> <span class="fu">birdsize</span><span class="fu">:::</span><span class="fu"><a href="../reference/add_estimated_sds.html">add_estimated_sds</a></span><span class="op">(</span>sd_pars <span class="op">=</span> <span class="fu">birdsize</span><span class="fu">:::</span><span class="fu"><a href="../reference/get_sd_parameters.html">get_sd_parameters</a></span><span class="op">(</span><span class="va">raw_masses</span><span class="op">)</span><span class="op">)</span> <span class="op">|></span></span> +<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span> +<span> log_mass <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="va">mass</span><span class="op">)</span>,</span> +<span> var <span class="op">=</span> <span class="va">sd</span><span class="op">^</span><span class="fl">2</span></span> +<span> <span class="op">)</span> <span class="op">|></span></span> +<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span> +<span> log_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="va">var</span><span class="op">)</span>,</span> +<span> `Estimated SD` <span class="op">=</span> <span class="va">estimated_sd</span></span> +<span> <span class="op">)</span></span> +<span></span> +<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">raw_masses_with_estimated_sd</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="va">log_mass</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="va">log_var</span><span class="op">)</span>, color <span class="op">=</span> <span class="va">`Estimated SD`</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_color_viridis_d</a></span><span class="op">(</span>option <span class="op">=</span> <span class="st">"viridis"</span>, begin <span class="op">=</span> <span class="fl">.1</span>, end <span class="op">=</span> <span class="fl">.7</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"Scaling of variance with mean, with estimates included"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"Mean body mass\n(note log scale)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"Variance of body mass\n(note log scale)"</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_x_log10</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_y_log10</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> +<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"bottom"</span><span class="op">)</span></span></code></pre></div> <p><img src="scaling_files/figure-html/unnamed-chunk-6-1.png" width="480"></p> <p>The internal function <code>birdsize:::species_estimate_sd</code> can -be used to estimate the standard deviation of body mass from the -mean:</p> -<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="co"># Using species_estimate:</span></span> +be used to estimate the standard deviation of body mass from the mean. +This function is called within <code>species_define</code> to add +estimated standard deviations to records of species that have body mass +but no sd measurements.</p> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="co"># Using species_estimate:</span></span> <span><span class="fu">birdsize</span><span class="fu">:::</span><span class="fu"><a href="../reference/species_estimate_sd.html">species_estimate_sd</a></span><span class="op">(</span>sp_mean <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span> <span><span class="co">#> [1] 7.061862</span></span> <span></span> <span></span> <span><span class="co"># Calculated manually - note slight numeric discrepancy due to truncating parameters:</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">0.0047</span> <span class="op">*</span> <span class="fl">100</span> <span class="op">^</span> <span class="fl">2.01</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">0.0047</span> <span class="op">*</span> <span class="fl">100</span><span class="op">^</span><span class="fl">2.01</span><span class="op">)</span></span> <span><span class="co">#> [1] 7.015343</span></span></code></pre></div> <p>See also Thibault et al. (2011) for this scaling relationship for a slightly different subset of the Breeding Bird Survey.</p> diff --git a/docs/articles/species.html b/docs/articles/species.html index 591cc38..3295442 100644 --- a/docs/articles/species.html +++ b/docs/articles/species.html @@ -62,6 +62,9 @@ <a href="../articles/species.html">species</a> </li> </ul> +</li> +<li> + <a href="../news/index.html">Changelog</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -115,8 +118,7 @@ <h2 id="species-known-to-birdsize">Species known to <code>birdsize</code><a clas view the list of species included, examine the <code>known_species</code> data table, included:</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">known_species</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">known_species</span><span class="op">)</span></span> <span><span class="co">#> <span style="color: #949494;"># A tibble: 6 × 3</span></span></span> <span><span class="co">#> AOU genus species </span></span> <span><span class="co">#> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span></span> @@ -133,8 +135,7 @@ <h2 id="species-known-to-birdsize">Species known to <code>birdsize</code><a clas <h3 id="aou-lookup">AOU lookup<a class="anchor" aria-label="anchor" href="#aou-lookup"></a> </h3> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">hummingbird_AOU_parameters</span> <span class="op"><-</span> <span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>AOU <span class="op">=</span> <span class="fl">4360</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="va">hummingbird_AOU_parameters</span> <span class="op"><-</span> <span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>AOU <span class="op">=</span> <span class="fl">4360</span><span class="op">)</span></span> <span></span> <span><span class="va">hummingbird_AOU_parameters</span></span> <span><span class="co">#> $AOU</span></span> @@ -159,8 +160,7 @@ <h3 id="aou-lookup">AOU lookup<a class="anchor" aria-label="anchor" href="#aou-l <h3 id="scientific-name-lookup">Scientific name lookup<a class="anchor" aria-label="anchor" href="#scientific-name-lookup"></a> </h3> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">hummingbird_name_parameters</span> <span class="op"><-</span> <span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>scientific_name <span class="op">=</span> <span class="st">"Selasphorus calliope"</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="va">hummingbird_name_parameters</span> <span class="op"><-</span> <span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>scientific_name <span class="op">=</span> <span class="st">"Selasphorus calliope"</span><span class="op">)</span></span> <span></span> <span><span class="va">hummingbird_name_parameters</span></span> <span><span class="co">#> $AOU</span></span> @@ -191,12 +191,10 @@ <h3 id="unknown-species-or-aous">Unknown species or AOUs<a class="anchor" aria-l <p>Attempting to use <code>species_define</code> with an AOU or species not known to <code>birdsize</code> will return an error:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="kw"><a href="https://rdrr.io/r/base/try.html" class="external-link">try</a></span><span class="op">(</span><span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>AOU <span class="op">=</span> <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/try.html" class="external-link">try</a></span><span class="op">(</span><span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>AOU <span class="op">=</span> <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span> <span><span class="co">#> Error in species_lookup(AOU = AOU) : `AOU` is invalid.</span></span></code></pre></div> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="kw"><a href="https://rdrr.io/r/base/try.html" class="external-link">try</a></span><span class="op">(</span><span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>scientific_name <span class="op">=</span> <span class="st">"Taylor swift"</span><span class="op">)</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/try.html" class="external-link">try</a></span><span class="op">(</span><span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>scientific_name <span class="op">=</span> <span class="st">"Swiftus Taylor"</span><span class="op">)</span><span class="op">)</span></span> <span><span class="co">#> Error in species_lookup(scientific_name = scientific_name) : </span></span> <span><span class="co">#> Scientific name is invalid.</span></span></code></pre></div> </div> @@ -220,8 +218,7 @@ <h3 id="manually-supplying-species-parameters">Manually supplying species parame doesn’t have a scientific name or AOU included in <code>birdsize</code>, we label it using the arbitrary <code>sim_species_id</code> of 1.</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">hypothetical_species_parameters</span> <span class="op"><-</span> <span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>mean_size <span class="op">=</span> <span class="fl">40</span>, sd_size <span class="op">=</span> <span class="fl">2.5</span>, sim_species_id <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="va">hypothetical_species_parameters</span> <span class="op"><-</span> <span class="fu"><a href="../reference/species_define.html">species_define</a></span><span class="op">(</span>mean_size <span class="op">=</span> <span class="fl">40</span>, sd_size <span class="op">=</span> <span class="fl">2.5</span>, sim_species_id <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> <span></span> <span><span class="va">hypothetical_species_parameters</span></span> <span><span class="co">#> $AOU</span></span> @@ -247,12 +244,11 @@ <h3 id="manually-supplying-species-parameters">Manually supplying species parame <code>sim_species_id</code> to generate parameters for each species. This happens under the hood in <code>community_generate</code>.</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">multiple_species_info</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> +<code class="sourceCode R"><span><span class="va">multiple_species_info</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> mean_size <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">40</span>, <span class="fl">50</span><span class="op">)</span>,</span> <span> sd_size <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2.5</span>, <span class="fl">3</span><span class="op">)</span>,</span> <span> sim_species_id <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">3</span></span> -<span><span class="op">)</span> </span> +<span><span class="op">)</span></span> <span></span> <span></span> <span><span class="fu">pmap_df</span><span class="op">(</span><span class="va">multiple_species_info</span>, <span class="va">species_define</span><span class="op">)</span></span> @@ -266,12 +262,10 @@ <h3 id="manually-supplying-species-parameters">Manually supplying species parame <code>species_define</code> will estimate it (see the <code>scaling</code> vignette):</p> <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span></span> -<span><span class="va">multiple_species_info_no_sd</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> +<code class="sourceCode R"><span><span class="va">multiple_species_info_no_sd</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> mean_size <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">40</span>, <span class="fl">50</span><span class="op">)</span>,</span> <span> sim_species_id <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">3</span></span> -<span><span class="op">)</span> </span> +<span><span class="op">)</span></span> <span></span> <span></span> <span><span class="fu">pmap_df</span><span class="op">(</span><span class="va">multiple_species_info_no_sd</span>, <span class="va">species_define</span><span class="op">)</span></span> diff --git a/docs/authors.html b/docs/authors.html index 3ce04c3..6bc10f4 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -44,6 +44,9 @@ <a href="articles/species.html">species</a> </li> </ul></li> +<li> + <a href="news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -68,6 +71,10 @@ <h1>Authors</h1> <p><strong>Renata Diaz</strong>. Author, maintainer. <a href="https://orcid.org/0000-0003-0803-4734" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </p> </li> + <li> + <p><strong>John Dunning</strong>. Data contributor. + </p> + </li> </ul></div> <div class="section level2 citation-section"> <div> diff --git a/docs/index.html b/docs/index.html index 467cd44..82c34b1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,11 @@ <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> <script src="pkgdown.js"></script><meta property="og:title" content="Estimate Avian Body Size Distributions"> -<meta property="og:description" content="Generate estimated body size distributions for populations or communities of birds, given either species ID or species' mean body size. Designed to work naturally with the North American Breeding Bird Survey, or with any dataset of bird species, abundance, and/or mean size data. "> +<meta property="og:description" content="Generate estimated body size distributions for populations or + communities of birds, given either species ID or species' mean body + size. Designed to work naturally with the North American Breeding Bird + Survey, or with any dataset of bird species, abundance, and/or mean + size data."> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> @@ -62,6 +66,9 @@ <a href="articles/species.html">species</a> </li> </ul> +</li> +<li> + <a href="news/index.html">Changelog</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -84,7 +91,7 @@ </header><div class="row"> <div class="contents col-md-9"> <div class="section level1"> -<div class="page-header"><h1 id="birdsize">birdsize<a class="anchor" aria-label="anchor" href="#birdsize"></a> +<div class="page-header"><h1 id="birdsize-estimate-avian-body-size-distributions">birdsize: Estimate avian body size distributions<a class="anchor" aria-label="anchor" href="#birdsize-estimate-avian-body-size-distributions"></a> </h1></div> <!-- badges: start --> @@ -111,9 +118,10 @@ <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i </h2> <p>To install the in-development version:</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">'diazrenata/birdsize'</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"diazrenata/birdsize"</span><span class="op">)</span></span></code></pre></div> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/diazrenata/birdsize" class="external-link">birdsize</a></span><span class="op">)</span></span></code></pre></div> +<p>Note that, while the package itself depends only on R>= 2.10, the vignettes use the base R pipe (<code>|></code>), which was introduced in R 4.1.0.</p> </div> <div class="section level2"> <h2 id="core-functions">Core functions<a class="anchor" aria-label="anchor" href="#core-functions"></a> @@ -128,23 +136,27 @@ <h2 id="estimating-body-masses-for-a-population">Estimating body masses for a po <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">13</span><span class="op">)</span></span> <span></span> -<span><span class="va">first_population</span> <span class="op"><-</span> <span class="fu"><a href="reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>,</span> -<span> mean_size <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span> +<span><span class="va">first_population</span> <span class="op"><-</span> <span class="fu"><a href="reference/pop_generate.html">pop_generate</a></span><span class="op">(</span></span> +<span> abundance <span class="op">=</span> <span class="fl">100</span>,</span> +<span> mean_size <span class="op">=</span> <span class="fl">10</span></span> +<span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></span><span class="op">(</span><span class="va">first_population</span><span class="op">$</span><span class="va">individual_mass</span>,</span> -<span> main <span class="op">=</span> <span class="st">"First population masses"</span>, </span> -<span> xlab <span class="op">=</span> <span class="st">"Body mass (g)"</span><span class="op">)</span></span></code></pre></div> +<span> main <span class="op">=</span> <span class="st">"First population masses"</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Body mass (g)"</span></span> +<span><span class="op">)</span></span></code></pre></div> <p><img src="reference/figures/README-unnamed-chunk-4-1.png" width="100%"></p> <p>Alternatively, for a species known to <code>birdsize</code>, we can simply provide the scientific name or AOU code. Here, <em>Melanerpes carolinus</em> is the red-headed woodpecker:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span></span> -<span><span class="va">woodpecker_population</span> <span class="op"><-</span> <span class="fu"><a href="reference/pop_generate.html">pop_generate</a></span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">100</span>,</span> -<span> scientific_name <span class="op">=</span> <span class="st">"Melanerpes carolinus"</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="va">woodpecker_population</span> <span class="op"><-</span> <span class="fu"><a href="reference/pop_generate.html">pop_generate</a></span><span class="op">(</span></span> +<span> abundance <span class="op">=</span> <span class="fl">100</span>,</span> +<span> scientific_name <span class="op">=</span> <span class="st">"Melanerpes carolinus"</span></span> +<span><span class="op">)</span></span> <span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></span><span class="op">(</span><span class="va">first_population</span><span class="op">$</span><span class="va">individual_mass</span>,</span> -<span> main <span class="op">=</span> <span class="st">"M. carolinus population masses"</span>, </span> -<span> xlab <span class="op">=</span> <span class="st">"Body mass (g)"</span><span class="op">)</span></span></code></pre></div> +<span> main <span class="op">=</span> <span class="st">"M. carolinus population masses"</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Body mass (g)"</span></span> +<span><span class="op">)</span></span></code></pre></div> <p><img src="reference/figures/README-unnamed-chunk-5-1.png" width="100%"></p> </div> <div class="section level2"> @@ -153,8 +165,7 @@ <h2 id="estimating-body-masses-for-a-whole-community">Estimating body masses for <p>To generate body size estimates for a whole community, we use the <code>community_generate</code> function. <code>community_generate</code> takes population sizes and species identifiers or parameters for multiple species, and simulates populations for each species.</p> <p>We can create estimates for a hypothetical community by providing population sizes and scientific names:</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span></span> -<span><span class="va">first_community</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> +<code class="sourceCode R"><span><span class="va">first_community</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> abundance <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">50</span>, <span class="fl">100</span>, <span class="fl">150</span><span class="op">)</span>,</span> <span> scientific_name <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Melanerpes carolinus"</span>, <span class="st">"Myiarchus crinitus"</span>, <span class="st">"Sayornis phoebe"</span><span class="op">)</span></span> <span><span class="op">)</span></span> @@ -207,6 +218,7 @@ <h2 data-toc-skip>Citation</h2> <h2 data-toc-skip>Developers</h2> <ul class="list-unstyled"> <li>Renata Diaz <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-0803-4734" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> +<li><a href="authors.html">More about authors...</a></li> </ul> </div> diff --git a/docs/news/index.html b/docs/news/index.html new file mode 100644 index 0000000..47c20cd --- /dev/null +++ b/docs/news/index.html @@ -0,0 +1,105 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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Major changes include: +<ul><li>Reorganization to vignettes</li> +<li>Fix to individual sampling mechanism to avoid negative masses</li> +<li>Addition of John Dunning as a Data Contributor</li> +<li>For more details on revisions, see the software review thread: <a href="https://github.com/ropensci/software-review/issues/577" class="external-link uri">https://github.com/ropensci/software-review/issues/577</a> +</li> +</ul></li> +<li>2/2023: ROpenSci submission.</li> +</ul></div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> + +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Renata Diaz.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index a63eb78..a5466ab 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: birdsize: birdsize.html scaling: scaling.html species: species.html -last_built: 2023-11-03T20:01Z +last_built: 2023-12-08T19:18Z diff --git a/docs/reference/add_estimated_sds.html b/docs/reference/add_estimated_sds.html index 2160aff..accc93e 100644 --- a/docs/reference/add_estimated_sds.html +++ b/docs/reference/add_estimated_sds.html @@ -1,5 +1,7 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Estimate missing records for standard deviation based on mean of body size — add_estimated_sds • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Estimate missing records for standard deviation based on mean of body size — add_estimated_sds"><meta property="og:description" content="Fill in missing records for the standard deviation of body mass for a species, based on its mean body size and the parameters estimated by the linear model fit by get_sd_parameters."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Estimate missing records for standard deviation based on mean of body size — add_estimated_sds • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Estimate missing records for standard deviation based on mean of body size — add_estimated_sds"><meta property="og:description" content="Fill in missing records for the standard deviation of body mass for a +species, based on its mean body size and the parameters estimated by the +linear model fit by get_sd_parameters."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +46,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +70,9 @@ <h1>Estimate missing records for standard deviation based on mean of body size</ </div> <div class="ref-description"> - <p>Fill in missing records for the standard deviation of body mass for a species, based on its mean body size and the parameters estimated by the linear model fit by <code>get_sd_parameters</code>.</p> + <p>Fill in missing records for the standard deviation of body mass for a +species, based on its mean body size and the parameters estimated by the +linear model fit by <code>get_sd_parameters</code>.</p> </div> <div id="ref-usage"> @@ -75,18 +82,24 @@ <h1>Estimate missing records for standard deviation based on mean of body size</ <div id="arguments"> <h2>Arguments</h2> <dl><dt>clean_size_data</dt> -<dd><p>dataframe of species' masses and standard deviations; as generated by <code>clean_sp_size_data</code></p></dd> +<dd><p>dataframe of species' masses and standard deviations; +as generated by <code>clean_sp_size_data</code></p></dd> <dt>sd_pars</dt> -<dd><p>parameters as list of <code>$slope</code>, <code>$intercept</code>; as generated by <code>get_sd_parameters</code></p></dd> +<dd><p>parameters as list of <code>$slope</code>, <code>$intercept</code>; as generated by +<code>get_sd_parameters</code></p></dd> </dl></div> <div id="value"> <h2>Value</h2> -<p>a dataframe of species' <code>species_id</code> (which matches the AOU in the Breeding Bird Survey), <code>mass</code> mean body mass, <code>sd</code> standard deviation body mass, and a new column for <code>estimated_sd</code>, a <code>TRUE</code>/<code>FALSE</code> flag for whether the standard deviation has been estimated using the parameters provided in <code>sd_pars</code>.</p> +<p>a dataframe of species' <code>species_id</code> (which matches the AOU in the +Breeding Bird Survey), <code>mass</code> mean body mass, <code>sd</code> standard deviation body +mass, and a new column for <code>estimated_sd</code>, a <code>TRUE</code>/<code>FALSE</code> flag for +whether the standard deviation has been estimated using the parameters +provided in <code>sd_pars</code>.</p> </div> </div> diff --git a/docs/reference/clean_sp_size_data.html b/docs/reference/clean_sp_size_data.html index c2e31cc..e96c235 100644 --- a/docs/reference/clean_sp_size_data.html +++ b/docs/reference/clean_sp_size_data.html @@ -1,5 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Reconcile taxonomic updates between 2008 and 2019 — clean_sp_size_data • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Reconcile taxonomic updates between 2008 and 2019 — clean_sp_size_data"><meta property="og:description" content="Six species have undergone name changes or other minor taxonomic rearrangements between 2008 and 2019, resulting in name mismatches between data from the Breeding Bird Survey (Paradieck et al. 2019) and the CRC Handbook (Dunning 2008). This function resolves those mismatches such that all species in the Breeding Bird Survey are associated with the appropriate size records from the CRC Handbook."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Reconcile taxonomic updates between 2008 and 2019 — clean_sp_size_data • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Reconcile taxonomic updates between 2008 and 2019 — clean_sp_size_data"><meta property="og:description" content="Six species have undergone name changes or other minor taxonomic +rearrangements between 2008 and 2019, resulting in name mismatches between +data from the Breeding Bird Survey (Paradieck et al. 2019) and the CRC +Handbook (Dunning 2008). This function resolves those mismatches such that +all species in the Breeding Bird Survey are associated with the appropriate +size records from the CRC Handbook."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +49,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +73,12 @@ <h1>Reconcile taxonomic updates between 2008 and 2019</h1> </div> <div class="ref-description"> - <p>Six species have undergone name changes or other minor taxonomic rearrangements between 2008 and 2019, resulting in name mismatches between data from the Breeding Bird Survey (Paradieck et al. 2019) and the CRC Handbook (Dunning 2008). This function resolves those mismatches such that all species in the Breeding Bird Survey are associated with the appropriate size records from the CRC Handbook.</p> + <p>Six species have undergone name changes or other minor taxonomic +rearrangements between 2008 and 2019, resulting in name mismatches between +data from the Breeding Bird Survey (Paradieck et al. 2019) and the CRC +Handbook (Dunning 2008). This function resolves those mismatches such that +all species in the Breeding Bird Survey are associated with the appropriate +size records from the CRC Handbook.</p> </div> <div id="ref-usage"> @@ -75,20 +88,26 @@ <h1>Reconcile taxonomic updates between 2008 and 2019</h1> <div id="arguments"> <h2>Arguments</h2> <dl><dt>raw_size_data</dt> -<dd><p>dataframe of species' mean and standard deviation body sizes; use the included <code>raw_masses</code> data table.</p></dd> +<dd><p>dataframe of species' mean and standard deviation body +sizes; use the included <code>raw_masses</code> data table.</p></dd> </dl></div> <div id="value"> <h2>Value</h2> -<p>dataframe of species' mean and standard deviation body sizes, with name mismatches resolved.</p> +<p>dataframe of species' mean and standard deviation body sizes, with +name mismatches resolved.</p> </div> <div id="references"> <h2>References</h2> -<ul><li><p>Dunning, J. B. (2008). CRC handbook of avian body masses (2nd ed.). CRC Press.</p></li> -<li><p>Pardieck, K. L., Ziolkowski, D. J., Lutmerding, M., Aponte, V., & Hudson, M.-A. (2019). North American Breeding Bird Survey Dataset 1966—2018, version 2018.0. U.S. Geological Survey. https://doi.org/10.5066/P9HE8XYJ</p></li> +<ul><li><p>Dunning, J. B. (2008). CRC handbook of avian body +masses (2nd ed.). CRC Press.</p></li> +<li><p>Pardieck, K. L., Ziolkowski, D. J., +Lutmerding, M., Aponte, V., & Hudson, M.-A. (2019). North American Breeding +Bird Survey Dataset 1966—2018, version 2018.0. U.S. Geological Survey. +https://doi.org/10.5066/P9HE8XYJ</p></li> </ul></div> </div> diff --git a/docs/reference/community_generate.html b/docs/reference/community_generate.html index 044e7cf..fce076f 100644 --- a/docs/reference/community_generate.html +++ b/docs/reference/community_generate.html @@ -1,5 +1,7 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Simulate individual measurements for many populations — community_generate • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate individual measurements for many populations — community_generate"><meta property="og:description" content="For a community (i.e. a collection of populations of different species, or of the same species at different points in time or locations, etc), simulate individual-level size and metabolic rate measurements."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Simulate individual measurements for many populations — community_generate • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate individual measurements for many populations — community_generate"><meta property="og:description" content="For a community (i.e. a collection of populations of different species, or of +the same species at different points in time or locations, etc), simulate +individual-level size and metabolic rate measurements."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +46,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +70,9 @@ <h1>Simulate individual measurements for many populations</h1> </div> <div class="ref-description"> - <p>For a community (i.e. a collection of populations of different species, or of the same species at different points in time or locations, etc), simulate individual-level size and metabolic rate measurements.</p> + <p>For a community (i.e. a collection of populations of different species, or of +the same species at different points in time or locations, etc), simulate +individual-level size and metabolic rate measurements.</p> </div> <div id="ref-usage"> @@ -78,18 +85,21 @@ <h1>Simulate individual measurements for many populations</h1> <div id="arguments"> <h2>Arguments</h2> <dl><dt>community_data_table</dt> -<dd><p>dataframe containing at least one of <code>AOU</code>, <code>scientific_name</code>, or <code>mean_size</code> and a column for species abundances</p></dd> +<dd><p>dataframe containing at least one of <code>AOU</code>, +<code>scientific_name</code>, or <code>mean_size</code> and a column for species abundances</p></dd> <dt>abundance_column_name</dt> -<dd><p>character, the name of the column with species abundances. Defaults to "speciestotal".</p></dd> +<dd><p>character, the name of the column with species +abundances. Defaults to "speciestotal".</p></dd> </dl></div> <div id="value"> <h2>Value</h2> -<p>a dataframe one row per individual, all columns from <code>community_data_table</code>, and additional columns for species attributes.</p> +<p>a dataframe one row per individual, all columns from +<code>community_data_table</code>, and additional columns for species attributes.</p> <p>Specifically:</p><ul><li><p><code>AOU</code>: the AOU, if provided</p></li> @@ -125,12 +135,12 @@ <h2>Examples</h2> <span class="r-out co"><span class="r-pr">#></span> 5 15 12 15 5 62 4730 4730</span> <span class="r-out co"><span class="r-pr">#></span> 6 15 12 15 5 62 4730 4730</span> <span class="r-out co"><span class="r-pr">#></span> individual_mass individual_bmr mean_size sd_size abundance sd_method</span> -<span class="r-out co"><span class="r-pr">#></span> 1 42.89634 153.1457 37.475 3.300613 62 AOU lookup</span> -<span class="r-out co"><span class="r-pr">#></span> 2 40.22053 146.2718 37.475 3.300613 62 AOU lookup</span> -<span class="r-out co"><span class="r-pr">#></span> 3 36.93396 137.6461 37.475 3.300613 62 AOU lookup</span> -<span class="r-out co"><span class="r-pr">#></span> 4 38.96666 143.0058 37.475 3.300613 62 AOU lookup</span> -<span class="r-out co"><span class="r-pr">#></span> 5 35.45900 133.7040 37.475 3.300613 62 AOU lookup</span> -<span class="r-out co"><span class="r-pr">#></span> 6 32.42222 125.4354 37.475 3.300613 62 AOU lookup</span> +<span class="r-out co"><span class="r-pr">#></span> 1 39.18252 143.5701 37.475 3.300613 62 AOU lookup</span> +<span class="r-out co"><span class="r-pr">#></span> 2 34.52951 131.1955 37.475 3.300613 62 AOU lookup</span> +<span class="r-out co"><span class="r-pr">#></span> 3 41.40308 149.3254 37.475 3.300613 62 AOU lookup</span> +<span class="r-out co"><span class="r-pr">#></span> 4 37.64058 139.5186 37.475 3.300613 62 AOU lookup</span> +<span class="r-out co"><span class="r-pr">#></span> 5 38.98820 143.0621 37.475 3.300613 62 AOU lookup</span> +<span class="r-out co"><span class="r-pr">#></span> 6 37.98640 140.4314 37.475 3.300613 62 AOU lookup</span> <span class="r-out co"><span class="r-pr">#></span> scientific_name</span> <span class="r-out co"><span class="r-pr">#></span> 1 Alauda arvensis</span> <span class="r-out co"><span class="r-pr">#></span> 2 Alauda arvensis</span> diff --git a/docs/reference/demo_route_clean.html b/docs/reference/demo_route_clean.html index 3feb1ce..fbf0ce1 100644 --- a/docs/reference/demo_route_clean.html +++ b/docs/reference/demo_route_clean.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/demo_route_raw.html b/docs/reference/demo_route_raw.html index 064b1cc..de62619 100644 --- a/docs/reference/demo_route_raw.html +++ b/docs/reference/demo_route_raw.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/figures/README-unnamed-chunk-4-1.png b/docs/reference/figures/README-unnamed-chunk-4-1.png index a026eaa..a53f822 100644 Binary files a/docs/reference/figures/README-unnamed-chunk-4-1.png and b/docs/reference/figures/README-unnamed-chunk-4-1.png differ diff --git a/docs/reference/figures/README-unnamed-chunk-5-1.png b/docs/reference/figures/README-unnamed-chunk-5-1.png index 295fa4d..c4a66dc 100644 Binary files a/docs/reference/figures/README-unnamed-chunk-5-1.png and b/docs/reference/figures/README-unnamed-chunk-5-1.png differ diff --git a/docs/reference/figures/README-unnamed-chunk-6-1.png b/docs/reference/figures/README-unnamed-chunk-6-1.png index da33554..1ea5a0f 100644 Binary files a/docs/reference/figures/README-unnamed-chunk-6-1.png and b/docs/reference/figures/README-unnamed-chunk-6-1.png differ diff --git a/docs/reference/filter_bbs_survey.html b/docs/reference/filter_bbs_survey.html index f9512dc..a716740 100644 --- a/docs/reference/filter_bbs_survey.html +++ b/docs/reference/filter_bbs_survey.html @@ -1,5 +1,7 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Clean raw Breeding Bird Survey survey data — filter_bbs_survey • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Clean raw Breeding Bird Survey survey data — filter_bbs_survey"><meta property="og:description" content="The raw data for the Breeding Bird Survey includes unidentified species and some species that are not well-sampled by the BBS methods. This function filters a dataframe to remove those species."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Clean raw Breeding Bird Survey survey data — filter_bbs_survey • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Clean raw Breeding Bird Survey survey data — filter_bbs_survey"><meta property="og:description" content="The raw data for the Breeding Bird Survey includes unidentified species and +some species that are not well-sampled by the BBS methods. This function +filters a dataframe to remove those species."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +46,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +70,9 @@ <h1>Clean raw Breeding Bird Survey survey data</h1> </div> <div class="ref-description"> - <p>The raw data for the Breeding Bird Survey includes unidentified species and some species that are not well-sampled by the BBS methods. This function filters a dataframe to remove those species.</p> + <p>The raw data for the Breeding Bird Survey includes unidentified species and +some species that are not well-sampled by the BBS methods. This function +filters a dataframe to remove those species.</p> </div> <div id="ref-usage"> @@ -82,13 +89,13 @@ <h2>Arguments</h2> <h2>Value</h2> -<p>bbs_survey_data with unidentified species, nightbirds, waterbirds, non-targets removed</p> +<p>bbs_survey_data with unidentified species, nightbirds, waterbirds, +non-targets removed</p> </div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">filter_bbs_survey</span><span class="op">(</span><span class="va">demo_route_raw</span><span class="op">)</span><span class="op">)</span></span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">filter_bbs_survey</span><span class="op">(</span><span class="va">demo_route_raw</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> record_id routedataid countrynum statenum route rpid year AOU count10</span> <span class="r-out co"><span class="r-pr">#></span> 1 900000 9009911011994 900 99 1 101 1994 4730 8</span> <span class="r-out co"><span class="r-pr">#></span> 2 900001 9009911011995 900 99 1 101 1995 4730 13</span> @@ -103,7 +110,6 @@ <h2>Examples</h2> <span class="r-out co"><span class="r-pr">#></span> 4 13 16 9 12 5 59</span> <span class="r-out co"><span class="r-pr">#></span> 5 6 12 8 7 5 43</span> <span class="r-out co"><span class="r-pr">#></span> 6 13 5 9 5 5 44</span> -<span class="r-in"><span></span></span> </code></pre></div> </div> </div> diff --git a/docs/reference/find_nontarget_species.html b/docs/reference/find_nontarget_species.html index d554c3e..7afc6ae 100644 --- a/docs/reference/find_nontarget_species.html +++ b/docs/reference/find_nontarget_species.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/find_unidentified_species.html b/docs/reference/find_unidentified_species.html index a1350b4..1a8d7e8 100644 --- a/docs/reference/find_unidentified_species.html +++ b/docs/reference/find_unidentified_species.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/generate_sd_table.html b/docs/reference/generate_sd_table.html index 0e5966d..4fe1006 100644 --- a/docs/reference/generate_sd_table.html +++ b/docs/reference/generate_sd_table.html @@ -1,5 +1,13 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Generate table of species-level means for the mean and standard deviation of body mass for species in the Breeding Bird Survey — generate_sd_table • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" 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standard deviation of body mass from the CRC Handbook (Dunning 2008) to a table of species-level means for the mean and standard deviation of body mass, incorporating estimates for missing standard deviation records and resolving taxonomic updates between the publication of the CRC Handbook and present releases of the Breeding Bird Survey dataset (Paradieck et al. 2019)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta 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--><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Generate table of species-level means for the mean and standard deviation of +body mass for species in the Breeding Bird Survey — generate_sd_table"><meta property="og:description" content="Goes from the raw_masses dataframe (included in bbssize) of records of +species' mean and (where provided) standard deviation of body mass from the +CRC Handbook (Dunning 2008) to a table of species-level means for the mean +and standard deviation of body mass, incorporating estimates for missing +standard deviation records and resolving taxonomic updates between the +publication of the CRC Handbook and present releases of the Breeding Bird +Survey dataset (Paradieck et al. 2019)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +52,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -59,13 +70,20 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Generate table of species-level means for the mean and standard deviation of body mass for species in the Breeding Bird Survey</h1> + <h1>Generate table of species-level means for the mean and standard deviation of +body mass for species in the Breeding Bird Survey</h1> <small class="dont-index">Source: <a href="https://github.com/diazrenata/birdsize/blob/HEAD/R/species_data_functions.R" class="external-link"><code>R/species_data_functions.R</code></a></small> <div class="hidden name"><code>generate_sd_table.Rd</code></div> </div> <div class="ref-description"> - <p>Goes from the <code>raw_masses</code> dataframe (included in <code>bbssize</code>) of records of species' mean and (where provided) standard deviation of body mass from the CRC Handbook (Dunning 2008) to a table of species-level means for the mean and standard deviation of body mass, incorporating estimates for missing standard deviation records and resolving taxonomic updates between the publication of the CRC Handbook and present releases of the Breeding Bird Survey dataset (Paradieck et al. 2019).</p> + <p>Goes from the <code>raw_masses</code> dataframe (included in <code>bbssize</code>) of records of +species' mean and (where provided) standard deviation of body mass from the +CRC Handbook (Dunning 2008) to a table of species-level means for the mean +and standard deviation of body mass, incorporating estimates for missing +standard deviation records and resolving taxonomic updates between the +publication of the CRC Handbook and present releases of the Breeding Bird +Survey dataset (Paradieck et al. 2019).</p> </div> <div id="ref-usage"> @@ -82,13 +100,18 @@ <h2>Arguments</h2> <h2>Value</h2> -<p>a dataframe of species-level means for mean body size and standard deviation of body size</p> +<p>a dataframe of species-level means for mean body size and standard +deviation of body size</p> </div> <div id="references"> <h2>References</h2> -<ul><li><p>Dunning, J. B. (2008). CRC handbook of avian body masses (2nd ed.). CRC Press.</p></li> -<li><p>Pardieck, K. L., Ziolkowski, D. J., Lutmerding, M., Aponte, V., & Hudson, M.-A. (2019). North American Breeding Bird Survey Dataset 1966—2018, version 2018.0. U.S. Geological Survey. https://doi.org/10.5066/P9HE8XYJ</p></li> +<ul><li><p>Dunning, J. B. (2008). CRC handbook of avian body +masses (2nd ed.). CRC Press.</p></li> +<li><p>Pardieck, K. L., Ziolkowski, D. J., +Lutmerding, M., Aponte, V., & Hudson, M.-A. (2019). North American Breeding +Bird Survey Dataset 1966—2018, version 2018.0. U.S. Geological Survey. +https://doi.org/10.5066/P9HE8XYJ</p></li> </ul></div> </div> diff --git a/docs/reference/get_sd_parameters.html b/docs/reference/get_sd_parameters.html index c8cc559..5da56f0 100644 --- a/docs/reference/get_sd_parameters.html +++ b/docs/reference/get_sd_parameters.html @@ -1,5 +1,12 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Estimate parameters for scaling of standard deviation with mean body size — get_sd_parameters • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Estimate parameters for scaling of standard deviation with mean body size — get_sd_parameters"><meta property="og:description" content="Calculates parameters for a (log-log linear) scaling relationship between the mean and standard deviation of a species' mean body size. Given a table of species with known mean and standard deviation body sizes, fits a linear model of the form log(var(body_size)) ~ log(mean(body_size)) and extracts parameter estimates, which can then be used to estimate the standard deviation of body mass for a species based only on its mean body mass. See also Thibault et al. (2011) for this method applied to the Breeding Bird Survey."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Estimate parameters for scaling of standard deviation with mean body size — get_sd_parameters • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Estimate parameters for scaling of standard deviation with mean body size — get_sd_parameters"><meta property="og:description" content="Calculates parameters for a (log-log linear) scaling relationship between the +mean and standard deviation of a species' mean body size. Given a table of +species with known mean and standard deviation body sizes, fits a linear +model of the form log(var(body_size)) ~ log(mean(body_size)) and extracts +parameter estimates, which can then be used to estimate the standard +deviation of body mass for a species based only on its mean body mass. See +also Thibault et al. (2011) for this method applied to the Breeding Bird +Survey."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +51,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +75,14 @@ <h1>Estimate parameters for scaling of standard deviation with mean body size</h </div> <div class="ref-description"> - <p>Calculates parameters for a (log-log linear) scaling relationship between the mean and standard deviation of a species' mean body size. Given a table of species with known mean and standard deviation body sizes, fits a linear model of the form <code>log(var(body_size)) ~ log(mean(body_size))</code> and extracts parameter estimates, which can then be used to estimate the standard deviation of body mass for a species based only on its mean body mass. See also Thibault et al. (2011) for this method applied to the Breeding Bird Survey.</p> + <p>Calculates parameters for a (log-log linear) scaling relationship between the +mean and standard deviation of a species' mean body size. Given a table of +species with known mean and standard deviation body sizes, fits a linear +model of the form <code>log(var(body_size)) ~ log(mean(body_size))</code> and extracts +parameter estimates, which can then be used to estimate the standard +deviation of body mass for a species based only on its mean body mass. See +also Thibault et al. (2011) for this method applied to the Breeding Bird +Survey.</p> </div> <div id="ref-usage"> @@ -75,7 +92,8 @@ <h1>Estimate parameters for scaling of standard deviation with mean body size</h <div id="arguments"> <h2>Arguments</h2> <dl><dt>raw_size_data</dt> -<dd><p>dataframe of species' mean and standard deviation body sizes; use the included <code>raw_masses</code> data table.</p></dd> +<dd><p>dataframe of species' mean and standard deviation body +sizes; use the included <code>raw_masses</code> data table.</p></dd> </dl></div> <div id="value"> @@ -87,7 +105,10 @@ <h2>Value</h2> <div id="references"> <h2>References</h2> -<ul><li><p>Thibault, K. M., White, E. P., Hurlbert, A. H., & Ernest, S. K. M. (2011). Multimodality in the individual size distributions of bird communities. Global Ecology and Biogeography, 20(1), 145–153. https://doi.org/10.1111/j.1466-8238.2010.00576.x</p></li> +<ul><li><p>Thibault, K. M., White, E. P., Hurlbert, A. H., & +Ernest, S. K. M. (2011). Multimodality in the individual size distributions +of bird communities. Global Ecology and Biogeography, 20(1), 145–153. +https://doi.org/10.1111/j.1466-8238.2010.00576.x</p></li> </ul></div> </div> diff --git a/docs/reference/get_sp_mean_size.html b/docs/reference/get_sp_mean_size.html index 0705f1f..bc6d033 100644 --- a/docs/reference/get_sp_mean_size.html +++ b/docs/reference/get_sp_mean_size.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summarize records of mean and standard deviation of body mass to species-level means — get_sp_mean_size • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize records of mean and standard deviation of body mass to species-level means — get_sp_mean_size"><meta property="og:description" content="The CRC Handbook (Dunning 2008) often contains multiple records for mean body mass (and standard deviation of body mass) for a species, drawn from different locations or for different sexes. This function summarizes across all records for each species to produce species-level means for the mean and standard deviation of body mass."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summarize records of mean and standard deviation of body mass to +species-level means — get_sp_mean_size • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize records of mean and standard deviation of body mass to +species-level means — get_sp_mean_size"><meta property="og:description" content="The CRC Handbook (Dunning 2008) often contains multiple records for mean body +mass (and standard deviation of body mass) for a species, drawn from +different locations or for different sexes. This function summarizes across +all records for each species to produce species-level means for the mean and +standard deviation of body mass."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +50,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -59,13 +68,18 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Summarize records of mean and standard deviation of body mass to species-level means</h1> + <h1>Summarize records of mean and standard deviation of body mass to +species-level means</h1> <small class="dont-index">Source: <a href="https://github.com/diazrenata/birdsize/blob/HEAD/R/species_data_functions.R" class="external-link"><code>R/species_data_functions.R</code></a></small> <div class="hidden name"><code>get_sp_mean_size.Rd</code></div> </div> <div class="ref-description"> - <p>The CRC Handbook (Dunning 2008) often contains multiple records for mean body mass (and standard deviation of body mass) for a species, drawn from different locations or for different sexes. This function summarizes across all records for each species to produce species-level means for the mean and standard deviation of body mass.</p> + <p>The CRC Handbook (Dunning 2008) often contains multiple records for mean body +mass (and standard deviation of body mass) for a species, drawn from +different locations or for different sexes. This function summarizes across +all records for each species to produce species-level means for the mean and +standard deviation of body mass.</p> </div> <div id="ref-usage"> @@ -75,19 +89,22 @@ <h1>Summarize records of mean and standard deviation of body mass to species-lev <div id="arguments"> <h2>Arguments</h2> <dl><dt>sd_dat</dt> -<dd><p>dataframe of mean and standard deviation of body mass for all records for all species; generated by <code>add_estimated_sds</code></p></dd> +<dd><p>dataframe of mean and standard deviation of body mass for all +records for all species; generated by <code>add_estimated_sds</code></p></dd> </dl></div> <div id="value"> <h2>Value</h2> -<p><code>sd_dat</code> summarized to species-level means for the mean and standard deviation of body mass</p> +<p><code>sd_dat</code> summarized to species-level means for the mean and standard +deviation of body mass</p> </div> <div id="references"> <h2>References</h2> -<ul><li><p>Dunning, J. B. (2008). CRC handbook of avian body masses (2nd ed.). CRC Press.</p></li> +<ul><li><p>Dunning, J. B. (2008). CRC handbook of avian body +masses (2nd ed.). CRC Press.</p></li> </ul></div> </div> diff --git a/docs/reference/ind_draw.html b/docs/reference/ind_draw.html index f8b28b3..163b2b3 100644 --- a/docs/reference/ind_draw.html +++ b/docs/reference/ind_draw.html @@ -1,5 +1,6 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Draw individuals to make a population. — ind_draw • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Draw individuals to make a population. — ind_draw"><meta property="og:description" content="This is not a user-facing function; it is the random number generator under-the-hood for pop_generate."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Draw individuals to make a population. — ind_draw • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Draw individuals to make a population. — ind_draw"><meta property="og:description" content="This is not a user-facing function; it is the random number generator +under-the-hood for pop_generate."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +45,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +69,8 @@ <h1>Draw individuals to make a population.</h1> </div> <div class="ref-description"> - <p>This is not a user-facing function; it is the random number generator under-the-hood for <a href="pop_generate.html">pop_generate</a>.</p> + <p>This is not a user-facing function; it is the random number generator +under-the-hood for <a href="pop_generate.html">pop_generate</a>.</p> </div> <div id="ref-usage"> diff --git a/docs/reference/index.html b/docs/reference/index.html index 7501008..9c763fe 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/individual_metabolic_rate.html b/docs/reference/individual_metabolic_rate.html index 09b4bbd..8eaf3d5 100644 --- a/docs/reference/individual_metabolic_rate.html +++ b/docs/reference/individual_metabolic_rate.html @@ -1,5 +1,6 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Estimate individual-level BMR — individual_metabolic_rate • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Estimate individual-level BMR — individual_metabolic_rate"><meta property="og:description" content="Given an individual's body mass (in grams), use allometric scaling (Fristoe 2015) to estimate basal metabolic rate."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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S. (2015). Energy use by migrants and residents in North American breeding bird communities. Global Ecology and Biogeography, 24(4), 406–415. https://doi.org/10.1111/geb.12262</p></li> +<ul><li><p>Fristoe, T. S. (2015). Energy use by migrants and +residents in North American breeding bird communities. Global Ecology and +Biogeography, 24(4), 406–415. https://doi.org/10.1111/geb.12262</p></li> </ul></div> <div id="ref-examples"> diff --git a/docs/reference/is_unidentified.html b/docs/reference/is_unidentified.html index ab4e5d4..35ede8c 100644 --- a/docs/reference/is_unidentified.html +++ b/docs/reference/is_unidentified.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/known_species.html b/docs/reference/known_species.html index 2ca7a24..294d755 100644 --- a/docs/reference/known_species.html +++ b/docs/reference/known_species.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/nontarget_species.html b/docs/reference/nontarget_species.html index 9bbf5e0..53f6861 100644 --- a/docs/reference/nontarget_species.html +++ b/docs/reference/nontarget_species.html @@ -46,6 +46,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/pop_generate.html b/docs/reference/pop_generate.html index ed05488..7793b93 100644 --- a/docs/reference/pop_generate.html +++ b/docs/reference/pop_generate.html @@ -1,5 +1,7 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Simulate body masses for a population — pop_generate • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link 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--><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate body masses for a population — pop_generate"><meta property="og:description" content="Draws body mass measurements for a population of birds (of all the same species) given the population size and either (1) the species AOU or (2) the mean and potentially standard deviation of body mass for that species."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Simulate body masses for a population — pop_generate • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" 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href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate body masses for a population — pop_generate"><meta property="og:description" content="Draws body mass measurements for a population of birds (of all the same +species) given the population size and either (1) the species AOU or (2) the +mean and potentially standard deviation of body mass for that species."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +46,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +70,9 @@ <h1>Simulate body masses for a population</h1> </div> <div class="ref-description"> - <p>Draws body mass measurements for a population of birds (of all the same species) given the population size and either (1) the species AOU or (2) the mean and potentially standard deviation of body mass for that species.</p> + <p>Draws body mass measurements for a population of birds (of all the same +species) given the population size and either (1) the species AOU or (2) the +mean and potentially standard deviation of body mass for that species.</p> </div> <div id="ref-usage"> @@ -86,7 +93,8 @@ <h2>Arguments</h2> <dt>AOU</dt> -<dd><p>AOU</p></dd> +<dd><p>the numeric AOU code used for this species in the Breeding Bird +Survey</p></dd> <dt>scientific_name</dt> @@ -109,7 +117,8 @@ <h2>Arguments</h2> <h2>Value</h2> -<p>a dataframe with <code>abundance</code> rows - one record per individual - and columns for species attributes.</p> +<p>a dataframe with <code>abundance</code> rows - one record per individual - and +columns for species attributes.</p> <p>Specifically:</p><ul><li><p><code>AOU</code>: the AOU, if provided</p></li> @@ -124,7 +133,8 @@ <h2>Value</h2> </ul></div> <div id="details"> <h2>Details</h2> - <p><code>abundance</code> is required, as well as <em>one of</em>: <code>AOU</code>, <code>scientific_name</code>, or <code>mean_size</code>.</p> + <p><code>abundance</code> is required, as well as <em>one of</em>: <code>AOU</code>, <code>scientific_name</code>, or +<code>mean_size</code>.</p> </div> <div id="ref-examples"> @@ -132,11 +142,11 @@ <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu">pop_generate</span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">5</span>, AOU <span class="op">=</span> <span class="fl">2881</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> AOU sim_species_id individual_mass individual_bmr mean_size sd_size</span> -<span class="r-out co"><span class="r-pr">#></span> 1 2881 2881 452.2041 821.1884 405.5 31</span> -<span class="r-out co"><span class="r-pr">#></span> 2 2881 2881 377.0726 721.4070 405.5 31</span> -<span class="r-out co"><span class="r-pr">#></span> 3 2881 2881 369.5527 711.1195 405.5 31</span> -<span class="r-out co"><span class="r-pr">#></span> 4 2881 2881 417.3716 775.5719 405.5 31</span> -<span class="r-out co"><span class="r-pr">#></span> 5 2881 2881 406.8111 761.5289 405.5 31</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2881 2881 369.6341 711.2311 405.5 31</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2881 2881 437.9375 802.6314 405.5 31</span> +<span class="r-out co"><span class="r-pr">#></span> 3 2881 2881 434.9881 798.7736 405.5 31</span> +<span class="r-out co"><span class="r-pr">#></span> 4 2881 2881 402.5902 755.8868 405.5 31</span> +<span class="r-out co"><span class="r-pr">#></span> 5 2881 2881 439.0888 804.1353 405.5 31</span> <span class="r-out co"><span class="r-pr">#></span> abundance sd_method scientific_name</span> <span class="r-out co"><span class="r-pr">#></span> 1 5 AOU lookup Perdix perdix</span> <span class="r-out co"><span class="r-pr">#></span> 2 5 AOU lookup Perdix perdix</span> @@ -145,11 +155,11 @@ <h2>Examples</h2> <span class="r-out co"><span class="r-pr">#></span> 5 5 AOU lookup Perdix perdix</span> <span class="r-in"><span><span class="fu">pop_generate</span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">5</span>, scientific_name <span class="op">=</span> <span class="st">"Selasphorus calliope"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> AOU sim_species_id individual_mass individual_bmr mean_size sd_size</span> -<span class="r-out co"><span class="r-pr">#></span> 1 4360 4360 2.473328 20.02623 2.65 0.1818394</span> -<span class="r-out co"><span class="r-pr">#></span> 2 4360 4360 2.515924 20.27153 2.65 0.1818394</span> -<span class="r-out co"><span class="r-pr">#></span> 3 4360 4360 2.935491 22.62798 2.65 0.1818394</span> -<span class="r-out co"><span class="r-pr">#></span> 4 4360 4360 2.359319 19.36360 2.65 0.1818394</span> -<span class="r-out co"><span class="r-pr">#></span> 5 4360 4360 2.667413 21.13448 2.65 0.1818394</span> +<span class="r-out co"><span class="r-pr">#></span> 1 4360 4360 2.631619 20.93188 2.65 0.1818394</span> +<span class="r-out co"><span class="r-pr">#></span> 2 4360 4360 2.718777 21.42386 2.65 0.1818394</span> +<span class="r-out co"><span class="r-pr">#></span> 3 4360 4360 2.705184 21.34743 2.65 0.1818394</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4360 4360 2.466374 19.98607 2.65 0.1818394</span> +<span class="r-out co"><span class="r-pr">#></span> 5 4360 4360 2.630751 20.92696 2.65 0.1818394</span> <span class="r-out co"><span class="r-pr">#></span> abundance sd_method scientific_name</span> <span class="r-out co"><span class="r-pr">#></span> 1 5 Scientific name lookup Selasphorus calliope</span> <span class="r-out co"><span class="r-pr">#></span> 2 5 Scientific name lookup Selasphorus calliope</span> @@ -158,11 +168,11 @@ <h2>Examples</h2> <span class="r-out co"><span class="r-pr">#></span> 5 5 Scientific name lookup Selasphorus calliope</span> <span class="r-in"><span><span class="fu">pop_generate</span><span class="op">(</span>abundance <span class="op">=</span> <span class="fl">5</span>, mean_size <span class="op">=</span> <span class="fl">20</span>, sd_size <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> AOU sim_species_id individual_mass individual_bmr mean_size sd_size abundance</span> -<span class="r-out co"><span class="r-pr">#></span> 1 NA 1 17.40227 80.48989 20 3 5</span> -<span class="r-out co"><span class="r-pr">#></span> 2 NA 1 13.71185 67.91078 20 3 5</span> -<span class="r-out co"><span class="r-pr">#></span> 3 NA 1 15.74589 74.94964 20 3 5</span> -<span class="r-out co"><span class="r-pr">#></span> 4 NA 1 18.25798 83.29235 20 3 5</span> -<span class="r-out co"><span class="r-pr">#></span> 5 NA 1 24.05238 101.38064 20 3 5</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1 22.61756 97.03069 20 3 5</span> +<span class="r-out co"><span class="r-pr">#></span> 2 NA 1 24.29249 102.10122 20 3 5</span> +<span class="r-out co"><span class="r-pr">#></span> 3 NA 1 12.65889 64.15012 20 3 5</span> +<span class="r-out co"><span class="r-pr">#></span> 4 NA 1 26.07664 107.39318 20 3 5</span> +<span class="r-out co"><span class="r-pr">#></span> 5 NA 1 23.57310 99.93610 20 3 5</span> <span class="r-out co"><span class="r-pr">#></span> sd_method scientific_name</span> <span class="r-out co"><span class="r-pr">#></span> 1 Mean and SD provided <NA></span> <span class="r-out co"><span class="r-pr">#></span> 2 Mean and SD provided <NA></span> diff --git a/docs/reference/raw_masses.html b/docs/reference/raw_masses.html index 63f032a..5637339 100644 --- a/docs/reference/raw_masses.html +++ b/docs/reference/raw_masses.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/sd_table.html b/docs/reference/sd_table.html index 840a1b1..dba7f47 100644 --- a/docs/reference/sd_table.html +++ b/docs/reference/sd_table.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/species_define.html b/docs/reference/species_define.html index 208c1f8..5cf2b71 100644 --- a/docs/reference/species_define.html +++ b/docs/reference/species_define.html @@ -1,5 +1,6 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Define a species — species_define • birdsize</title><!-- jquery --><script 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body mass."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +45,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +69,8 @@ <h1>Define a species</h1> </div> <div class="ref-description"> - <p>Creates a list with taxonomic/identifying information and parameters for mean and standard deviation of body mass.</p> + <p>Creates a list with taxonomic/identifying information and parameters for mean +and standard deviation of body mass.</p> </div> <div id="ref-usage"> @@ -81,7 +86,8 @@ <h1>Define a species</h1> <div id="arguments"> <h2>Arguments</h2> <dl><dt>AOU</dt> -<dd><p>AOU</p></dd> +<dd><p>the numeric AOU code used for this species in the Breeding Bird +Survey</p></dd> <dt>scientific_name</dt> @@ -97,7 +103,9 @@ <h2>Arguments</h2> <dt>sim_species_id</dt> -<dd><p>identifier; if using taxonomic info, defaults to AOU. If not, defaults to 1. Supplying other values can be useful for simulation models.</p></dd> +<dd><p>identifier; if using taxonomic info, defaults to AOU. +If not, defaults to 1. Supplying other values can be useful for simulation +models.</p></dd> </dl></div> <div id="value"> @@ -108,7 +116,9 @@ <h2>Value</h2> </div> <div id="details"> <h2>Details</h2> - <p>The identifying information used depends on which parameters are provided, with the following order of preference: AOU > scientific name > user provided mean and sd > user provided mean and estimated sd.</p> + <p>The identifying information used depends on which parameters are provided, +with the following order of preference: AOU > scientific name > user provided +mean and sd > user provided mean and estimated sd.</p> </div> <div id="ref-examples"> diff --git a/docs/reference/species_estimate_sd.html b/docs/reference/species_estimate_sd.html index 042aeb9..449f66b 100644 --- a/docs/reference/species_estimate_sd.html +++ b/docs/reference/species_estimate_sd.html @@ -1,5 +1,8 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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If not provided, estimated by running <code>get_sd_parameters(raw_masses)</code>.</p></dd> +<dd><p>list containing <code>$slope</code> and <code>$intercept</code>, generated by +<code><a href="get_sd_parameters.html">get_sd_parameters()</a></code>. If not provided, estimated by running +<code>get_sd_parameters(raw_masses)</code>.</p></dd> </dl></div> <div id="value"> diff --git a/docs/reference/species_lookup.html b/docs/reference/species_lookup.html index d113f89..4d6a3e3 100644 --- a/docs/reference/species_lookup.html +++ b/docs/reference/species_lookup.html @@ -1,5 +1,6 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Species lookup — species_lookup • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" 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src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Species lookup — species_lookup • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" 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src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Species lookup — species_lookup"><meta property="og:description" content="Given either AOU or scientific name, looks up a species' taxonomic +information and mean and standard deviation of body size in sd_table."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +45,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +69,8 @@ <h1>Species lookup</h1> </div> <div class="ref-description"> - <p>Given either AOU or scientific name, looks up a species' taxonomic information and mean and standard deviation of body size in <a href="sd_table.html">sd_table</a>.</p> + <p>Given either AOU or scientific name, looks up a species' taxonomic +information and mean and standard deviation of body size in <a href="sd_table.html">sd_table</a>.</p> </div> <div id="ref-usage"> @@ -75,7 +80,8 @@ <h1>Species lookup</h1> <div id="arguments"> <h2>Arguments</h2> <dl><dt>AOU</dt> -<dd><p>AOU species code as specified in the Breeding Bird Survey</p></dd> +<dd><p>the numeric AOU code used for this species in the Breeding Bird +Survey</p></dd> <dt>scientific_name</dt> @@ -86,7 +92,8 @@ <h2>Arguments</h2> <h2>Value</h2> -<p>data frame with columns AOU, genus, species, mean_mass, mean_sd, contains_estimates, scientific_name</p> +<p>data frame with columns AOU, genus, species, mean_mass, mean_sd, +contains_estimates, scientific_name</p> </div> <div id="ref-examples"> diff --git a/docs/reference/toy_aou_community.html b/docs/reference/toy_aou_community.html index 71f14a8..6ce43f1 100644 --- a/docs/reference/toy_aou_community.html +++ b/docs/reference/toy_aou_community.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/reference/toy_size_community.html b/docs/reference/toy_size_community.html index b3787a8..0337220 100644 --- a/docs/reference/toy_size_community.html +++ b/docs/reference/toy_size_community.html @@ -1,5 +1,6 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" 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It has abundances and AOU codes for 5 species to make up a hypothetical community."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Toy data frame of abundances and species mean sizes (for vignettes) — toy_size_community • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Toy data frame of abundances and species mean sizes (for vignettes) — toy_size_community"><meta property="og:description" content="This data table is a toy data frame for the vignettes. It has abundances and +mean body sizes for 5 species to make up a hypothetical community."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +45,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +69,8 @@ <h1>Toy data frame of abundances and species mean sizes (for vignettes)</h1> </div> <div class="ref-description"> - <p>This data table is a toy data frame for the vignettes. It has abundances and AOU codes for 5 species to make up a hypothetical community.</p> + <p>This data table is a toy data frame for the vignettes. It has abundances and +mean body sizes for 5 species to make up a hypothetical community.</p> </div> <div id="ref-usage"> diff --git a/docs/reference/toy_species_name_community.html b/docs/reference/toy_species_name_community.html index 51d8b06..31c46c1 100644 --- a/docs/reference/toy_species_name_community.html +++ b/docs/reference/toy_species_name_community.html @@ -1,5 +1,6 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Toy data frame of abundances and species names (for vignettes) — toy_species_name_community • birdsize</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Toy data frame of abundances and species names (for vignettes) — toy_species_name_community"><meta property="og:description" content="This data table is a toy data frame for the vignettes. 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It has abundances and +scientific names for 5 species to make up a hypothetical community."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -44,6 +45,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -65,7 +69,8 @@ <h1>Toy data frame of abundances and species names (for vignettes)</h1> </div> <div class="ref-description"> - <p>This data table is a toy data frame for the vignettes. It has abundances and AOU codes for 5 species to make up a hypothetical community.</p> + <p>This data table is a toy data frame for the vignettes. It has abundances and +scientific names for 5 species to make up a hypothetical community.</p> </div> <div id="ref-usage"> diff --git a/docs/reference/unidentified_species.html b/docs/reference/unidentified_species.html index 20c7f19..520f126 100644 --- a/docs/reference/unidentified_species.html +++ b/docs/reference/unidentified_species.html @@ -44,6 +44,9 @@ <a href="../articles/species.html">species</a> </li> </ul></li> +<li> + <a href="../news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/review_edits.html b/docs/review_edits.html index 2872388..17fe08d 100644 --- a/docs/review_edits.html +++ b/docs/review_edits.html @@ -44,6 +44,9 @@ <a href="articles/species.html">species</a> </li> </ul></li> +<li> + <a href="news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> @@ -82,12 +85,12 @@ <h1>R1</h1> </ul><blockquote> <p>Defining species in function arguments could be clarified. In the arguments to pop_generate() and species_define(), species can be identified either by AOU code or scientific name. Given that both genus and species are required, it feels more intuitive to me to use a single argument (e.g. scientific_name). The documentation also doesn’t make it clear that species is the species’ epithet and not the scientific or common name. As it stands, it feels like you should be able to call pop_generate(100, species = “Selasphorus calliope”) or even pop_generate(100, species = “Calliope Hummingbird”).</p> </blockquote> -<p>+1 on combining genus and species as <code>scientific_name</code>.</p> -<p>I am of two minds on the common name lookup. It does seem intuitive and nice, but I wonder how accurate the matching would be? It would be easy to implement <em>perfect</em> matching. Or, to clarify in the docs that it has to be the scientific name.</p> +<p>In this version, the <code>genus</code> + <code>species</code> designation has been replaced by a single argument, <code>scientific_name</code>.</p> +<p>In this revision, I did <em>not</em> try to implement name matching based on the common name. My reasoning here was that the common name would be more prone to variations in spelling, etc, and so matching common names would be another layer of computational infrastructure. This does seem like a good feature to add in later iterations, or one that I could put more thought into if it seems like it would be very widely used!</p> <blockquote> <p>I wonder if the _summarize() functions are necessary since they’re essentially just calling group_by() %>% summarize(). Personally I’d prefer to do this directly myself with dplyr so I know exactly what’s going on and the vignettes could demonstrate exactly how users should do it. However, I can imagine that some users aren’t as comfortable with dplyr so these convenience functions could be useful.</p> </blockquote> -<p>Always a tough call. I like the idea of scooting it to the vignette for transparency. This would also help reduce, or at least compartmentalize, tidyverse deps.</p> +<p>I agree. In this version, the <code>*summarize</code> functions are removed. I added a short demo of computing summary values using <code>dplyr</code> in the Getting Started vignette. (This also made it easier to remove tidyverse dependencies, see later comments!)</p> <blockquote> <p>The internal function ind_draw() seems dangerous to me since it has a while loop to get rid of negative sizes with potential to run for a very long time. This is especially true because there appears to be no checks to ensure the mean size is positive. For example the following will run indefinitely:</p> </blockquote> @@ -97,38 +100,35 @@ <h1>R1</h1> <blockquote> <p>At the very least, please add a check to ensure mean_size and sd_size are positive and some method to ensure the while loop won’t run forever, e.g. after a certain number of iterations maybe it should stop and raise an error. Even better would be re-writing this function to use a less brute force method to ensure the sizes generated aren’t negative. It’s not immediately clear what that would look like, since simple solutions like take the absolute value, won’t preserve the desired normal distribution.</p> </blockquote> -<p>This completely didn’t occur to me and is completely on point 😆.</p> -<p>To-do:</p> -<ul><li>test a truncated normal vs. rejection sampling with rules</li> -<li>add protections so the functions won’t take negative means</li> -<li>update docs</li> -</ul><blockquote> +<p>Wow, thank you for recognizing this! This completely did not occur to me, but is of course a significant potential bug!</p> +<p>In this version, I’ve taken the suggestion to use <code><a href="https://rdrr.io/pkg/truncnorm/man/dtruncnorm.html" class="external-link">truncnorm::rtruncnorm</a></code> to draw from a normal distribution truncated with a lower bound of 1 (i.e. 1 gram of bird). Additionally, <code>pop_generate</code> now issues a message if the combined mean and standard deviations provided are likely to produce negative values.</p> +<blockquote> <p>Some additional, specific comments about the code:</p> </blockquote> <blockquote> <pre><code>I believe the standard for documenting package datasets is to document them all in R/data.R rather than individual R files. Not a huge issue, but I think this would help anyone interested find the source for the documentation more easily. See https://r-pkgs.org/data.html#sec-documenting-data.</code></pre> </blockquote> -<p>Ah, ok!</p> +<p>Ah, ok! The dataset documentation is now all in R/data.R.</p> <blockquote> <pre><code>Related to the previous point, you might consider renaming or re-grouping some of the other source files. For example, the only exported function in R/simulate_populations.R is pop_generate(), so why not call that file R/pop_generate.R so it's more obvious what's in the file?</code></pre> </blockquote> -<p>To-do: revisit grouping of functions in .R files, thinking about readability.</p> +<p>I’ve rearranged the functions and tried to create a closer match between the functions in a file and the file name. I’ve kept some single-function scripts (ind_draw.R, pop_generate.R) and grouped others thematically. I hope this is easier to navigate?</p> <blockquote> <p>dplyr has deprecated or superseded a lot of the “scoped” verbs, e.g. group_by_at(). Please replace these as appropriate to future proof your package. See <a href="https://dplyr.tidyverse.org/reference/scoped.html" class="external-link uri">https://dplyr.tidyverse.org/reference/scoped.html</a></p> </blockquote> -<p>Yikes. To-do: check this, unless it gets addressed as part of a de-tidyversing (see R2).</p> +<p>Yikes, and this is good to keep in mind. I’ve removed all <code>dplyr</code> verbs except for those in the vignette.</p> <blockquote> <p>I see some inconsistency in code styling. For example, in some places you use if() and in other places if (). I recommend picking one method of formatting your code and sticking with it. See <a href="https://style.tidyverse.org/" class="external-link uri">https://style.tidyverse.org/</a>.</p> </blockquote> -<p>To-do: catch the styling</p> +<p>I’ve reformatted the code using <code>styler</code>.</p> <blockquote> <p>In a few places I see you’re using as.numeric(NA) or is.character(NA) (e.g. <a href="https://github.com/diazrenata/birdsize/blob/main/R/species_define.R#L56" class="external-link uri">https://github.com/diazrenata/birdsize/blob/main/R/species_define.R#L56</a>). Note that there are NAs specifically for different data types, i.e. NA_real_ and NA_character_. It seems cleaner to use these rather than casting NA to different data types.</p> </blockquote> -<p>I’ve never done this, but seems good to start! To-do: NA_character/NA_real.</p> +<p>I’ve replaced nonspecific NAs with data-type-specific NAs.</p> <blockquote> <p>There are a handful of unnecessarily nested if statements (e.g. <a href="https://github.com/diazrenata/birdsize/blob/main/R/species_define.R#L54" class="external-link uri">https://github.com/diazrenata/birdsize/blob/main/R/species_define.R#L54</a>). Anywhere you have if (A) {if (B) {…}} I think it’s cleaner to use if (A && B) {…}, but that may just be personal preference.</p> </blockquote> -<p>To-do: check these. I think I personally find it easier to use the nested logic than the combination for some vague personal cognitive-flow thing, but it’s definitely more verbose.</p> +<p>I’ve kept these mostly as written, perhaps because it’s just much easier for me to parse. I’m happy to revisit this!</p> </div> <div class="section level1"> <h1 id="r2">R2<a class="anchor" aria-label="anchor" href="#r2"></a></h1> @@ -141,11 +141,11 @@ <h1 id="r2">R2<a class="anchor" aria-label="anchor" href="#r2"></a></h1> <blockquote> <p>The DESCRIPTION file states that the package depends on R >=2.10 but the tidyverse dependencies require R >= 3.3.</p> </blockquote> -<p>🤔 See below, I think the solution to this <em>may</em> be to untidy.</p> +<p>With the removal of tidyverse dependencies, I <em>believe</em> R >= 2.10 will be sufficient.</p> <blockquote> <p>I agree with Matt that the documentation of the package datasets should be in one data.R file which is a little easier to navigate (though this is not too relevant to users as they won’t ever see that, but it would be helpful for contributors)</p> </blockquote> -<p>+1 on consolidating data documentation to data.R</p> +<p>Absolutely! The dataset documentation is now consolidated in data.R.</p> <blockquote> <p>This is a tough one, but I generally try to shy away from having tidyverse dependencies in packages. For example the lines with dplyr::mutate() could be rewritten from</p> </blockquote> @@ -160,57 +160,58 @@ <h1 id="r2">R2<a class="anchor" aria-label="anchor" href="#r2"></a></h1> <blockquote> <pre><code>Also, having tidyverse dependencies greatly increases the number of downstream dependencies for the package which might not be desirable.</code></pre> </blockquote> -<p>These comments (and conversations outside this) encourage me to move away from tidyverse dependencies. Most of the operations here are pretty simple and should translate to base reasonably easily, so <em>todo</em> start by reverting to base, and revisit this if there are components that really seem to need tidyverse.</p> +<p>These comments (and conversations outside this) encourage me to move away from tidyverse dependencies. In this revision, the tidyverse packages are removed, except for examples shown in the vignettes.</p> <blockquote> <p>I also agree with Matt that it would be good to at least rewrite the code not to use the magrittr pipes %>% for the reasons he cited.</p> </blockquote> -<p>I think most of the pipes are in tidyverse paragraphs! <em>todo</em> make sure, though.</p> +<p>This revision has removed the magrittr pipe. The examples use the new base R pipe (<code>|></code>).</p> <blockquote> <pre><code>In filter_bbs_survey(), package data are loaded with unidentified_species <- unidentified_species. I am not sure that is the recommended way to internally use package data. I noticed Matt also brought this up so I would follow his advice there.</code></pre> </blockquote> -<p><em>Todo</em> fix how this is called.</p> +<p>I’ve removed these calls loading internal data. This has introduced the NOTES of “no visible binding for global variable”.</p> <blockquote> <p>In simulate_populations(), the error checking routines that cause failure if things like mean and standard deviation aren’t provided is one level down in the ind_draw() function. To me it would make more sense if the input is checked for errors right away instead of further down.</p> </blockquote> -<p>Can do!</p> +<p>This version has the error checking occurring at both levels. This makes it slightly easier to trace if a user is running <code>pop_generate</code> (new name for <code>simulate_populations</code>), and keeps the guardrails on within <code>ind_draw</code> as well.</p> <blockquote> <p>Line 33 of species_data_functions.R: the argument data to lm() should be named.</p> </blockquote> -<p>Can do!</p> +<p>Done! (Now at line 24).</p> <blockquote> <p>Documentation review</p> </blockquote> <blockquote> <pre><code>I thought the vignettes were well-organized and do a good job of providing examples of all the functions. One suggestion is that the vignettes could have more informative titles. Just the word community does not make it clear exactly what can be learned from going through the vignette.</code></pre> </blockquote> -<p>I think this would be well-addressed by refocusing on topics (see above)</p> +<p>I hope this is addressed by re-organizing the vignettes so most of the general-purpose information is in “Getting Started”, and the remaining vignettes have clear, specific content (BBS data, scaling relationship, species definitions).</p> <blockquote> <p>I also liked the Taylor Swift example but shouldn’t the species be Taylor and the genus Swift? :-D</p> </blockquote> -<p>Here for it.</p> +<p>Noted, and updated. :D</p> <blockquote> <p>A user copying and pasting code from the vignettes will not be able to run the code containing tidyverse functions including select() and pmap_df() because those packages are not explicitly loaded in the vignette.</p> </blockquote> -<p><em>Todo</em> if any tidyverse stays in the vignettes, make sure they are loaded visibly in the vignettes.</p> +<p>The package calls have been made visible in the vignettes.</p> <blockquote> <p>The term “AOU” should be defined somewhere - it is known to North Americans but not otherwise. I understand this package is most intended for use with BBS so users will be familiar but it can’t hurt to define so that other people can understand what it is (maybe not necessarily the user but someone looking over the code). A related minor point: in some of the functions where AOU is an argument, it is in lowercase aou but I think it would be more consistent to make it capitalized AOU.</p> </blockquote> -<p><em>Todo</em> Make sure to explain AOU (maybe as part of wider explanation of BBS data), and capitalize the argument.</p> +<p>I’ve expanded references to the AOU in the vignettes and code documentation to the “AOU numeric code” and added links to the BBS page. I’ve also capitalized user-facing instances of “AOU”.</p> +<p>Interestingly, in doing this I found that the BBS AOUs appear to differ from the (more recent) codes put out by the American Ornithological Union. It looks to me like the AOU itself has switched to four-letter alpha character codes, but the BBS has kept with the (original, I believe) numeric codes. So the only lookup table for the AOU numbers to species is the BBS list, which I have linked to.</p> <blockquote> <p>The bar plot with total biomass by AOU in the community vignette, as Matt mentioned, would be more informative with species names instead of AOU codes. Also, because the fill color legend is redundant with the axis labels, it would be cleaner to just label the x axis with the species names and suppress the legend of fill colors.</p> </blockquote> -<p><em>Todo</em> Make sure this plot gets updated.</p> +<p>This plot has been removed with the vignette rearrangement, but I’ve updated the other plot legends to use scientific names instead of AOUs.</p> <blockquote> <p>Comments on science stuff</p> </blockquote> <blockquote> <p>I would feel better about it if you explicitly incorporated uncertainty in the scaling relationships. The parameters for the relationship between body mass mean and standard deviation are average expectations, so you would end up underestimating the variation in body mass if you only use that mean expectation to impute missing standard deviations. Is there any way of incorporating uncertainty in those scaling parameters?</p> </blockquote> -<p>I need to think about this one. Generally when I work with this method, I take the estimated mass and sd as the limit of the precision of this approach. The uncertainty is also variable among species - for some we have estimates and some measurements; for some species many measurements and some just one; and from different locations and times and investigators. For these reasons, I handle these estimates as “best-guesses suitable for broad-scale questions, but with some significant limitations as things get precise”….more thought needed.</p> +<p>This is a tough question. Generally when <em>I</em> work with this method, I take the estimated mass and sd as the limit of the precision of this approach. The uncertainty is also variable among species - for some we have estimates and some measurements; for some species many measurements and some just one; and from different locations and times and investigators. For these reasons, I handle these estimates as “best-guesses suitable for broad-scale questions, but with some significant limitations as things get precise”. I’ve added language to this effect in the vignettes and README.</p> <blockquote> <p>It would be nice to allow filter_bbs_survey() to take arguments so that the user could customize removing specific species groups. For instance it would be interesting if the user could remove only waterbirds and keep nocturnal birds, if they were so inclined.</p> </blockquote> -<p><em>Todo</em> Check this out. I might need to go back to Dunning to get masses for waterbirds and nocturnal birds :)</p> +<p>This is an interesting suggestion. To implement it I would need to expand the database of masses included in the package, which would mean going back to Dunning (2008) - which invites expanding the data further than (necessarily) just the Breeding Bird Survey species. I think this becomes a wider conversation about the scope of data reproduction in the package vs. shifting that onto a user. I haven’t implemented it in this revision, but if it seems like a necessary value-add it would be possible.</p> <blockquote> <p>The real heart of the body mass distribution simulation is in the file simulate_populations.R in ind_draw() at line 34:</p> </blockquote> @@ -224,17 +225,59 @@ <h1 id="r2">R2<a class="anchor" aria-label="anchor" href="#r2"></a></h1> <blockquote> <pre><code>To further address the point about the rejection sampling method, Matt mentioned in his review that it would be good to use a "less brute force" method to ensure the values are >0. Actually, the method of rejection sampling that you are currently using is a well-accepted method. It is used by the R package truncnorm. For almost any realistic values of body mass mean and sd, you will get very few negative values on the initial sample, so the while loop would hardly ever even be necessary. However, if you are interested in a more direct method of sampling from a truncated normal without the while loop, I would check out [this Stackoverflow thread](https://stats.stackexchange.com/questions/56747/simulate-constrained-normal-on-lower-or-upper-bound-in-r) especially [this answer](https://stats.stackexchange.com/a/510821/54923). There are also the existing functions msm::tnorm() and truncnorm::truncnorm() but you may not want to add a dependency to your package.</code></pre> </blockquote> -<p>!!!! see above.</p> -<p>Additional todos:</p> -<ul><li>make sure the normal assumption is made crystal clear in the documentation</li> -<li>look into a user-specified lower limit other than 0</li> -</ul></div> +<p>This is a really good and important observation (see the earlier response to Matt’s comment)! I went ahead and switched over to <code><a href="https://rdrr.io/pkg/truncnorm/man/dtruncnorm.html" class="external-link">truncnorm::rtruncnorm</a></code> to avoid the negative-values problem.</p> +<p>I’ve also added sections right at the beginning of both the README and Getting Started vignette clarifying the assumption of the normal distribution.</p> +</div> <div class="section level1"> <h1 id="others">Others<a class="anchor" aria-label="anchor" href="#others"></a></h1> -<ul><li>make sure test file names // source files names</li> +<ul><li>Regarding @ maelle’s comment regarding test files and source file names: I have renamed the test files to correspond more closely to the file names.</li> <li>tests fail due to an issue with unzip on windows. 👀</li> -<li>reach out to Dunning re: contributor-ship</li> -<li>and see the Small Fixes PR (which looks extremely helpful and above-and-beyond for peer review! <span class="emoji" data-emoji="raised_hands">🙌</span>)</li> +<li>I’ve reached out to Dr. Dunning and he agreed to be listed as a Data Contributor. I’ve added him with this revision.</li> +<li>I reviewed the Small Fixes PR from @ mstrimas. Because of the scope of revisions, I ended up not merging that pull request and instead implementing the same changes on the revised codebase. Specifically, I tidied up the DESCRIPTION using desc::desc_normalize(), removed <code><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">remotes::install_github</a></code> from the README, switched T/F to TRUE/FALSE, and switched 1:nrow() to seq_len(nrow()). = was changed to <- via the lintr cleanup, and use of .data$ was removed with the removal of tidyverse functions.</li> +</ul></div> +<div class="section level1"> +<h1 id="from-editor">From editor:<a class="anchor" aria-label="anchor" href="#from-editor"></a></h1> +<ul><li>I’d recommend running desc::desc_normalize(): it will order DESCRIPTION fields in a standard way and order dependencies alphabetically. +<ul><li> +<em>Response</em>: Done!</li> +</ul></li> +<li>You can remove the {remotes} installation instructions and keep the {devtools} ones only as {devtools} calls {remotes} (might call {pak} in the future?) and is the interface for users. +<ul><li> +<em>Response</em>: Done!</li> +</ul></li> +<li>It’d be nice to add grouping to the reference index <a href="https://pkgdown.r-lib.org/reference/build_reference.html#reference-index" class="external-link uri">https://pkgdown.r-lib.org/reference/build_reference.html#reference-index</a> Given your package’s naming scheme, you might want to use the starts_with() helper. +<ul><li> +<em>Response</em>: I haven’t done this because there are so few functions, it seems to me like it verges on redundant. I’m happy to revisit this!</li> +</ul></li> +<li>In the test filenames, why use numbers? If the R files and test files have the same basename, it’s easier to navigate between the two in RStudio IDE. <a href="https://r-pkgs.org/testing-basics.html#test-organisation" class="external-link uri">https://r-pkgs.org/testing-basics.html#test-organisation</a> * <em>Response</em>: Ah, I learned to use the numbers so that tests fail informatively in order. The tests also don’t - all - correspond directly to RScripts. Is this a major barrier? If so, I’m happy to revisit!</li> +<li>In your test files and scripts I see a lot of vertical space, more than one empty lines between some elements. I’d recommend using one empty line only as it increases the amount of code one can see at a time on the screen. It’s still nice to organize the code in paragraphs, I am not suggesting to remove all empty lines. 😁 +<ul><li> +<em>Response</em>: I think this has been largely addressed via the re-styling I’ve done, but please let me know if the issue persists!</li> +</ul></li> +<li>In the README instead of “Package summary” as a header you could use the same text as this issue “birdsize: Estimate avian body size distributions” which is more informative. +<ul><li> +<em>Response</em>: Done!</li> +</ul></li> +<li>Regarding data yes it might make sense to contact the author of the included dataset? +<ul><li> +<em>Response:</em> Done! I’ve reached out and Dr. Dunning agreed to be listed as a contributor. I’ve sent a more recent-follow up with the revisions and giving him the opportunity to confirm. I’m still waiting to hear back there, and will let you know.</li> +</ul></li> +<li>For comments such as <a href="https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/R/simulate_community.R#L51" class="external-link uri">https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/R/simulate_community.R#L51</a> if you add 4 hyphens afterwards —-, the comment will appear in the script outline on the right in RStudio IDE (if you use that IDE), helping code navigation. <a href="https://blog.r-hub.io/2023/01/26/code-comments-self-explaining-code/#use-comments-for-the-scripts-outline" class="external-link uri">https://blog.r-hub.io/2023/01/26/code-comments-self-explaining-code/#use-comments-for-the-scripts-outline</a> +<ul><li> +<em>Response</em>: I’ve added these to the long community_generate script.</li> +</ul></li> +<li>why have this “trivial” test file? <a href="https://github.com/diazrenata/birdsize/blob/main/tests/testthat/test-01_trivial.R" class="external-link uri">https://github.com/diazrenata/birdsize/blob/main/tests/testthat/test-01_trivial.R</a> +<ul><li> +<em>Response</em>: I use this to test that CI is working, but it’s not needed now the package is built. Deleted!</li> +</ul></li> +<li>in test code you don’t need to write birdsize::: as testthat loads your package code. Example <a href="https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/tests/testthat/test-02_included_data.R#L13" class="external-link uri">https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/tests/testthat/test-02_included_data.R#L13</a> +<ul><li> +<em>Response</em>: These are removed!</li> +</ul></li> +<li>why are some expectations commented out? <a href="https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/tests/testthat/test-07_simulate_community.R#L34" class="external-link uri">https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/tests/testthat/test-07_simulate_community.R#L34</a> +<ul><li> +<em>Response</em>: These were vestigial, removed!</li> +</ul></li> </ul></div> diff --git a/docs/review_template.html b/docs/review_template.html index c63fff1..32ae479 100644 --- a/docs/review_template.html +++ b/docs/review_template.html @@ -44,6 +44,9 @@ <a href="articles/species.html">species</a> </li> </ul></li> +<li> + <a href="news/index.html">Changelog</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/diazrenata/birdsize/" class="external-link"> <span class="fab fa-github fa-lg"></span> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index ef516a2..fa50681 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -54,6 +54,9 @@ <url> <loc>/LICENSE.html</loc> </url> + <url> + <loc>/news/index.html</loc> + </url> <url> <loc>/reference/add_estimated_sds.html</loc> </url> diff --git a/manuscript/application_ms.Rmd b/manuscript/application_ms.Rmd deleted file mode 100644 index 262f4e7..0000000 --- a/manuscript/application_ms.Rmd +++ /dev/null @@ -1,215 +0,0 @@ ---- -title: "Simulating avian body mass measurements using the R package `birdsize`" -author: "Renata M. Diaz" -output: - word_document: default - pdf_document: default -csl: ecology.csl -bibliography: refs.bib ---- - -# Introduction - -Different currencies of measurement - e.g. total number of individuals, total biomass, or total metabolic flux or energy use - provide linked, but qualitatively very different, perspectives on the structure and function of ecological systems (@white2007). The study of the interrelated dynamics of size structure, species composition, individual abundance, and biomass and energy use is well-established for systems for which data on both individuals' body sizes and individual organismal abundance are widely available, including aquatic systems, terrestrial forest systems, and, to a lesser extent, small mammal systems (@kerr2001, @white2007). Work in these systems has yielded important insight into - for example - how ecological degradation can manifest in the relationship between total abundance and total biomass (@warwick1994), or how shifts in community-wide mean body size can buffer total energy use against apparent changes in total individual abundance (@white2004). Efforts to generalize these efforts to terrestrial vertebrate systems have been constrained due to the lack of body size measurements for these communities (@white2007, @thibault2011). Sampling methodologies for avian communities often rely on visual or auditory point-counts, which provide information about species abundance and diversity but do not directly capture information about body size or energy use. - -The `birdsize` R package offers a way around this limitation by estimating individual-level (and, from there, population or community-wide) body size measurements for birds given either species identity or a species' mean and/or standard deviation of body size. Birds exhibit determinate growth, and `birdsize` assumes that intraspecific body size distributions for birds are, to a first approximation, well-described by normal distributions parameterized with a species-specific mean and standard deviation (see also @thibault2011). Moreover, there is a strong scaling relationship between a species' mean body size and its standard deviation of body size, meaning that, for species for which the standard deviation is not known, the standard deviation can be estimated from the mean (see also @thibault2011). Estimates obtained in this way are, of course, considerably less precise than those that could be obtained through exhaustive field sampling, and may not be appropriate for all use cases. However, given the logistical constraints on field operations of this scale (and the even harsher constraint of time, which prevents us from retroactively taking these measurements for ecological timeseries), `birdsize` makes it possible to conduct macroecological-scale analyses of avian communities that would not otherwise be possible. This approach was first used at scale by @thibault2011 and subsequently by @diaz2022b (in review). `birdsize` formalizes this method and makes it accessible via a straightforward user interface, in order to facilitate use by other research groups with diverse use cases. - -# The estimation procedure in `birdsize` - -The core functionality of `birdsize` is to generate estimates of individual body size for populations of birds by drawing from a normal distribution parameterized with a species-level mean and standard deviation of body size. It includes built-in values for these parameters for 443 species found in the North American Breeding Bird Survey (@pardieck2019), and can accept user-supplied parameter values for additional species. - -For the 443 species included with `birdsize`, mean and standard deviation values were manually obtained from the CRC Handbook of Avian Body Masses (@dunning2008). These species are listed in the data frame `birdsize::known_species`. Many species in @dunning2008 have multiple records from different time periods, locations, and subspecies. In these instances, parameter values are averaged across records to obtain a single species-wide value. For records in @dunning2008 with mean, but no standard deviation, reported, the standard deviation is estimated via a scaling relationship between the mean and standard deviation of body mass (see also @thibault2011). Specifically, a linear model of the form `log(variance(body_size)) ~ log(mean(body_size))` has a model R^2 of 0.89, and produces the scaling relationship of `variance(body_size) = 0.0047(body_size) ^ 2.01`. This scaling relationship is used to generate estimated standard deviations for records without standard deviation recorded, affecting 353 of 928 raw records. - -A user may also manually supply parameter values, in order to generate estimates for species not included in `birdsize::knownspecies`, or to use different parameter values than those included with `birdsize`. This may be of particular interest for users wishing to explore questions related to (for example) intraspecific variation in body size across different populations of the same species, or extending to species not common to North America. In this case, if both mean and standard deviation are supplied, they will be used, and if only the mean is provided, the standard deviation is estimated via the scaling relationship explained above. - -# Population and community-wide summaries - -While `birdsize` generates estimated body size measurements at the level of individual birds, in many instances the quantity of interest is actually the population or community-wide total biomass or metabolic rate. Indeed, given the several layers of estimation involved in obtaining measurements via `birdsize`, it is likely to generally be more appropriate to focus on these aggregate properties than on estimates for "individuals". Accordingly, `birdsize` includes functions to compute these summaries, grouping by species, year, or other variables supplied by the user. These are demonstrated in the package vignettes and use cases, below. - -# Integration with the Breeding Bird Survey - -The methodology in `birdsize` was first developed and applied to the North American Breeding Bird Survey, and `birdsize` is built to naturally accommodate Breeding Bird Survey data obtained from ScienceBase (@pardieck2019) or tools such as the Data Retriever (@senyondo2017). There is no actual data from the Breeding Bird Survey included in the `birdsize` package, and users are encouraged to access the most up-to-date data from the creators directly. To facilitate this, the `bbs-data` and demonstration vignettes illustrate how to access these data and use them with `birdsize`, and the example data tables in `birdsize` (i.e. `demo_route_raw` and `demo_route_clean`) contain synthetic data matching the format of the Breeding Bird Survey. - -However, `birdsize` is not constrained to work _only_ with Breeding Bird Survey data. It accepts any dataset, real or synthetic, that includes population sizes and species identity and/or body size parameters (see above); see Use case #3, below. - -# Use case 1: Simulation over the Breeding Bird Survey timeseries - -```{r setup, include = F, echo = F} - -library(birdsize) -library(dplyr) -library(ggplot2) -theme_set(theme_bw()) - -``` - -A common anticipated use case for `birdsize` is to generate estimates of species- and community- level biomass and metabolic rate for a Breeding Bird Survey route over time. Here, we generate these estimates using the `demo_route_raw` dataset, which has the same shape and structure as data from the Breeding Bird Survey, but contains simulated values for the actual data. - -First, it is recommended to clean the raw data to remove species poorly sampled via Breeding Bird Survey methods and remove records not identified to species. This is accomplished using the `filter_bbs_survey` function: - -```{r} - -clean_data = filter_bbs_survey(demo_route_raw) -head(clean_data) - -``` - -For the purposes of simulating body size and metabolic rate, the relevant columns in these data are `year`, `aou`, and `speciestotal`, which refer to the year of the survey, the species identity, and the total number of individuals of that species recorded on that route in that year, respectively. - -Given a dataframe like this, `birdsize::community_generate` iterates over rows and draw `speciestotal` individuals of the appropriate species (identified by the `aou`, or species code). The resulting data frame has one row per simulated individual. It retains all columns from the original data frame, and adds columns for `sim_species_id`, `genus`, `species`, `individual_mass`, `individual_bmr`, `mean_size`, `sd_size`, `abundance`, and `sd_method`. Most of these are bookkeeping columns explained in the package documentation (see `?birdsize::community_generate`). Of particular relevance are the `individual_mass` and `individual_bmr` columns, which include the estimated body mass (in grams) and estimated basal metabolic rate for each simulated "individual". The `sd_method` column notes which method (see above) was used to obtain parameters for the species' mean and standard deviation body size. In this instance, it is `AOU lookup`, meaning parameters were obtained based on the `aou` column. - -```{r} - -simulated_community <- community_generate(clean_data) - -head(simulated_community) - -``` - -These individual-level estimates can be condensed into year and species totals using `birdsize::community_summarize`. Summarizing by `"species_and_year"` will produce species-level totals for each year surveyed: - -```{r} - -annual_species_summaries <- community_summarize(simulated_community, level = "species_and_year") - -head(annual_species_summaries) - -``` - -Summarizing by only `"year"` will produce community-wide totals (over all species) for each year:: - -```{r} - -annual_summaries <- community_summarize(simulated_community, level = "year") - -head(annual_summaries) -``` - -Similarly, summarizing by only `"species"` will produce species-level totals over all years: - - -```{r} - -species_summaries <- community_summarize(simulated_community, level = "species") - -head(species_summaries) - -``` - - -Finally, `community_summarize` can group by other variables as specified by setting `level = "custom"` and supplying column names via the `id_vars` argument. Here, we group by `genus` and `year`: - -```{r} - -genus_year_summaries <- community_summarize(simulated_community, level = "custom", id_vars = c("year", "genus")) - -head(genus_year_summaries) -``` - -These functions can be used to generate plots of species or community level biomass over time. For example, here we plot community-wide biomass in each year surveyed: - -```{r} - -ggplot(annual_summaries, aes(year, total_biomass)) + - geom_line() - -``` - -# Use case 2: Using user-provided parameters to simulate changes in body size over time - -The data tables provided in `birdsize` contain geographically- and time-averaged estimates of mean and standard deviation of body size for each species. In order to investigate - for example - how changes in these parameters over space or time affect the body size distributions and ecosystem function for these systems, a user can provide customized parameter values. - -To do this based on the species data provided in `birdsize`, we can modify the mean body size associated with each species in our toy dataset such that mean body size decreases over time. - -First, we obtain the mean masses for each species in our dataset as provided in `birdsize::sd_table`: - -```{r} - -species_to_simulate <- clean_data |> - select(year, aou) |> - left_join(sd_table) - -head(species_to_simulate) - -``` - -For this example, we can introduce a simple adjustment where `mean_mass` decreases by 1% of its starting value each year, beginning in 1994: - - -```{r} -species_to_simulate <- species_to_simulate |> - mutate(modified_mass = mean_mass - (.01 * (year - 1994) * mean_mass)) |> - mutate(mean_size = modified_mass) - -``` - - - -We can provide these modified `mean_size` values to `community_generate` by adding the `mean_size` column to our original dataset (`clean_data`). Note that, if `aou` or `species` and `genus` are provided, `community_generate` will use these parameters to look up `mean_size` and ignore the user-provided values. To avoid this, we must remove or rename these columns before passing the data: - -```{r} - -parameters_to_add <- species_to_simulate |> - select(aou, mean_size, year) - -clean_data_with_size_change <- clean_data |> - left_join(parameters_to_add) |> - rename(speciescode = aou) - -simulated_size_change <- community_generate(clean_data_with_size_change) - -``` - - -Here, we can examine how the mean body size of each species behaves over time in the simulated data, and see a (fuzzy) decline consistent with the decline we introduced via modification to the parameters: - - -```{r} - -simulated_mean_change <- simulated_size_change |> - group_by(speciescode, year) |> - summarize(mean_mass = mean(individual_mass)) |> - ungroup() - -ggplot(simulated_mean_change, aes(year, mean_mass)) + - geom_point() + - facet_wrap(vars(speciescode), scales = "free") - -``` - - -# Use case 3: Simulating imaginary birds - -Finally, the core `community_generate` functionality of `birdsize` can apply to any dataframe that contains species abundances and mean size values. Here, we manually construct such a table for a set of purely simulated bird species: - -```{r} - -fictional_abundance_data <- - data.frame( - sim_species_id = 1:10, - mean_size = sample.int(500, size = 10), - speciestotal = round(rlnorm(10, 4, 1)) - ) - -fictional_community_data <- community_generate(fictional_abundance_data) - - -``` - -```{r} - -fictional_community_summary <- community_summarize(fictional_community_data, level = "species") |> - mutate(sim_species_id = as.factor(sim_species_id)) - - -ggplot(fictional_community_summary, aes(sim_species_id, total_abundance)) + - geom_col() + - ggtitle("Total abundance for each fictional species") - -ggplot(fictional_community_summary, aes(sim_species_id, total_biomass)) + - geom_col() + - ggtitle("Total simulated biomass for each fictional species") - -``` - -# References diff --git a/manuscript/application_ms.docx b/manuscript/application_ms.docx deleted file mode 100644 index a009b4b..0000000 Binary files a/manuscript/application_ms.docx and /dev/null differ diff --git a/manuscript/application_ms.pdf b/manuscript/application_ms.pdf deleted file mode 100644 index 52c6468..0000000 Binary files a/manuscript/application_ms.pdf and /dev/null differ diff --git a/manuscript/ecology.csl b/manuscript/ecology.csl deleted file mode 100644 index 452c44a..0000000 --- a/manuscript/ecology.csl +++ /dev/null @@ -1,188 +0,0 @@ -<?xml version="1.0" encoding="utf-8"?> -<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" default-locale="en-US" version="1.0" demote-non-dropping-particle="sort-only"> - <info> - <title>Ecology</title> - <id>http://www.zotero.org/styles/ecology</id> - <link href="http://www.zotero.org/styles/ecology" rel="self"/> - <link href="http://esapubs.org/esapubs/AuthorInstructions.htm" rel="documentation"/> - <author> - <name>Rintze Zelle</name> - <uri>http://twitter.com/rintzezelle</uri> - </author> - <category citation-format="author-date"/> - <category field="biology"/> - <issn>0012-9658</issn> - <updated>2015-07-27T08:57:33+00:00</updated> - <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights> - </info> - <macro name="container-contributors"> - <choose> - <if type="chapter paper-conference" match="any"> - <text term="in" suffix=" " font-style="italic"/> - <names variable="editor translator" delimiter=", "> - <name and="text" initialize-with=". 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" prefix=". "> - <text macro="edition"/> - <text macro="publisher"/> - <text macro="access"/> - </group> - </layout> - </bibliography> -</style> diff --git a/manuscript/refs.bib b/manuscript/refs.bib deleted file mode 100644 index eb58b2c..0000000 --- a/manuscript/refs.bib +++ /dev/null @@ -1,7857 +0,0 @@ -@misc{2014, - title = {Manipulated {{Animal Community Database}}}, - year = {2014}, - month = mar, - publisher = {{figshare}}, - doi = {10.6084/m9.figshare.969831.v1}, - abstract = {6,698 records indicated the presence and abundance of animal species, including representatives across trophic groups and size classes documented at 254 sites throughout the world, encompassing a variety of habitats. We accessed peer-reviewed articles, government publications, and theses that were freely available with the Utah State University library subscription and were published in English. We extracted data from articles that reported species-level abundance for a control community and at least one manipulated community.~The data here represent a single data point each for the control treatment and the manipulated treatment(s) in each study. Data came from a wide variety of sites including artificial experiments (i.e., caged exclosures, habitat modules, nutrient addition) and human-mediated ``natural'' experiments (e.g., wildfire or controlled burn, logging, grazed plots, pollution). Sites represent all continents except Antarctica, and widely varying terrestrial animal groups (arachnid, insect, herpetofauna [reptiles and amphibians], mammal, and bird).}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/27EVNG7C/969831.html} -} - -@misc{2020, - title = {How {{Eugenics Shaped Statistics}}}, - year = {2020}, - month = oct, - journal = {Nautilus | Science Connected}, - abstract = {Exposing the damned lies of three science pioneers.}, - howpublished = {https://nautil.us/how-eugenics-shaped-statistics-9365/}, - langid = {american}, - file = {/Users/renatadiaz/Zotero/storage/8WG6S5KQ/how-eugenics-shaped-statistics-9365.html} -} - -@article{2022, - title = {Process-Explicit Models Reveal the Structure and Dynamics of Biodiversity Patterns}, - year = {2022}, - journal = {SCIENCE ADVANCES}, - pages = {13}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/CMPE664V/2022 - Process-explicit models reveal the structure and d.pdf} -} - -@misc{2022a, - type = {Text.{{Article}}}, - title = {Blue {{Marble}}: {{Next Generation}} +{{Topography}} and {{Bathymetry}} | {{NASA}}}, - shorttitle = {Blue {{Marble}}}, - year = {2022}, - month = apr, - journal = {Blue Marble: Next Generation +Topography and Bathymetry | NASA}, - publisher = {{NASA Earth Observations (NEO)}}, - abstract = {Welcome to NASA Earth Observations, where you can browse and download imagery of satellite data from NASAs Earth Observing System. Over 50 different global datasets are represented with daily, weekly, and monthly snapshots, and images are available in a variety of formats.}, - howpublished = {https://neo.gsfc.nasa.gov/view.php?datasetId=BlueMarbleNG-TB\&date=2004-12-01}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/UJ4LKJUE/view.html} -} - -@misc{2022b, - type = {Text.{{Article}}}, - title = {Sea {{Ice Concentration}} and {{Snow Extent}}, {{Global}} (1 Day - {{SSM}}/{{I}} / {{DMSP}}) | {{NASA}}}, - year = {2022}, - month = apr, - journal = {Sea Ice Concentration and Snow Extent, Global (1 day - SSM/I / DMSP) | NASA}, - publisher = {{NASA Earth Observations (NEO)}}, - abstract = {Welcome to NASA Earth Observations, where you can browse and download imagery of satellite data from NASAs Earth Observing System. Over 50 different global datasets are represented with daily, weekly, and monthly snapshots, and images are available in a variety of formats.}, - howpublished = {https://neo.gsfc.nasa.gov/view.php?datasetId=NISE\_D\&year=2021}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/53TNV3WN/view.html} -} - -@article{acevedo2020, - title = {Teaching Quantitative Ecology Online: {{An}} Evidence-Based Prescription of Best Practices}, - shorttitle = {Teaching Quantitative Ecology Online}, - author = {Acevedo, Miguel A.}, - year = {2020}, - journal = {Ecology and Evolution}, - volume = {10}, - number = {22}, - pages = {12457--12464}, - issn = {2045-7758}, - doi = {10.1002/ece3.6607}, - abstract = {Quantitative skills are becoming central to the undergraduate and graduate curriculum in ecology and evolutionary biology. While previous studies acknowledge that students perceive their quantitative training to be inadequate, there is little guidance on best practices. Moreover, with the recent COVID-19 sudden transition to online learning, there is even less guidance on how to effectively teach quantitative ecology online. Here, I synthesize a prescription of pedagogical best practices for teaching quantitative ecology online based on a broad review of the literature on multiple quantitative disciplines. These best practices include the following: (1) design and implement the class to meet learning goals using online strategies specifically; (2) create an open, inclusive, and welcoming online environment that promotes a sense of learning community; (3) acknowledge the diversity of talents and learning strategies; (4) use real-world examples and assessments; (5) account for gaps in knowledge; (6) emphasize the modeling cycle process; (7) focus on developing ideas rather than tools or procedures; (8) if needed, introduce computational tools thoroughly before combining them with mathematical or statistical concepts; (9) evaluate the course constantly; and (10) put your heart and soul into the class. I hope these practices help fellow instructors of quantitative ecology facing similar challenges in providing our students with the knowledge and skills needed to meet the challenges of the future.}, - langid = {english}, - keywords = {active learning,ecological modeling,online learning,pedagogy,quantitative ecology,statistics}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.6607}, - file = {/Users/renatadiaz/Zotero/storage/982GUHX4/Acevedo - 2020 - Teaching quantitative ecology online An evidence-.pdf;/Users/renatadiaz/Zotero/storage/ZV4EPKE4/ece3.html} -} - -@article{allington2013, - title = {Niche Opportunities and Invasion Dynamics in a Desert Annual Community}, - author = {Allington, Ginger R. H. and Koons, David N. and Ernest, S. K. Morgan and Schutzenhofer, Michele R. and Valone, Thomas J.}, - year = {2013}, - journal = {Ecology Letters}, - volume = {16}, - number = {2}, - pages = {158--166}, - issn = {1461-0248}, - doi = {10.1111/ele.12023}, - abstract = {Although many factors influence the ability of exotics to invade successfully, most studies focus on only a few variables to explain invasion; attempts at theoretical synthesis are largely untested. The niche opportunities framework proposes that the demographic success of an invader is largely affected by the availability of resources and the abundance of its enemies. Here, we use a 31-year study from a desert ecosystem to examine the niche opportunities framework via the invasion of the annual plant Erodium cicutarium. While the invader remained rare for two decades, a decline in granivory combined with an ideal climate window created an opportunity for E. cicutarium to escape control and become the dominant annual plant in the community. We show that fluctuations in consumption and resources can create niche opportunities for invaders and highlight the need for additional long-term studies to track the influence of changing climate and community dynamics on invasions.}, - langid = {english}, - keywords = {Community reorganisation,competition,Erodium cicutarium,exotic species,granivory,rodents}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12023} -} - -@article{andres, - title = {Combining Sampling Gear to Optimally Inventory Species Highlights the Efficiency of {{eDNA}} Metabarcoding}, - author = {Andres, Kara J. and Lambert, Timothy D. and Lodge, David M. and Andr{\'e}s, Jose and Jackson, James R.}, - journal = {Environmental DNA}, - volume = {n/a}, - number = {n/a}, - issn = {2637-4943}, - doi = {10.1002/edn3.366}, - abstract = {Biodiversity surveys may require the use of multiple types of sampling gear to maximize the efficiency of species detections, yet few studies have investigated how to optimally distribute effort among gear. In this study, we conducted eDNA metabarcoding and capture-based sampling surveys (electrofishing, fyke netting, gillnetting, and seining) to sample fish species richness in a large northern temperate lake. We evaluated the success of the sampling methods individually and in combination to determine the allocation of effort and cost across sampling gear that provides the optimal approach for lake-wide species inventories. We found that eDNA metabarcoding detected more species than any other sampling method, including 11 species that were not detected with any capture-based approach. Optimal gear combination analyses revealed that detected species richness is maximized when most of the effort or budget is allocated to eDNA metabarcoding, with smaller allocations to seining and fyke netting. eDNA metabarcoding and capture sampling gear showed similar patterns of spatial heterogeneity in the fish community across habitat types, with pelagic samples forming a group that was distinct from nearshore samples. Our results indicate that eDNA metabarcoding is a rapid and cost-efficient tool for biodiversity monitoring and that assessing the complementarity of multiple sampling types can inform the development of optimal approaches for measuring fish species richness.}, - langid = {english}, - keywords = {biodiversity,cost efficiency,environmental DNA,fisheries,optimal gear combination,sampling effort,species richness}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.366}, - file = {/Users/renatadiaz/Zotero/storage/WSH696W3/Andres et al. - Combining sampling gear to optimally inventory spe.pdf;/Users/renatadiaz/Zotero/storage/2WDS4C2S/edn3.html} -} - -@article{appling2022, - title = {Machine Learning for Understanding Inland Water Quantity, Quality, and Ecology}, - author = {Appling, Alison Paige and Oliver, Samantha Kay and Read, Jordan S. and Sadler, Jeffrey Michael and Zwart, Jacob}, - year = {2022}, - month = sep, - publisher = {{EarthArXiv}}, - abstract = {This chapter provides an overview of machine learning models and their applications to the science of inland waters. Such models serve a wide range of purposes for science and management: predicting water quality, quantity, or ecological dynamics across space, time, or hypothetical scenarios; vetting and distilling raw data for further modeling or analysis; generating and exploring hypotheses; estimating physically or biologically meaningful parameters for use in further modeling; and revealing patterns in complex, multidimensional data or model outputs. An important research frontier is the injection of limnological knowledge into machine-learning models, which has shown great promise for increasing such models' accuracy, trustworthiness, and interpretability. Here we describe a few of the most powerful machine learning tools, describe best practices for employing these tools and injecting knowledge guidance, and give examples of their applications to advance understanding of inland waters.}, - copyright = {CC0 1.0 Universal - Public Domain Dedication}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/IAVQFDNC/Appling et al. - 2022 - Machine learning for understanding inland water qu.pdf;/Users/renatadiaz/Zotero/storage/XWXSNGWP/3565.html} -} - -@article{arranz, - title = {Species Compositions Mediate Biomass Conservation: The Case of Lake Fish Communities}, - shorttitle = {Species Compositions Mediate Biomass Conservation}, - author = {Arranz, Ignasi and Fournier, Bertrand and Lester, Nigel P. and Shuter, Brian J. and {Peres-Neto}, Pedro R.}, - journal = {Ecology}, - volume = {n/a}, - number = {n/a}, - pages = {e3608}, - issn = {1939-9170}, - doi = {10.1002/ecy.3608}, - abstract = {Environmental and geographical factors are known to influence the number, distribution and combination of species that coexist within ecological communities. This, in turn, should influence ecosystem functions such as biomass conservation, or the ability of a community to sustain biomass from small to large organisms. We tested this hypothesis by assessing the role of environmental factors in determining how biomass is conserved in over 600 limnetic fish communities spread across a broad geographic gradient in Canada. Comprehensive and accurate information on water conditions and community characteristics such as taxonomy, abundance, biomass and size distributions were used in our assessment. Results showed that species combinations emerge as one of the main predictors of biomass conservation among the effects of individual species and abiotic factors. Our study highlights the strong role that geographic patterns in the distribution of species can play in shaping key ecosystem functions, with consequences for ecosystem services such as the provision of harvestable fish biomass.}, - langid = {english}, - keywords = {Biomass distribution,community composition,diversity patterns,environmental filtering,species effect,trophic food web}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3608}, - file = {/Users/renatadiaz/Zotero/storage/WU37LDK4/ecy.html} -} - -@article{arribas2021, - title = {The Limited Spatial Scale of Dispersal in Soil Arthropods Revealed with Whole-Community Haplotype-Level Metabarcoding}, - author = {Arribas, Paula and And{\'u}jar, Carmelo and {Salces-Castellano}, Antonia and Emerson, Brent C. and Vogler, Alfried P.}, - year = {2021}, - journal = {Molecular Ecology}, - volume = {30}, - number = {1}, - pages = {48--61}, - issn = {1365-294X}, - doi = {10.1111/mec.15591}, - abstract = {Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype-level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for {$>$}1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.}, - langid = {english}, - keywords = {cMBC,dispersal,distance decay,endemism,haplotype,soil mesofauna,speciation scale}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.15591}, - file = {/Users/renatadiaz/Zotero/storage/ZYEHCMDI/Arribas et al. - 2021 - The limited spatial scale of dispersal in soil art.pdf;/Users/renatadiaz/Zotero/storage/XDUE3KWQ/mec.html} -} - -@article{attina2021, - title = {Genetic Variation in Neotropical Butterflies Is Associated with Sampling Scale, Species Distributions, and Historical Forest Dynamics}, - author = {Attin{\'a}, Natal{\'i} and N{\'u}{\~n}ez Bustos, Ezequiel O. and Lijtmaer, Dar{\'i}o A. and Hebert, Paul D. N. and Tubaro, Pablo L. and Lavinia, Pablo D.}, - year = {2021}, - journal = {Molecular Ecology Resources}, - volume = {21}, - number = {7}, - pages = {2333--2349}, - issn = {1755-0998}, - doi = {10.1111/1755-0998.13441}, - abstract = {Previous studies of butterfly diversification in the Neotropics have focused on Amazonia and the tropical Andes, while southern regions of the continent have received little attention. To address the gap in knowledge about the Lepidoptera of temperate South America, we analysed over 3000 specimens representing nearly 500 species from Argentina for a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Representing 42\% of the country's butterfly fauna, collections targeted species from the Atlantic and Andean forests, and biodiversity hotspots that were previously connected but are now isolated. We assessed COI effectiveness for species discrimination and identification and how its performance was affected by geographic distances and taxon coverage. COI data also allowed to study patterns of genetic variation across Argentina, particularly between populations in the Atlantic and Andean forests. Our results show that COI discriminates species well, but that identification success is reduced on average by 20\% as spatial and taxonomic coverage rises. We also found that levels of genetic variation are associated with species' spatial distribution type, a pattern which might reflect differences in their dispersal and colonization abilities. In particular, intraspecific distance between populations in the Atlantic and Andean forests was significantly higher in species with disjunct distributions than in those with a continuous range. All splits between lineages in these forests dated to the Pleistocene, but divergence dates varied considerably, suggesting that historical connections between the Atlantic and Andean forests have differentially affected their shared butterfly fauna. Our study supports the fact that large-scale assessments of mitochondrial DNA variation are a powerful tool for evolutionary studies.}, - langid = {english}, - keywords = {butterflies,diversification,DNA barcoding,Neotropics,South American forests,species traits}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13441}, - file = {/Users/renatadiaz/Zotero/storage/ADIQ4EDB/Attiná et al. - 2021 - Genetic variation in neotropical butterflies is as.pdf;/Users/renatadiaz/Zotero/storage/Q8F84B89/1755-0998.html} -} - -@article{auker2020, - title = {Teaching {{R}} in the Undergraduate Ecology Classroom: Approaches, Lessons Learned, and Recommendations}, - shorttitle = {Teaching {{R}} in the Undergraduate Ecology Classroom}, - author = {Auker, Linda A. and Barthelmess, Erika L.}, - year = {2020}, - journal = {Ecosphere}, - volume = {11}, - number = {4}, - pages = {e03060}, - issn = {2150-8925}, - doi = {10.1002/ecs2.3060}, - abstract = {Learning ecology requires training in data management and analysis. Because of its transparent and flexible nature, R is increasingly used for data management and analysis in the field of ecology. Consequently, job postings targeting candidates with a bachelor's degree and a required knowledge of R have increased over the past ten years. In this paper, we begin by presenting data from the last ten years demonstrating the increase in the use of R, an open-source programming environment, in ecology and its prevalence as a required skill in job descriptions. We then discuss our experiences teaching undergraduates R in two advanced ecology classes using different approaches. One approach, in a course with a field laboratory, focused on collecting, cleaning, and preparing data for analysis. The other approach, in a course without a field laboratory, focused on analyzing existing datasets and applying the results to content discussed in the lecture portion of the course. Our experiences determined that each approach had strengths and weaknesses. We recommend that above all, instructors of ecology and related subjects should be encouraged to include R in their coursework. Furthermore, instructors should be aware of the following: Learning R is a separate skill from learning statistics; writing R assignments is a significant time commitment for course preparation; and there is a tradeoff between teaching R and teaching content. Determining how one's course fits into the curriculum and identifying resources outside of the classroom for students' continued practice will ensure that R training is successful and will extend beyond a one-semester course.}, - langid = {english}, - keywords = {data analysis,data management,pedagogy,R,repeatability,statistics,teaching}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3060}, - file = {/Users/renatadiaz/Zotero/storage/72KY6KY4/Auker and Barthelmess - 2020 - Teaching R in the undergraduate ecology classroom.pdf;/Users/renatadiaz/Zotero/storage/QPUPS8UW/ecs2.html} -} - -@article{austin2006, - title = {Linking {{Movement}}, {{Diving}}, and {{Habitat}} to {{Foraging Success}} in a {{Large Marine Predator}}}, - author = {Austin, Deborah and Bowen, W. Don and McMillan, Jim I. and Iverson, Sara J.}, - year = {2006}, - journal = {Ecology}, - volume = {87}, - number = {12}, - pages = {3095--3108}, - issn = {1939-9170}, - doi = {10.1890/0012-9658(2006)87[3095:LMDAHT]2.0.CO;2}, - abstract = {Establishing where and when predators forage is essential to understanding trophic interactions, yet foraging behavior remains poorly understood in large marine carnivores. We investigated the factors leading to foraging success in gray seals (Halichoerus grypus) in the Northwest Atlantic in the first study to use simultaneous deployments of satellite transmitters, time depth recorders, and stomach-temperature loggers on a free-ranging marine mammal. Thirty-two seals were each fitted with the three types of instrumentation; however, complete records from all three instruments were obtained from only 13 individuals, underscoring the difficulty of such a multi-instrument approach. Our goal was to determine the characteristics of diving, habitat, and movement that predict feeding. We linked diving behavior to foraging success at two temporal scales: trips (days) and bouts (hours) to test models of optimal diving, which indicate that feeding can be predicted by time spent at the bottom of a dive. Using an information-theoretic approach, a Generalized Linear Mixed Model with trip duration and accumulated bottom time per day best explained the number of feeding events per trip, whereas the best predictor of the number of feeding events per bout was accumulated bottom time. We then tested whether characteristics of movement were predictive of feeding. Significant predictors of the number of feeding events per trip were angular variance (i.e., path tortuosity) and distance traveled per day. Finally, we integrated measures of diving, movement, and habitat at four temporal scales to determine overall predictors of feeding. At the 3-h scale, mean bottom time and distance traveled were the most important predictors of feeding frequency, whereas at the 6-h and 24-h time scales, distance traveled alone was most important. Bathymetry was the most significant predictor of feeding at the 12-h interval, with feeding more likely to occur at deeper depths. Our findings indicate that several factors predict feeding in gray seals, but predictor variables differ across temporal scales such that environmental variation becomes important at some scales and not others. Overall, our results illustrate the value of simultaneously recording and integrating multiple types of information to better understand the circumstances leading to foraging success.}, - langid = {english}, - keywords = {bathymetry,feeding probability,gray seals,Halichoerus grypus,Northwest Atlantic,satellite tracking,stomach-temperature telemetry,wildlife telemetry}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9658\%282006\%2987\%5B3095\%3ALMDAHT\%5D2.0.CO\%3B2}, - file = {/Users/renatadiaz/Zotero/storage/66M727MF/Austin et al. - 2006 - Linking Movement, Diving, and Habitat to Foraging .pdf;/Users/renatadiaz/Zotero/storage/BBSG3SZM/0012-9658(2006)87[3095LMDAHT]2.0.html} -} - -@article{azaele2016, - title = {Statistical Mechanics of Ecological Systems: {{Neutral}} Theory and Beyond}, - shorttitle = {Statistical Mechanics of Ecological Systems}, - author = {Azaele, Sandro and Suweis, Samir and Grilli, Jacopo and Volkov, Igor and Banavar, Jayanth R. and Maritan, Amos}, - year = {2016}, - month = jul, - journal = {Reviews of Modern Physics}, - volume = {88}, - number = {3}, - pages = {035003}, - issn = {0034-6861, 1539-0756}, - doi = {10.1103/RevModPhys.88.035003}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/U8PGLRIZ/Azaele et al. - 2016 - Statistical mechanics of ecological systems Neutr.pdf} -} - -@article{bahlai2021, - title = {The Broken Window: {{An}} Algorithm for Quantifying and Characterizing Misleading Trajectories in Ecological Processes}, - shorttitle = {The Broken Window}, - author = {Bahlai, Christie A. and White, Easton R. and Perrone, Julia D. and Cusser, Sarah and Stack Whitney, Kaitlin}, - year = {2021}, - month = sep, - journal = {Ecological Informatics}, - volume = {64}, - pages = {101336}, - issn = {1574-9541}, - doi = {10.1016/j.ecoinf.2021.101336}, - abstract = {A core issue in temporal ecology is the concept of trajectory\textemdash that is, when can ecologists have reasonable assurance that they know where a system is going? In this paper, we describe a non-random resampling method to directly address the temporal aspects of scaling ecological observations by leveraging existing data. Findings from long-term research sites have been hugely influential in ecology because of their unprecedented longitudinal perspective, yet short-term studies more consistent with typical grant cycles and graduate programs are still the norm. We use long-term insights to create `broken windows,' that is, reanalyze long-term studies from short-term observational perspectives to examine discontinuities in trends at differing temporal scales. The broken window algorithm connects our observations between the short-term and the long-term with an automated, systematic resampling approach: in short, we repeatedly `sample' moving windows of data from existing long-term time series, and analyze these sampled data as if they represented the entire dataset. We then compile typical statistics used to describe the relationship in the sampled data, through repeated samplings, and then use these derived data to gain insights to the questions: 1) how often are the trends observed in short-term data misleading, and 2) can characteristics of these trends be used to predict our likelihood of being misled? We develop a systematic resampling approach, the `broken\_window algorithm, and illustrate its utility with a case study of firefly observations produced at the Kellogg Biological Station Long-Term Ecological Research Site (KBS LTER). Through a variety of visualizations, summary statistics, and downstream analyses, we provide a standardized approach to evaluating the trajectory of a system, the amount of observation required to find a meaningful trajectory in similar systems, and a means of evaluating our confidence in our conclusions.}, - langid = {english}, - keywords = {Data mining,Firefly,Lampyridae,Population,Scaling,Time series,Trajectory}, - file = {/Users/renatadiaz/Zotero/storage/62GIRUAY/Bahlai et al. - 2021 - The broken window An algorithm for quantifying an.pdf;/Users/renatadiaz/Zotero/storage/XIC22G8S/S1574954121001278.html} -} - -@misc{baldridge2015, - title = {{{MiscAbundanceDB}}\_main}, - author = {Baldridge, Elita}, - year = {2015}, - month = apr, - doi = {10.6084/m9.figshare.95843.v4}, - abstract = {Main table with species identity and abundance for MiscAbundanceDB.}, - keywords = {abundance,ecoinformatics,open data,Open data}, - file = {/Users/renatadiaz/Zotero/storage/YUI3BQRZ/95843.pdf} -} - -@article{baldridge2016, - title = {An Extensive Comparison of Species-Abundance Distribution Models}, - author = {Baldridge, Elita and Harris, David J. and Xiao, Xiao and White, Ethan P.}, - year = {2016}, - month = dec, - journal = {PeerJ}, - volume = {4}, - pages = {e2823}, - issn = {2167-8359}, - doi = {10.7717/peerj.2823}, - abstract = {A number of different models have been proposed as descriptions of the species-abundance distribution (SAD). Most evaluations of these models use only one or two models, focus on only a single ecosystem or taxonomic group, or fail to use appropriate statistical methods. We use likelihood and AIC to compare the fit of four of the most widely used models to data on over 16,000 communities from a diverse array of taxonomic groups and ecosystems. Across all datasets combined the log-series, Poisson lognormal, and negative binomial all yield similar overall fits to the data. Therefore, when correcting for differences in the number of parameters the log-series generally provides the best fit to data. Within individual datasets some other distributions performed nearly as well as the log-series even after correcting for the number of parameters. The Zipf distribution is generally a poor characterization of the SAD.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/34XBFZI4/Baldridge et al. - 2016 - An extensive comparison of species-abundance distr.pdf;/Users/renatadiaz/Zotero/storage/TCIXRWYH/Baldridge et al. - 2016 - An extensive comparison of species-abundance distr.pdf;/Users/renatadiaz/Zotero/storage/BPS7VR3K/2823.html;/Users/renatadiaz/Zotero/storage/WLWKVR6C/2823.html} -} - -@article{bannar-martin2018, - title = {Integrating Community Assembly and Biodiversity to Better Understand Ecosystem Function: The {{Community Assembly}} and the {{Functioning}} of {{Ecosystems}} ({{CAFE}}) Approach}, - shorttitle = {Integrating Community Assembly and Biodiversity to Better Understand Ecosystem Function}, - author = {Bannar-Martin, Katherine H. and Kremer, Colin T. and Ernest, S. K. Morgan and Leibold, Mathew A. and Auge, Harald and Chase, Jonathan and Declerck, Steven A. J. and Eisenhauer, Nico and Harpole, Stanley and Hillebrand, Helmut and Isbell, Forest and Koffel, Thomas and Larsen, Stefano and Narwani, Anita and Petermann, Jana S. and Roscher, Christiane and Cabral, Juliano Sarmento and Supp, Sarah R.}, - year = {2018}, - journal = {Ecology Letters}, - volume = {21}, - number = {2}, - pages = {167--180}, - issn = {1461-0248}, - doi = {10.1111/ele.12895}, - abstract = {The research of a generation of ecologists was catalysed by the recognition that the number and identity of species in communities influences the functioning of ecosystems. The relationship between biodiversity and ecosystem functioning (BEF) is most often examined by controlling species richness and randomising community composition. In natural systems, biodiversity changes are often part of a bigger community assembly dynamic. Therefore, focusing on community assembly and the functioning of ecosystems (CAFE), by integrating both species richness and composition through species gains, losses and changes in abundance, will better reveal how community changes affect ecosystem function. We synthesise the BEF and CAFE perspectives using an ecological application of the Price equation, which partitions the contributions of richness and composition to function. Using empirical examples, we show how the CAFE approach reveals important contributions of composition to function. These examples show how changes in species richness and composition driven by environmental perturbations can work in concert or antagonistically to influence ecosystem function. Considering how communities change in an integrative fashion, rather than focusing on one axis of community structure at a time, will improve our ability to anticipate and predict changes in ecosystem function.}, - langid = {english}, - keywords = {Biodiversity,community assembly,composition,dispersal,ecosystem function,metacommunity,Price equation}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12895}, - file = {/Users/renatadiaz/Zotero/storage/I9Q2SP78/Bannar‐Martin et al. - 2018 - Integrating community assembly and biodiversity to.pdf;/Users/renatadiaz/Zotero/storage/KYBKIMLI/ele.html} -} - -@article{bar-on2018, - title = {The Biomass Distribution on {{Earth}}}, - author = {{Bar-On}, Yinon M. and Phillips, Rob and Milo, Ron}, - year = {2018}, - month = jun, - journal = {Proceedings of the National Academy of Sciences}, - volume = {115}, - number = {25}, - pages = {6506--6511}, - publisher = {{National Academy of Sciences}}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.1711842115}, - abstract = {A census of the biomass on Earth is key for understanding the structure and dynamics of the biosphere. However, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. Here, we assemble the overall biomass composition of the biosphere, establishing a census of the {$\approx$}550 gigatons of carbon (Gt C) of biomass distributed among all of the kingdoms of life. We find that the kingdoms of life concentrate at different locations on the planet; plants ({$\approx$}450 Gt C, the dominant kingdom) are primarily terrestrial, whereas animals ({$\approx$}2 Gt C) are mainly marine, and bacteria ({$\approx$}70 Gt C) and archaea ({$\approx$}7 Gt C) are predominantly located in deep subsurface environments. We show that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of {$\approx$}6 Gt C of marine biota, doubling the previous estimated quantity. Our analysis reveals that the global marine biomass pyramid contains more consumers than producers, thus increasing the scope of previous observations on inverse food pyramids. Finally, we highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined and report the historical impact of humanity on the global biomass of prominent taxa, including mammals, fish, and plants.}, - chapter = {Biological Sciences}, - copyright = {Copyright \textcopyright{} 2018 the Author(s). Published by PNAS.. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).}, - langid = {english}, - pmid = {29784790}, - keywords = {biomass,biosphere,ecology,quantitative biology}, - file = {/Users/renatadiaz/Zotero/storage/4M6MRTSH/Bar-On et al. - 2018 - The biomass distribution on Earth.pdf;/Users/renatadiaz/Zotero/storage/Z4AG28XX/6506.html} -} - -@article{barberan2014, - title = {The Microbial Contribution to Macroecology}, - author = {Barber{\'a}n, Albert and Casamayor, Emilio O. and Fierer, Noah}, - year = {2014}, - journal = {Frontiers in Microbiology}, - volume = {5}, - pages = {203}, - issn = {1664-302X}, - doi = {10.3389/fmicb.2014.00203}, - abstract = {There has been a recent explosion of research within the field of microbial ecology that has been fueled, in part, by methodological improvements that make it feasible to characterize microbial communities to an extent that was inconceivable only a few years ago. Furthermore, there is increasing recognition within the field of ecology that microorganisms play a critical role in the health of organisms and ecosystems. Despite these developments, an important gap still persists between the theoretical framework of macroecology and microbial ecology. We highlight two idiosyncrasies of microorganisms that are fundamental to understanding macroecological patterns and their mechanistic drivers. First, high dispersal rates provide novel opportunities to test the relative importance of niche, stochastic, and historical processes in structuring biological communities. Second, high speciation rates potentially lead to the convergence of ecological and evolutionary time scales. After reviewing these unique aspects, we discuss strategies for improving the conceptual integration of microbes into macroecology. As examples, we discuss the use of phylogenetic ecology as an integrative approach to explore patterns across the tree of life. Then we demonstrate how two general theories of biodiversity (i.e., the recently developed theory of stochastic geometry and the neutral theory) can be adapted to microorganisms. We demonstrate how conceptual models that integrate evolutionary and ecological mechanisms can contribute to the unification of microbial ecology and macroecology.}, - file = {/Users/renatadiaz/Zotero/storage/Z2HY7BNQ/Barberán et al. - 2014 - The microbial contribution to macroecology.pdf} -} - -@article{barker2022, - title = {Introducing the {{FAIR Principles}} for Research Software}, - author = {Barker, Michelle and Chue Hong, Neil P. and Katz, Daniel S. and Lamprecht, Anna-Lena and {Martinez-Ortiz}, Carlos and Psomopoulos, Fotis and Harrow, Jennifer and Castro, Leyla Jael and Gruenpeter, Morane and Martinez, Paula Andrea and Honeyman, Tom}, - year = {2022}, - month = oct, - journal = {Scientific Data}, - volume = {9}, - number = {1}, - pages = {622}, - publisher = {{Nature Publishing Group}}, - issn = {2052-4463}, - doi = {10.1038/s41597-022-01710-x}, - abstract = {Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value. The FAIR for Research Software (FAIR4RS) Working Group has adapted the FAIR Guiding Principles to create the FAIR Principles for Research Software (FAIR4RS Principles). The contents and context of the FAIR4RS Principles are summarised here to provide the basis for discussion of their adoption. Examples of implementation by organisations are provided to share information on how to maximise the value of research outputs, and to encourage others to amplify the importance and impact of this work.}, - copyright = {2022 The Author(s)}, - langid = {english}, - keywords = {Policy,Research management}, - file = {/Users/renatadiaz/Zotero/storage/84Q3BXFL/Barker et al. - 2022 - Introducing the FAIR Principles for research softw.pdf;/Users/renatadiaz/Zotero/storage/U98YXUVT/s41597-022-01710-x.html} -} - -@article{baselga2013, - title = {Whole-Community {{DNA}} Barcoding Reveals a Spatio-Temporal Continuum of Biodiversity at Species and Genetic Levels}, - author = {Baselga, Andr{\'e}s and Fujisawa, Tomochika and {Crampton-Platt}, Alexandra and Bergsten, Johannes and Foster, Peter G. and Monaghan, Michael T. and Vogler, Alfried P.}, - year = {2013}, - month = may, - journal = {Nature Communications}, - volume = {4}, - number = {1}, - pages = {1892}, - publisher = {{Nature Publishing Group}}, - issn = {2041-1723}, - doi = {10.1038/ncomms2881}, - abstract = {A correlation of species and genetic diversity has been proposed but not uniformly supported. Large-scale DNA barcoding provides qualitatively novel data to test for correlations across hierarchical levels (genes, genealogies and species), and may help to unveil the underlying processes. Here we analyse sequence variation in communities of aquatic beetles across Europe ({$>$}5,000 individuals) to test for self-similarity of beta diversity patterns at multiple hierarchical levels. We show that community similarity at all levels decreases exponentially with geographic distance, and initial similarity is correlated with the lineage age, consistent with a molecular clock. Log\textendash log correlations between lineage age, number of lineages, and range sizes, reveal a fractal geometry in time and space, indicating a spatio-temporal continuum of biodiversity across scales. Simulations show that these findings mirror dispersal-constrained models of haplotype distributions. These novel macroecological patterns may be explained by neutral evolutionary processes, acting continuously over time to produce multi-scale regularities of biodiversity.}, - copyright = {2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, - langid = {english}, - keywords = {Biodiversity,Ecological genetics}, - annotation = {Bandiera\_abtest: a Cg\_type: Nature Research Journals Primary\_atype: Research Subject\_term: Biodiversity;Ecological genetics Subject\_term\_id: biodiversity;ecological-genetics}, - file = {/Users/renatadiaz/Zotero/storage/Q3PWPRA7/Baselga et al. - 2013 - Whole-community DNA barcoding reveals a spatio-tem.pdf;/Users/renatadiaz/Zotero/storage/F3NC9BYS/ncomms2881.html} -} - -@article{baselga2015, - title = {Temporal {{Beta Diversity}} of {{Bird Assemblages}} in {{Agricultural Landscapes}}: {{Land Cover Change}} vs. {{Stochastic Processes}}}, - shorttitle = {Temporal {{Beta Diversity}} of {{Bird Assemblages}} in {{Agricultural Landscapes}}}, - author = {Baselga, Andr{\'e}s and Bonthoux, S{\'e}bastien and Balent, G{\'e}rard}, - year = {2015}, - month = may, - journal = {PLOS ONE}, - volume = {10}, - number = {5}, - pages = {e0127913}, - publisher = {{Public Library of Science}}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0127913}, - abstract = {Temporal variation in the composition of species assemblages could be the result of deterministic processes driven by environmental change and/or stochastic processes of colonization and local extinction. Here, we analyzed the relative roles of deterministic and stochastic processes on bird assemblages in an agricultural landscape of southwestern France. We first assessed the impact of land cover change that occurred between 1982 and 2007 on (i) the species composition (presence/absence) of bird assemblages and (ii) the spatial pattern of taxonomic beta diversity. We also compared the observed temporal change of bird assemblages with a null model accounting for the effect of stochastic dynamics on temporal beta diversity. Temporal assemblage dissimilarity was partitioned into two separate components, accounting for the replacement of species (i.e. turnover) and for the nested species losses (or gains) from one time to the other (i.e. nestedness-resultant dissimilarity), respectively. Neither the turnover nor the nestedness-resultant components of temporal variation were accurately explained by any of the measured variables accounting for land cover change (r2{$<$}0.06 in all cases). Additionally, the amount of spatial assemblage heterogeneity in the region did not significantly change between 1982 and 2007, and site-specific observed temporal dissimilarities were larger than null expectations in only 1\% of sites for temporal turnover and 13\% of sites for nestedness-resultant dissimilarity. Taken together, our results suggest that land cover change in this agricultural landscape had little impact on temporal beta diversity of bird assemblages. Although other unmeasured deterministic process could be driving the observed patterns, it is also possible that the observed changes in presence/absence species composition of local bird assemblages might be the consequence of stochastic processes in which species populations appeared and disappeared from specific localities in a random-like way. Our results might be case-specific, but if stochastic dynamics are generally dominant, the ability of correlative and mechanistic models to predict land cover change effects on species composition would be compromised.}, - langid = {english}, - keywords = {Birds,Census,Cereal crops,Crops,Grasslands,Mathematical models,Species diversity,Stochastic processes}, - file = {/Users/renatadiaz/Zotero/storage/NZA6F2L4/Baselga et al. - 2015 - Temporal Beta Diversity of Bird Assemblages in Agr.pdf;/Users/renatadiaz/Zotero/storage/ZSSGDEKU/article.html} -} - -@article{beare2020, - title = {On the Emergence of a Power Law in the Distribution of {{COVID-19}} Cases}, - author = {Beare, Brendan K. and Toda, Alexis Akira}, - year = {2020}, - month = nov, - journal = {Physica D: Nonlinear Phenomena}, - volume = {412}, - pages = {132649}, - issn = {0167-2789}, - doi = {10.1016/j.physd.2020.132649}, - abstract = {The first confirmed case of Coronavirus Disease 2019 (COVID-19) in the US was reported on January 21, 2020. By the end of March, 2020, there were more than 180,000 confirmed cases in the US, distributed across more than 2000 counties. We find that the right tail of this distribution exhibits a power law, with Pareto exponent close to one. We investigate whether a simple model of the growth of COVID-19 cases involving Gibrat's law can explain the emergence of this power law. The model is calibrated to match (i) the growth rates of confirmed cases, and (ii) the varying lengths of time during which COVID-19 had been present within each county. Thus calibrated, the model generates a power law with Pareto exponent nearly exactly equal to the exponent estimated directly from the distribution of confirmed cases across counties at the end of March.}, - langid = {english}, - keywords = {Coronavirus,COVID-19,Gibrat’s law,Mathematical modeling of epidemics,Power law,Tauberian theorem}, - file = {/Users/renatadiaz/Zotero/storage/MIFKZCEC/Beare and Toda - 2020 - On the emergence of a power law in the distributio.pdf;/Users/renatadiaz/Zotero/storage/73TV8XJU/S0167278920304711.html} -} - -@misc{begueria2017, - title = {{{SPEI}}: {{Calculation}} of the {{Standardised Precipitation-Evapotranspiration Index}}}, - author = {Beguer{\'i}a, Santiago and {Vicente-Serrano}, Sergio M.}, - year = {2017} -} - -@article{beisner2006, - title = {The {{Role}} of {{Environmental}} and {{Spatial Processes}} in {{Structuring Lake Communities}} from {{Bacteria}} to {{Fish}}}, - author = {Beisner, Beatrix E. and {Peres-Neto}, Pedro R. and Lindstr{\"o}m, Eva S. and Barnett, Allain and Longhi, Maria Lorena}, - year = {2006}, - journal = {Ecology}, - volume = {87}, - number = {12}, - pages = {2985--2991}, - issn = {1939-9170}, - doi = {10.1890/0012-9658(2006)87[2985:TROEAS]2.0.CO;2}, - abstract = {We assessed the relative roles of local environmental conditions and dispersal on community structure in a landscape of lakes for the major trophic groups. We use taxonomic presence\textendash absence and abundance data for bacteria, phytoplankton, zooplankton, and fish from 18 lakes in southern Quebec, Canada. The question of interest was whether communities composed of organisms with more limited dispersal abilities, because of size and life history (zooplankton and fish) would show a different effect of lake distribution than communities composed of good dispersers (bacteria and phytoplankton). We examine the variation in structure attributable to local environmental (i.e., lake chemical and physical variables) vs. dispersal predictors (i.e., overland and watercourse distances between lakes) using variation partitioning techniques. Overall, we show that less motile species (crustacean zooplankton and fish) are better predicted by spatial factors than by local environmental ones. Furthermore, we show that for zooplankton abundances, both overland and watercourse dispersal pathways are equally strong, though they may select for different components of the community, while for fish, only watercourses are relevant dispersal pathways. These results suggest that crustacean zooplankton and fish are more constrained by dispersal and therefore more likely to operate as a metacommunity than are bacteria and phytoplankton within this studied landscape.}, - langid = {english}, - keywords = {bacteria,dispersal,environmental predictors,fish,lakes,metacommunities,multivariate analysis,phytoplankton,zooplankton}, - file = {/Users/renatadiaz/Zotero/storage/CBNUR8WG/Beisner et al. - 2006 - The Role of Environmental and Spatial Processes in.pdf;/Users/renatadiaz/Zotero/storage/MZWYHNGM/0012-9658(2006)87[2985TROEAS]2.0.html} -} - -@article{bello2012, - title = {The Quest for Trait Convergence and Divergence in Community Assembly: Are Null-Models the Magic Wand?}, - shorttitle = {The Quest for Trait Convergence and Divergence in Community Assembly}, - author = {de Bello, Francesco}, - year = {2012}, - journal = {Global Ecology and Biogeography}, - volume = {21}, - number = {3}, - pages = {312--317}, - issn = {1466-8238}, - doi = {10.1111/j.1466-8238.2011.00682.x}, - abstract = {The relevance of neutral versus niche-based community assembly rules (i.e. the processes sorting species present in a larger geographical region into local communities) remains to be demonstrated in ecology and biogeography. To attempt to do this, a number of complex null models are increasingly being used that compare observed community functional diversity (FD, i.e. the extent of trait dissimilarity between coexisting species) with randomly simulated FD. However, little is known about the performance of these null models in detecting non-neutral community assembly rules such as trait convergence and divergence of communities (supposedly revealing habitat selection and limiting similarity, respectively). Here, using both simulated and field communities, I show that assembly rule detection varies systematically with the magnitude of the observed FD, so that these null models do not really succeed in breaking down the observed functional relationships between species. This is a particular concern, making detection of community assembly dependent on: (1) the pool of samples considered, and (2) the capacity of observed FD to correctly discriminate these rules. Null models should be more thoroughly described and validated before being considered as a magic wand to reveal assembly patterns.}, - langid = {english}, - keywords = {Biodiversity,community assembly,functional trait,neutral theory,species niche,species pool}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1466-8238.2011.00682.x}, - file = {/Users/renatadiaz/Zotero/storage/GW38DWGJ/Bello - 2012 - The quest for trait convergence and divergence in .pdf;/Users/renatadiaz/Zotero/storage/II7SI27C/j.1466-8238.2011.00682.html} -} - -@misc{bernhardt2014, - title = {Pre-Fire and {{Post-re}} Species Abundance ({{Braun-blaunquet}} Abundance Methods) for 14 Sites from 2001-2006.}, - author = {Bernhardt, Emily and Bonanza Creek LTER}, - year = {2014}, - publisher = {{Environmental Data Initiative}}, - doi = {10.6073/PASTA/E32EA21226801A893ADAE1E8B42BFB48} -} - -@article{bertram2019, - title = {Comparison of Two Maximum Entropy Models Highlights the Metabolic Structure of Metacommunities as a Key Determinant of Local Community Assembly}, - author = {Bertram, Jason and Newman, Erica A. and Dewar, Roderick C.}, - year = {2019}, - month = sep, - journal = {Ecological Modelling}, - volume = {407}, - pages = {108720}, - issn = {0304-3800}, - doi = {10.1016/j.ecolmodel.2019.108720}, - abstract = {The principle of Maximum Entropy (MaxEnt) promises a novel approach for understanding community assembly. Despite reproducing a variety of observed species abundance patterns, MaxEnt models in ecology have been hampered by disparate model assumptions and interpretations. A recurring challenge is that MaxEnt predictions are highly sensitive to the level of detail used to describe the community being modeled, and there seems to be no reason to prefer one level of detail over another. Here we present of formal unification of two previously developed MaxEnt models which differ in their level of detail, but which are otherwise mathematically similar. The less detailed model, ``Maximum Entropy Theory of Ecology'' (METE), does not resolve species identity or explicitly represent species-specific traits. The more detailed model, ``Very Entropic Growth'' (VEG), defines each separate species by its per capita metabolic rate \,{$\epsilon$} and assumes a ``density of species'' function {$\rho$}({$\epsilon$}) representing the distribution of {$\epsilon$} in the metacommunity. A formal comparison of METE and VEG then highlights {$\rho$}({$\epsilon$}) as a key determinant of local community assembly. In particular, appropriate choice of {$\rho$}({$\epsilon$}) in VEG can produce more realistic predictions for the metabolic-rank distribution of local communities than METE, which does not explicitly account for metacommunity structure. This opens new avenues of inquiry about what determines metacommunity structure in nature and suggests possible ways to improve METE.}, - langid = {english}, - keywords = {Community assembly,Macroecology,Metabolic requirements,Resource partitioning,Species-abundance distribution,Statistical aggregation} -} - -@article{bestelmeyer, - title = {Variation in Ecological Resilience: A Fundamental Concept for Rangeland Ecology}, - author = {Bestelmeyer, Brandon and Briske, David D and Brown, Joel R and Havstad, Kris M and Skaggs, Rhonda K}, - pages = {23}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/AN8LLBFW/Bestelmeyer et al. - Variation in ecological resilience a fundamental .pdf} -} - -@article{blackburn2018, - title = {Abundance, Biomass and Energy Use of Native and Alien Breeding Birds in {{Britain}}}, - author = {Blackburn, Tim M. and Gaston, Kevin J.}, - year = {2018}, - month = dec, - journal = {Biological Invasions}, - volume = {20}, - number = {12}, - pages = {3563--3573}, - issn = {1573-1464}, - doi = {10.1007/s10530-018-1795-z}, - abstract = {We quantify the contribution of alien species to the total breeding population numbers, biomass and energy use of an entire taxonomic assemblage at a large spatial scale, using data on British birds from 1997 and 2013. A total of 216 native and 16 alien bird species were recorded as breeding in Great Britain across the two census years. Only 2.8\textendash 3.7\% of British breeding bird individuals were alien, but alien species co-opted 11.9\textendash 13.8\% of the energy used by the assemblage, and contributed 19.1\textendash 21.1\% of assemblage biomass. Neither the population sizes nor biomasses of native and alien species differed, on average, in either census, but alien species biomass is higher than native species biomass for a given population size. Species richness underestimates the potential effects of alien bird species in Britain, which have disproportionately high overall biomass and population energy use. The main driver of these effects is the ring-necked pheasant (Phasianus colchicus), which comprised 74\textendash 81\% of alien biomass, yet the breeding population of this species is still only a small fraction of the estimated 35 million birds released in the UK in autumn. The biomass of this release exceeds that of the entire breeding avifauna, and suggests that the pheasant should have an important role in structuring the communities in which it is embedded.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/5KMLR32S/Blackburn and Gaston - 2018 - Abundance, biomass and energy use of native and al.pdf} -} - -@article{bledsoe2019, - title = {Temporal Changes in Species Composition Affect a Ubiquitous Species' Use of Habitat Patches}, - author = {Bledsoe, Ellen K. and Ernest, S. K. Morgan}, - year = {2019}, - journal = {Ecology}, - volume = {100}, - number = {11}, - pages = {e02869}, - issn = {1939-9170}, - doi = {10.1002/ecy.2869}, - abstract = {Across landscapes, shifts in species composition often co-occur with shifts in structural or abiotic habitat features, making it difficult to disentangle the role of competitors and environment on assessments of patch quality. Using over two decades of rodent community data from a long-term experiment, we show that a small, ubiquitous granivore (Chaetodipus penicillatus) shifted its use of different experimental treatments with the establishment of a novel competitor, C. baileyi. Shifts in residency, probability of movement between patches, and the arrival of new individuals in patches altered which treatment supported the highest abundances of C. penicillatus. Our results suggest that the establishment of a new species worsened the quality of the originally preferred treatment, likely by impacting resource availability. Paradoxically, the presence of the new species also increased C. penicillatus' use of the less preferred treatment, potentially through shifts in the competitive network on those plots.}, - langid = {english}, - keywords = {habitat selection,metacommunity,patch preference,patch quality,species composition,species interactions}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2869}, - file = {/Users/renatadiaz/Zotero/storage/FHCU7XG7/Bledsoe and Ernest - 2019 - Temporal changes in species composition affect a u.pdf;/Users/renatadiaz/Zotero/storage/IKJMYKT8/ecy.html} -} - -@article{blonder, - title = {Carrying the {{Moral Burden}} of {{Safe Fieldwork}}}, - author = {Blonder, Benjamin Wong}, - journal = {The Bulletin of the Ecological Society of America}, - volume = {n/a}, - number = {n/a}, - pages = {e2031}, - issn = {2327-6096}, - doi = {10.1002/bes2.2031}, - abstract = {Fieldwork in ecology and the environmental sciences often leads to negative physical and emotional outcomes for workers. I argue that this is largely due to an abdication of responsibility on the part of their supervisors, and that supervisors are charged with carrying three interlinked moral burdens: first, the duty of promoting safety; second, the duty of ensuring safe experiences are accessible to all; and third, the duty of continuing to learn and improve. To help, I offer a set of safety actions that supervisors can easily implement. I then offer a set of personal reflections on how we should think about failure, accountability, learning, repair, and forgiveness in the scientific workplace.}, - langid = {english}, - keywords = {equity,ethics,field safety,field work,inclusion,supervisor}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/bes2.2031}, - file = {/Users/renatadiaz/Zotero/storage/VTXM86BX/Blonder - Carrying the Moral Burden of Safe Fieldwork.pdf;/Users/renatadiaz/Zotero/storage/864SZ7WW/bes2.html} -} - -@article{blonder2014, - title = {Separating {{Macroecological Pattern}} and {{Process}}: {{Comparing Ecological}}, {{Economic}}, and {{Geological Systems}}}, - shorttitle = {Separating {{Macroecological Pattern}} and {{Process}}}, - author = {Blonder, Benjamin and Sloat, Lindsey and Enquist, Brian J. and McGill, Brian}, - year = {2014}, - month = nov, - journal = {PLOS ONE}, - volume = {9}, - number = {11}, - pages = {e112850}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0112850}, - abstract = {Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form (`first-order effects'), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns (`second-order effects'). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.}, - langid = {english}, - keywords = {Biodiversity,Birds,Ecological economics,Economics,Ecosystems,Environmental economics,Geology,Spatial and landscape ecology,Species diversity,Theoretical ecology,United States}, - file = {/Users/renatadiaz/Zotero/storage/CILEX5MJ/Blonder et al. - 2014 - Separating Macroecological Pattern and Process Co.pdf;/Users/renatadiaz/Zotero/storage/U838BTWD/Blonder et al. - 2014 - Separating Macroecological Pattern and Process Co.pdf;/Users/renatadiaz/Zotero/storage/D5IXY4H9/article.html;/Users/renatadiaz/Zotero/storage/TC74G8UY/article.html} -} - -@article{blowes2019, - title = {The Geography of Biodiversity Change in Marine and Terrestrial Assemblages}, - author = {Blowes, Shane A. and Supp, Sarah R. and Ant{\~a}o, Laura H. and Bates, Amanda and Bruelheide, Helge and Chase, Jonathan M. and Moyes, Faye and Magurran, Anne and McGill, Brian and {Myers-Smith}, Isla H. and Winter, Marten and Bjorkman, Anne D. and Bowler, Diana E. and Byrnes, Jarrett E. K. and Gonzalez, Andrew and Hines, Jes and Isbell, Forest and Jones, Holly P. and Navarro, Laetitia M. and Thompson, Patrick L. and Vellend, Mark and Waldock, Conor and Dornelas, Maria}, - year = {2019}, - month = oct, - journal = {Science}, - volume = {366}, - number = {6463}, - pages = {339--345}, - publisher = {{American Association for the Advancement of Science}}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.aaw1620}, - abstract = {Spatial structure of species change Biodiversity is undergoing rapid change driven by climate change and other human influences. Blowes et al. analyze the global patterns in temporal change in biodiversity using a large quantity of time-series data from different regions (see the Perspective by Eriksson and Hillebrand). Their findings reveal clear spatial patterns in richness and composition change, where marine taxa exhibit the highest rates of change. The marine tropics, in particular, emerge as hotspots of species richness losses. Given that human activities are affecting biodiversity in magnitudes and directions that differ across the planet, these findings will provide a much needed biogeographic understanding of biodiversity change that can help inform conservation prioritization. Science, this issue p. 339; see also p. 308 Human activities are fundamentally altering biodiversity. Projections of declines at the global scale are contrasted by highly variable trends at local scales, suggesting that biodiversity change may be spatially structured. Here, we examined spatial variation in species richness and composition change using more than 50,000 biodiversity time series from 239 studies and found clear geographic variation in biodiversity change. Rapid compositional change is prevalent, with marine biomes exceeding and terrestrial biomes trailing the overall trend. Assemblage richness is not changing on average, although locations exhibiting increasing and decreasing trends of up to about 20\% per year were found in some marine studies. At local scales, widespread compositional reorganization is most often decoupled from richness change, and biodiversity change is strongest and most variable in the oceans. Biodiversity change in the marine realm outpaces that in terrestrial systems, and loss is most prevalent in the tropics. Biodiversity change in the marine realm outpaces that in terrestrial systems, and loss is most prevalent in the tropics.}, - chapter = {Research Article}, - copyright = {Copyright \textcopyright{} 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. http://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.}, - langid = {english}, - pmid = {31624208}, - file = {/Users/renatadiaz/Zotero/storage/8L5KQWIJ/Blowes et al. - 2019 - The geography of biodiversity change in marine and.pdf;/Users/renatadiaz/Zotero/storage/LHCN2QA4/Blowes et al. - 2019 - The geography of biodiversity change in marine and.pdf;/Users/renatadiaz/Zotero/storage/96IULWTY/tab-pdf.html;/Users/renatadiaz/Zotero/storage/XKTCUTUF/339.html} -} - -@article{bodmer2021, - title = {The Outstanding Scientist, {{R}}.{{A}}. {{Fisher}}: His Views on Eugenics and Race}, - shorttitle = {The Outstanding Scientist, {{R}}.{{A}}. {{Fisher}}}, - author = {Bodmer, Walter and Bailey, R. A. and Charlesworth, Brian and {Eyre-Walker}, Adam and Farewell, Vernon and Mead, Andrew and Senn, Stephen}, - year = {2021}, - month = apr, - journal = {Heredity}, - volume = {126}, - number = {4}, - pages = {565--576}, - publisher = {{Nature Publishing Group}}, - issn = {1365-2540}, - doi = {10.1038/s41437-020-00394-6}, - copyright = {2021 The Author(s), under exclusive licence to The Genetics Society}, - langid = {english}, - keywords = {Evolution,Genetics}, - file = {/Users/renatadiaz/Zotero/storage/AQD56YAH/Bodmer et al. - 2021 - The outstanding scientist, R.A. Fisher his views .pdf;/Users/renatadiaz/Zotero/storage/RSVHKNEA/s41437-020-00394-6.html} -} - -@incollection{bonar2011, - title = {An Overview of Sampling Issues in Species Diversity and Abundance Surveys}, - booktitle = {Biological {{Diversity}}: {{Frontiers}} in {{Measurement}} and {{Assessment}}}, - author = {Bonar, Scott A. and Fehmi, Jeffrey S. and {Mercado-Silva}, Norman}, - editor = {Magurran, Anne E. and McGill, Brian J.}, - year = {2011}, - pages = {11--24}, - publisher = {{Oxford University Press}}, - address = {{Oxford, UNITED KINGDOM}}, - isbn = {978-0-19-157684-3}, - keywords = {Biodiversity -- Monitoring.,Biodiversity conservation.,Biodiversity.} -} - -@article{borregaard2016, - title = {The General Dynamic Model: Towards a Unified Theory of Island Biogeography?}, - shorttitle = {The General Dynamic Model}, - author = {Borregaard, Michael K. and Matthews, Thomas J. and Whittaker, Robert J.}, - year = {2016}, - journal = {Global Ecology and Biogeography}, - volume = {25}, - number = {7}, - pages = {805--816}, - issn = {1466-8238}, - doi = {10.1111/geb.12348}, - abstract = {Aim Island biogeography focuses on understanding the processes that underlie a set of well-described patterns on islands, but it lacks a unified theoretical framework for integrating these processes. The recently proposed general dynamic model (GDM) of oceanic island biogeography offers a step towards this goal. Here, we present an analysis of causality within the GDM and investigate its potential for the further development of island biogeographical theory. Further, we extend the GDM to include subduction-based island arcs and continental fragment islands. Location A conceptual analysis and a simulation of oceanic islands. Methods We describe the causal relationships between evolutionary and ecological processes implied by the GDM, implement them as a computer simulation and use this to simulate two alternative geological scenarios. Results The dynamics of species richness and rates of evolutionary processes in simulations derived from the mechanistic assumptions of the GDM corresponded broadly to those initially suggested, with the exception of trends in extinction rates. Expanding the model to incorporate different scenarios of island ontogeny and isolation revealed a sensitivity of evolutionary dynamics to attributes of island geology. Main conclusions We argue that the GDM of oceanic island biogeography has the potential to provide a unified framework for island biogeography, integrating geological, ecological and evolutionary processes. Our simulations highlight how the geological dynamics of distinct island types are predicted to lead to markedly different evolutionary dynamics. This sets the stage for a more predictive theory incorporating the processes governing temporal dynamics of species diversity on islands.}, - langid = {english}, - keywords = {Carrying capacity,causal model,GDM,general dynamic theory,island biogeography,oceanic islands,simulation model,species richness,theory of ecology,volcanic islands}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12348}, - file = {/Users/renatadiaz/Zotero/storage/4SWX43LQ/Borregaard et al. - 2016 - The general dynamic model towards a unified theor.pdf;/Users/renatadiaz/Zotero/storage/7WHRSCFC/geb.html} -} - -@article{bowers1987, - title = {Spatial Organization of a Desert Rodent Community: Food Addition and Species Removal}, - shorttitle = {Spatial Organization of a Desert Rodent Community}, - author = {Bowers, M. A. and Thompson, D. B. and Brown, J. H.}, - year = {1987}, - month = apr, - journal = {Oecologia}, - volume = {72}, - number = {1}, - pages = {77--82}, - issn = {1432-1939}, - doi = {10.1007/BF00385048}, - abstract = {From 1977 through 1983 we conducted experiments on a desert rodent community where supplemental seeds were added or certain rodent species and ants were removed from 0.25-ha fenced plots in a Chihuahuan Desert site in southeastern Arizona, USA. In this paper we examine the patterns of microhabitat use relative to vegetative cover by 11 rodent species. The results show that: i) removal of the largest seed-eating species, Dipodomys spectabilis, produced the most pervasive and dramatic shifts in microhabitat use by the remaining rodent species; ii) adding seeds or removing ants had little effect on the spatial use of microhabitats by rodents in this community; and iii) non-granivores were just as likely as granivores to shift microhabitat use when other granivores were removed. We believe these results indicate that both food and foraging microsites are limited but the relegation of subdominant species to lesspreferred microhabitats by the large Dipodomys spectabilis is the major factor underlying the spatial organization of this community. Results also demonstrate that strong interactions among species increase the probability that pathways of indirect interactions through intermediary species are important; these complex linkages may include species that overlap little in food preferences.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2HWKBG2Y/Bowers et al. - 1987 - Spatial organization of a desert rodent community.pdf} -} - -@article{bradford2012, - title = {Contingency in Ecosystem but Not Plant Community Response to Multiple Global Change Factors}, - author = {Bradford, Mark A. and Wood, Stephen A. and Maestre, Fernando T. and Reynolds, James F. and Warren, Robert J.}, - year = {2012}, - journal = {New Phytologist}, - volume = {196}, - number = {2}, - pages = {462--471}, - issn = {1469-8137}, - doi = {10.1111/j.1469-8137.2012.04271.x}, - abstract = {Community and ecosystem responses to global environmental change are contingent on the magnitude of change and interacting global change factors. To reveal whether responses are also contingent on the magnitude of each interacting factor, multifactor, multilevel experiments are required, but are rarely conducted. We exposed model grassland ecosystems to six levels of atmospheric CO2 and six levels of nitrogen enrichment, applying the latter both chronically (simulating deposition) and acutely (simulating fertilization). The 66 treatments were maintained for 6 months under controlled growing conditions, with biomass harvested every 28 d and sorted to species. Aboveground plant productivity responses to CO2 were contingent on nitrogen amount, and the responses to nitrogen amount were dependent on whether applications were chronic or acute. Specifically, productivity responses to increasing CO2 concentrations were accentuated with higher nitrogen enrichments, and productivity was greater when higher nitrogen enrichments were applied acutely. Plant community composition was influenced only by nitrogen enrichment, where the co-dominant grass species with the greatest leaf trait plasticity increasingly dominated with higher nitrogen amounts. Community processes are considered to be unpredictable, but our data suggest that the prediction of the impacts of simultaneous global changes is more complex for ecosystem processes, given that their responses are contingent on the levels of interacting factors.}, - copyright = {\textcopyright{} 2012 The Authors. New Phytologist \textcopyright{} 2012 New Phytologist Trust}, - langid = {english}, - keywords = {carbon dioxide,context dependence,functional leaf traits,global environmental change,interaction,nitrogen deposition,nitrogen fertilization,nonlinear}, - file = {/Users/renatadiaz/Zotero/storage/8VPEZIDY/Bradford et al. - 2012 - Contingency in ecosystem but not plant community r.pdf;/Users/renatadiaz/Zotero/storage/AAG5CVAA/j.1469-8137.2012.04271.html} -} - -@article{brenden2008, - title = {Comment: {{Use}} of {{Piecewise Regression Models}} to {{Estimate Changing Relationships}} in {{Fisheries}}}, - shorttitle = {Comment}, - author = {Brenden, Travis O. and Bence, James R.}, - year = {2008}, - month = jun, - journal = {North American Journal of Fisheries Management}, - volume = {28}, - number = {3}, - pages = {844--846}, - issn = {0275-5947, 1548-8675}, - doi = {10.1577/M07-157.1}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2G259NKN/Brenden and Bence - 2008 - Comment Use of Piecewise Regression Models to Est.pdf} -} - -@article{brommer2015, - title = {Bergmann on the Move: A Temporal Change in the Latitudinal Gradient in Body Mass of a Wild Passerine}, - shorttitle = {Bergmann on the Move}, - author = {Brommer, Jon E. and Hanski, Ilpo K. and Kekkonen, Jaana and V{\"a}is{\"a}nen, Risto A.}, - year = {2015}, - month = oct, - journal = {Journal of Ornithology}, - volume = {156}, - number = {4}, - pages = {1105--1112}, - issn = {2193-7206}, - doi = {10.1007/s10336-015-1211-8}, - abstract = {The latitudinal gradient in body mass, which many organisms show (Bergmann's rule), is thought to be a response to local environmental conditions varying across latitude. Hence, temporal changes in environmental conditions are expected to lead to a shift in Bergmann's rule. We compared house sparrow Passer domesticus body mass measures taken in 1984/85 with measures in 2009 to show that the mean body mass decreased in eight and nine populations (for females and males, respectively) out of ten Finnish populations. Consequently, the latitudinal cline in body mass shifted poleward. The decrease in body mass was large (1.5~g reduction in a 33-g bird). Temperatures during sampling did not differ between sampling periods, suggesting that at least the immediate effect of temperature did not explain the reduction in body mass. House sparrows have declined in abundance in Finland and worldwide in recent decades. We here suggest that the deterioration of the (unknown) environmental conditions associated with this population decline (which may include climatic drivers) has led to a poleward shift in Bergmann's rule in house sparrows.}, - langid = {english}, - keywords = {Bergmann’s rule,Body mass,House sparrow,Passer domesticus,Temperature} -} - -@article{brown1985, - title = {Experimental {{Manipulation}} of a {{Desert Rodent Community}}: {{Food Addition}} and {{Species Removal}}}, - shorttitle = {Experimental {{Manipulation}} of a {{Desert Rodent Community}}}, - author = {Brown, James H. and Munger, James C.}, - year = {1985}, - journal = {Ecology}, - volume = {66}, - number = {5}, - pages = {1545--1563}, - issn = {1939-9170}, - doi = {10.2307/1938017}, - abstract = {Since 1977 we have been conducting experiments in which we add supplemental seeds or remove certain combinations of species of seed\textemdash eating rodents and ants from 0.25\textemdash ha plots in the Chihuahuan Desert of southeastern Arizona. These experiments evaluate the extent to which food availability and interspecific competition influence rodent populations. Monitoring with live traps revealed that: (1) the addition of seed at the rate of 96 kg\textdegree plot\textemdash 1\textdegree yr\textemdash 1 resulted in an increased density of the largest granivorous rodent species (Dipodomys spectabilis), decreases in the densities of the two next\textemdash to\textemdash largest species (D. merriami and D. ordii), and no detectable changes in the densities of other rodents; (2) the removal of D. spectabilis, as well as other experimentally induced changes in the abundance of this species, resulted in reciprocal shifts in the densities of the two congeneric species, D. merriami and D. ordii, and no significant changes in densities of other rodents; and (3) the removal of all three Dipodomys species resulted in large increases in density of four of the five species of smaller seed\textemdash eating rodents, but had no effect on two species of insectivorous rodents. Taken together, these results indicate that limited food resources and interspecific competition pay major roles in regulating the density of rodent populations and determining the organization of desert rodent communities. However, the responses of the rodent populations to our manipulations were unexpectedly complex; they included long time lags, asymmetrical interactions, and little compensation in energy consumption. This indicates how much remains to be learned about the processes that determine the structure and function of even this relatively simple and well\textemdash studied community.}, - copyright = {\textcopyright{} 1985 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1938017}, - file = {/Users/renatadiaz/Zotero/storage/BDDKVL25/Brown and Munger - 1985 - Experimental Manipulation of a Desert Rodent Commu.pdf;/Users/renatadiaz/Zotero/storage/VFTMWXIM/1938017.html} -} - -@article{brown1989, - title = {Macroecology: {{The Division}} of {{Food}} and {{Space Among Species}} on {{Continents}}}, - shorttitle = {Macroecology}, - author = {Brown, James H. and Maurer, Brian A.}, - year = {1989}, - month = mar, - journal = {Science}, - volume = {243}, - number = {4895}, - pages = {1145--1150}, - publisher = {{American Association for the Advancement of Science}}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.243.4895.1145}, - abstract = {Analyses of statistical distributions of body mass, population density, and size and shape of geographic range offer insights into the empirical patterns and causal mechanisms that characterize the allocation of food and space among the diverse species in continental biotas. These analyses also provide evidence of the processes that couple ecological phenomena that occur on disparate spatial and temporal scales\textemdash from the activities of individual organisms within local populations to the dynamics of continent-wide speciation, colonization, and extinction events.}, - chapter = {Articles}, - copyright = {1989 by the American Association for the Advancement of Science.}, - langid = {english}, - pmid = {17799895}, - file = {/Users/renatadiaz/Zotero/storage/2TE5GSRF/1145.html} -} - -@book{brown1995, - title = {Macroecology}, - author = {Brown, James H.}, - year = {1995}, - publisher = {{University of Chicago Press}}, - abstract = {Introduction -- The macroecological approach -- Species, niches, and communities -- The abundance and distribution of species -- The composition of biotas: patterns of body size, abundance, and energetics -- The assembly of continental biotas: geographic range -- Mechanisms: structure and function of individuals -- Mechanisms: population dynamics and interspecific interactions -- Mechanisms: species dynamics -- Synthesis: ecological implications -- Synthesis: biogeographic and macroevolutionary implications -- Applications: human ecology and conservation biology -- Reflections and prospects.}, - isbn = {978-0-226-07614-0}, - keywords = {Ecology} -} - -@incollection{brown1995a, - title = {Organisms and {{Species}} as {{Complex Adaptive Systems}}: {{Linking}} the {{Biology}} of {{Populations}} with the {{Physics}} of {{Ecosystems}}}, - shorttitle = {Organisms and {{Species}} as {{Complex Adaptive Systems}}}, - booktitle = {Linking {{Species}} \& {{Ecosystems}}}, - author = {Brown, James H.}, - editor = {Jones, Clive G. and Lawton, John H.}, - year = {1995}, - pages = {16--24}, - publisher = {{Springer US}}, - address = {{Boston, MA}}, - doi = {10.1007/978-1-4615-1773-3_2}, - abstract = {SummaryHistorical constraints of paradigms, approaches, training, and methodology currently prevent the conceptual unification of ecology. They inhibit communication and collaboration between the biologists who study the structure and dynamics of populations and communities and the earth scientists, physicists, chemists, and biologists who study the distribution and fluxes of energy and materials in ecosystems. To link the attributes of individual organisms and species with the biogeochemical processes that occur in their environments requires an integration of biology and the physical sciences.To make these linkages, I suggest that individuals and species be considered a special class of complex adaptive systems (CASs) with some uniquely biological attributes. This view encourages a focus on the physical relationships of the biological CAS: on developing an energetic/thermodynamic currency that can be used to characterize population growth and fitness in terms of basic physical processes; on characterizing the niche in terms of the environmental requirements of the CAS for survival and reproduction; and on understanding the impacts of species on ecosystems in terms of work performed in meeting these requirements.}, - isbn = {978-1-4615-1773-3}, - langid = {english}, - keywords = {Complex Adaptive System,Ecosystem Ecology,Emergent Feature,Individual Organism,Spin Glass} -} - -@article{brown1997, - title = {Reorganization of an Arid Ecosystem in Response to Recent Climate Change}, - author = {Brown, J. H. and Valone, T. J. and Curtin, C. G.}, - year = {1997}, - month = sep, - journal = {Proceedings of the National Academy of Sciences}, - volume = {94}, - number = {18}, - pages = {9729--9733}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.94.18.9729}, - abstract = {Natural ecosystems contain many individuals and species interacting with each other and with their abiotic environment. Such systems can be expected to exhibit complex dynamics in which small perturbations can be amplified to cause large changes. Here, we document the reorganization of an arid ecosystem that has occurred since the late 1970s. The density of woody shrubs increased 3-fold. Several previously common animal species went locally extinct, while other previously rare species increased. While these changes are symptomatic of desertification, they were not caused by livestock grazing or drought, the principal causes of historical desertification. The changes apparently were caused by a shift in regional climate: since 1977 winter precipitation throughout the region was substantially higher than average for this century. These changes illustrate the kinds of large, unexpected responses of complex natural ecosystems that can occur in response to both natural perturbations and human activities.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/7BCFF9B7/Brown et al. - 1997 - Reorganization of an arid ecosystem in response to.pdf;/Users/renatadiaz/Zotero/storage/HX47F49V/Brown et al. - 1997 - Reorganization of an arid ecosystem in response to.pdf;/Users/renatadiaz/Zotero/storage/JKH4WU2W/Brown et al. - 1997 - Reorganization of an arid ecosystem in response to.pdf} -} - -@article{brown2001, - title = {Complex {{Species Interactions}} and the {{Dynamics}} of {{Ecological Systems}}: {{Long-Term Experiments}}}, - author = {Brown, James H. and Whitham, Thomas G. and Ernest, S. K. Morgan and Gehring, Catherine A.}, - year = {2001}, - journal = {Science, New Series}, - volume = {293}, - number = {5530}, - pages = {643--650}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/SB6NXLY4/Brown et al. - 2001 - Complex Species Interactions and the Dynamics of E.pdf} -} - -@article{brown2002, - title = {The {{Fractal Nature}} of {{Nature}}: {{Power Laws}}, {{Ecological Complexity}} and {{Biodiversity}}}, - shorttitle = {The {{Fractal Nature}} of {{Nature}}}, - author = {Brown, James H. and Gupta, Vijay K. and Li, Bai-Lian and Milne, Bruce T. and Restrepo, Carla and West, Geoffrey B.}, - year = {2002}, - journal = {Philosophical Transactions: Biological Sciences}, - volume = {357}, - number = {1421}, - pages = {619--626}, - publisher = {{The Royal Society}}, - issn = {0962-8436}, - abstract = {Underlying the diversity of life and the complexity of ecology is order that reflects the operation of fundamental physical and biological processes. Power laws describe empirical scaling relationships that are emergent quantitative features of biodiversity. These features are patterns of structure or dynamics that are self-similar or fractal-like over many orders of magnitude. Power laws allow extrapolation and prediction over a wide range of scales. Some appear to be universal, occurring in virtually all taxa of organisms and types of environments. They offer clues to underlying mechanisms that powerfully constrain biodiversity. We describe recent progress and future prospects for understanding the mechanisms that generate these power laws, and for explaining the diversity of species and complexity of ecosystems in terms of fundamental principles of physical and biological science.}, - file = {/Users/renatadiaz/Zotero/storage/XJTXPEY7/Brown et al. - 2002 - The fractal nature of nature power laws, ecologic.pdf} -} - -@article{brzezinski2014, - title = {Do Wealth Distributions Follow Power Laws? {{Evidence}} from `Rich Lists'}, - shorttitle = {Do Wealth Distributions Follow Power Laws?}, - author = {Brzezinski, Michal}, - year = {2014}, - month = jul, - journal = {Physica A: Statistical Mechanics and its Applications}, - volume = {406}, - pages = {155--162}, - issn = {0378-4371}, - doi = {10.1016/j.physa.2014.03.052}, - abstract = {We use data on the wealth of the richest persons taken from the `rich lists' provided by business magazines like Forbes to verify if the upper tails of wealth distributions follow, as often claimed, a power-law behaviour. The data sets used cover the world's richest persons over 1996\textendash 2012, the richest Americans over 1988\textendash 2012, the richest Chinese over 2006\textendash 2012, and the richest Russians over 2004\textendash 2011. Using a recently introduced comprehensive empirical methodology for detecting power laws, which allows for testing the goodness of fit as well as for comparing the power-law model with rival distributions, we find that a power-law model is consistent with data only in 35\% of the analysed data sets. Moreover, even if wealth data are consistent with the power-law model, they are usually also consistent with some rivals like the log-normal or stretched exponential distributions.}, - langid = {english}, - keywords = {Goodness-of-fit,Model selection,Pareto model,Power-law model,Wealth distribution}, - file = {/Users/renatadiaz/Zotero/storage/9A4JNQQE/Brzezinski - 2014 - Do wealth distributions follow power laws Evidenc.pdf;/Users/renatadiaz/Zotero/storage/APKDXJXM/S0378437114002544.html} -} - -@article{burkle2015, - title = {Wildfire Disturbance and Productivity as Drivers of Plant Species Diversity across Spatial Scales}, - author = {Burkle, Laura A. and Myers, Jonathan A. and Belote, R. Travis}, - year = {2015}, - month = oct, - journal = {Ecosphere}, - volume = {6}, - number = {10}, - pages = {art202}, - issn = {2150-8925}, - doi = {10.1890/ES15-00438.1}, - abstract = {Wildfires influence many temperate terrestrial ecosystems worldwide. Historical environmental heterogeneity created by wildfires has been altered by human activities and will be impacted by future climate change. Our ability to predict the impact of wildfire-created heterogeneity on biodiversity is limited because few studies have investigated variation in community composition (beta-diversity) in response to fire. Wildfires may influence beta-diversity through several ecological mechanisms. First, highseverity fires may decrease beta-diversity by homogenizing species composition when they create landscapes dominated by disturbance-tolerant or rapidly colonizing species. In contrast, mixed-severity fires may increase beta-diversity by creating mosaic landscapes containing habitats that support species with differing environmental tolerances and dispersal traits. Moreover, the effects of fire severity on betadiversity may change depending on site conditions. Disturbance is hypothesized to increase local species richness at higher productivity and decrease local species richness at lower productivity, a process that can have important, but largely unexamined, consequences on beta-diversity in fire-prone ecosystems. We tested these hypotheses by comparing patterns of beta-diversity and species richness across 162 plant communities in three sites that span a large-scale gradient in climate and productivity in the Northern Rockies of Montana. Within each site, we used spatially explicit fire-severity data to stratify sampling across unburned forests and forests burned with mixed- and high-severity wildfires. We found that betadiversity (community dispersion) of forbs was higher in mixed-severity compared to high-severity fire, regardless of productivity. Counter to our predictions, local species richness of forbs was higher in burned landscapes compared to unburned landscapes at the low-productivity site, but lower in burned landscapes at the high-productivity site. This pattern may be explained by rapid regeneration of woody plants after fire in high-productivity forests. Moreover, forbs and woody plants had disproportionately higher overall species richness in mixed-severity fire compared to high-severity fire, but only at the low-productivity site. These patterns suggest that mixed-severity fires promote higher landscape-level biodiversity in lowproductivity sites by increasing species turnover across landscapes with a diverse mosaic of habitats. Our study illustrates the importance of understanding the mechanisms by which patterns of wildfire severity interact with environmental gradients to influence patterns of biodiversity across spatial scales.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2EYWD8WL/Burkle et al. - 2015 - Wildfire disturbance and productivity as drivers o.pdf} -} - -@article{burns2022, - title = {The Psychology of Natural History}, - author = {Burns, K.C. and Low, Jason}, - year = {2022}, - month = dec, - journal = {Trends in Ecology \& Evolution}, - volume = {37}, - number = {12}, - pages = {1029--1031}, - issn = {01695347}, - doi = {10.1016/j.tree.2022.09.001}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/YJEKI53R/Burns and Low - 2022 - The psychology of natural history.pdf} -} - -@article{caceres2019, - title = {Trajectory Analysis in Community Ecology}, - author = {C{\'a}ceres, Miquel De and Coll, Llu{\'i}s and Legendre, Pierre and Allen, Robert B. and Wiser, Susan K. and Fortin, Marie-Jos{\'e}e and Condit, Richard and Hubbell, Stephen}, - year = {2019}, - journal = {Ecological Monographs}, - volume = {89}, - number = {2}, - pages = {e01350}, - issn = {1557-7015}, - doi = {10.1002/ecm.1350}, - abstract = {Ecologists have long been interested in how communities change over time. Addressing questions about community dynamics requires ways of representing and comparing the variety of dynamics observed across space. Until now, most analytical frameworks have been based on the comparison of synchronous observations across sites and between repeated surveys. An alternative perspective considers community dynamics as trajectories in a chosen space of community resemblance and utilizes trajectories as objects to be analyzed and compared using their geometry. While methods that take this second perspective exist, for example to test for particular trajectory shapes, there is a need for formal analytical frameworks that fully develop the potential of this approach. By adapting concepts and procedures used for the analysis of spatial trajectories, we present a framework for describing and comparing community trajectories. A key element of our contribution is the means to assess the geometric resemblance between trajectories, which allows users to describe, quantify, and analyze variation in community dynamics. We illustrate the behavior of our framework using simulated data and two spatiotemporal community data sets differing in the community properties of interest (species composition vs. size distribution of individuals). We conclude by evaluating the advantages and limitations of our community trajectory analysis framework, highlighting its broad domain of application and anticipating potential extensions.}, - langid = {english}, - keywords = {beta diversity,community dynamics,dissimilarity,distance matrices,forest dynamics,stand size structure,trajectory data mining}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecm.1350}, - file = {/Users/renatadiaz/Zotero/storage/EATFB8GM/Cáceres et al. - 2019 - Trajectory analysis in community ecology.pdf;/Users/renatadiaz/Zotero/storage/YAD8XIYS/ecm.html} -} - -@article{cadotte2006, - title = {Metacommunity {{Influences}} on {{Community Richness}} at {{Multiple Spatial Scales}}: {{A Microcosm Experiment}}}, - shorttitle = {Metacommunity {{Influences}} on {{Community Richness}} at {{Multiple Spatial Scales}}}, - author = {Cadotte, Marc W.}, - year = {2006}, - journal = {Ecology}, - volume = {87}, - number = {4}, - pages = {1008--1016}, - issn = {1939-9170}, - doi = {10.1890/0012-9658(2006)87[1008:MIOCRA]2.0.CO;2}, - abstract = {Large-scale processes are known to be important for patterns of species richness, yet the ways in which local and larger scale processes interact is not clear. I used metacommunities consisting of five interconnected microbial aquatic communities to examine the manner in which processes at different scales affect local and metacommunity richness. Specifically, I manipulated the potential dispersal rate, whether dispersal was localized or global, and variation in initial community composition. A repeated-measures ANOVA showed that a low dispersal rate and intermediate distance dispersal enhanced local richness. Initial assembly variation had no effect on local richness, while a lack of dispersal or global dispersal reduced local richness. At the metacommunity scale, richness was enhanced throughout the time course of the experiment by initial compositional variation and was reduced by high or global dispersal. The effects of dispersal were contingent on the presence of initial compositional variation. The treatments also affected individual species occupancy patterns, with some benefiting from large-scale processes and others being adversely impacted. These results indicate that the effects of dispersal on species richness have a complex relationship with scale and are not solely divisible into ``regional'' vs. ``local'' scales. Finally, predictions of the manner in which dispersal rate structures communities appear dependent upon species compositional variation among communities.}, - copyright = {\textcopyright{} 2006 by the Ecological Society of America}, - langid = {english}, - keywords = {community assembly,dispersal,metacommunity,migration,regional effects,spatial scale,species diversity,temporal dynamics}, - file = {/Users/renatadiaz/Zotero/storage/ZAVQSFSG/Cadotte - 2006 - Metacommunity Influences on Community Richness at .pdf;/Users/renatadiaz/Zotero/storage/CMDUUDEV/0012-9658(2006)87[1008MIOCRA]2.0.html} -} - -@article{cardenas2021, - title = {Declines in Rodent Abundance and Diversity Track Regional Climate Variability in {{North American}} Drylands}, - author = {C{\'a}rdenas, Pablo A. and Christensen, Erica and Ernest, S. K. Morgan and Lightfoot, David C. and Schooley, Robert L. and Stapp, Paul and Rudgers, Jennifer A.}, - year = {2021}, - month = sep, - journal = {Global Change Biology}, - volume = {27}, - number = {17}, - pages = {4005--4023}, - issn = {1354-1013, 1365-2486}, - doi = {10.1111/gcb.15672}, - abstract = {Regional long-term monitoring can enhance the detection of biodiversity declines associated with climate change, improving future projections by reducing reliance on space-for-time substitution and increasing scalability. Rodents are diverse and important consumers in drylands, regions defined by the scarcity of water that cover 45\% of Earth's land surface and face increasingly drier and more variable climates. We analyzed abundance data for 22 rodent species across grassland, shrubland, ecotone, and woodland ecosystems in the southwestern USA. Two time series (1995-2006, 20042013) coincided with phases of the Pacific Decadal Oscillation (PDO), which influences drought in southwestern North America. Regionally, rodent species diversity declined 20-35\%, with greater losses during the later time period. Abundance also declined regionally, but only during 2004-2013, with losses of 5\% of animals captured. During the first time series (wetter climate), plant productivity outranked climate variables as the best regional predictor of rodent abundance for 70\% of taxa, whereas during the second period (drier climate), climate best explained variation in abundance for 60\% of taxa. Temporal dynamics in diversity and abundance differed spatially among ecosystems, with the largest declines in woodlands and shrublands of central New Mexico and Colorado. Which species were winners or losers under increasing drought and amplified interannual variability in drought depended on ecosystem type and the phase of the PDO. Fewer taxa were significant winners (18\%) than losers (30\%) under drought, but the identities of winners and losers differed among ecosystems for 70\% of taxa. Our results suggest that the sensitivities of rodent species to climate contributed to regional declines in diversity and abundance during 1995 - 2013. Whether these changes portend future declines in drought-sensitive consumers in the southwestern USA will depend on the climate during the next major PDO cycle.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/5B29WW82/Cárdenas et al. - 2021 - Declines in rodent abundance and diversity track r.pdf;/Users/renatadiaz/Zotero/storage/CVQ6XGCK/Cárdenas et al. - 2021 - Declines in rodent abundance and diversity track r.pdf} -} - -@article{carey2019, - title = {Enhancing Collaboration between Ecologists and Computer Scientists: Lessons Learned and Recommendations Forward}, - shorttitle = {Enhancing Collaboration between Ecologists and Computer Scientists}, - author = {Carey, Cayelan C. and Ward, Nicole K. and Farrell, Kaitlin J. and Lofton, Mary E. and Krinos, Arianna I. and McClure, Ryan P. and Subratie, Kensworth C. and Figueiredo, Renato J. and Doubek, Jonathan P. and Hanson, Paul C. and Papadopoulos, Philip and Arzberger, Peter}, - year = {2019}, - journal = {Ecosphere}, - volume = {10}, - number = {5}, - pages = {e02753}, - issn = {2150-8925}, - doi = {10.1002/ecs2.2753}, - abstract = {In the era of big data, ecologists are increasingly relying on computational approaches and tools to answer existing questions and pose new research questions. These include both software applications (e.g., simulation models, databases and machine learning algorithms) and hardware systems (e.g., wireless sensor networks, supercomputing, drones and satellites), motivating the need for greater collaboration between computer scientists and ecologists. Here, we outline some synergistic opportunities for scientists in both disciplines that can be gained by building collaborations between the computer science and ecology research communities, with a focus on the benefits to ecology specifically. We also identify past contributions of computer science to ecology, including high-frequency environmental sensor technology, advanced supercomputing capacity for ecological modeling, databases for long-term and high-frequency datasets, and software programs for ecological analyses, to anticipate future potential contributions. These examples highlight the power and potential for further integration of computer science technology and ideas into the ecological research community. Finally, we translate our own experiences working together as a team of computer scientists and ecologists over the past decade into a conceptual framework with recommendations for supporting productive collaborations at the interface of the two disciplines. We specifically focus on how to apply best practices of team science for bridging computer science and ecology, which we advocate will substantially benefit ecology long-term.}, - langid = {english}, - keywords = {big data,computational ecology,computer programming,cyberinfrastructure,information technology,interdisciplinary,modeling,quantitative literacy,software,team science}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.2753}, - file = {/Users/renatadiaz/Zotero/storage/GESEICRM/Carey et al. - 2019 - Enhancing collaboration between ecologists and com.pdf;/Users/renatadiaz/Zotero/storage/CUMXMGWI/ecs2.html} -} - -@article{carlson2022, - title = {Climate Change Increases Cross-Species Viral Transmission Risk}, - author = {Carlson, Colin J. and Albery, Gregory F. and Merow, Cory and Trisos, Christopher H. and Zipfel, Casey M. and Eskew, Evan A. and Olival, Kevin J. and Ross, Noam and Bansal, Shweta}, - year = {2022}, - month = jul, - journal = {Nature}, - volume = {607}, - number = {7919}, - pages = {555--562}, - publisher = {{Nature Publishing Group}}, - issn = {1476-4687}, - doi = {10.1038/s41586-022-04788-w}, - abstract = {At least 10,000 virus species have the ability to infect humans but, at present, the vast majority are circulating silently in wild mammals1,2. However, changes in climate and land use will lead to opportunities for viral sharing among previously geographically isolated species of wildlife3,4. In some cases, this will facilitate zoonotic spillover\textemdash a mechanistic link between global environmental change and disease emergence. Here we simulate potential hotspots of future viral sharing, using a phylogeographical model of the mammal\textendash virus network, and projections of geographical range shifts for 3,139 mammal species under climate-change and land-use scenarios for the year 2070. We predict that species will aggregate in new combinations at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, causing the cross-species transmission of their associated viruses an estimated 4,000 times. Owing to their unique dispersal ability, bats account for the majority of novel viral sharing and are likely to share viruses along evolutionary pathways that will facilitate future emergence in humans. Notably, we find that this ecological transition may already be underway, and holding warming under 2\,\textdegree C within the twenty-first century will not reduce future viral sharing. Our findings highlight an urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking the range shifts of species, especially in tropical regions that contain the most zoonoses and are experiencing rapid warming.}, - copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited}, - langid = {english}, - keywords = {Biogeography,Environmental health,Microbial ecology,Viral reservoirs,Virus–host interactions}, - file = {/Users/renatadiaz/Zotero/storage/F83JBA87/Carlson et al. - 2022 - Climate change increases cross-species viral trans.pdf;/Users/renatadiaz/Zotero/storage/GS527A2T/s41586-022-04788-w.html} -} - -@article{carroll2020, - title = {The {{CARE Principles}} for {{Indigenous Data Governance}}}, - author = {Carroll, Stephanie Russo and Garba, Ibrahim and {Figueroa-Rodr{\'i}guez}, Oscar L. and Holbrook, Jarita and Lovett, Raymond and Materechera, Simeon and Parsons, Mark and Raseroka, Kay and {Rodriguez-Lonebear}, Desi and Rowe, Robyn and Sara, Rodrigo and Walker, Jennifer D. and Anderson, Jane and Hudson, Maui}, - year = {2020}, - month = nov, - journal = {Data Science Journal}, - volume = {19}, - number = {1}, - pages = {43}, - publisher = {{Ubiquity Press}}, - issn = {1683-1470}, - doi = {10.5334/dsj-2020-043}, - abstract = {Concerns about secondary use of data and limited opportunities for benefit-sharing have focused attention on the tension that Indigenous communities feel between (1) protecting Indigenous rights and interests in Indigenous data (including traditional knowledges) and (2) supporting open data, machine learning, broad data sharing, and big data initiatives. The International Indigenous Data Sovereignty Interest Group (within the Research Data Alliance) is a network of nation-state based Indigenous data sovereignty networks and individuals that developed the `CARE Principles for Indigenous Data Governance' (Collective Benefit, Authority to Control, Responsibility, and Ethics) in consultation with Indigenous Peoples, scholars, non-profit organizations, and governments. The CARE Principles are people\textendash{} and purpose-oriented, reflecting the crucial role of data in advancing innovation, governance, and self-determination among Indigenous Peoples. The Principles complement the existing data-centric approach represented in the `FAIR Guiding Principles for scientific data management and stewardship' (Findable, Accessible, Interoperable, Reusable). The CARE Principles build upon earlier work by the Te Mana Raraunga Maori Data Sovereignty Network, US Indigenous Data Sovereignty Network, Maiam nayri Wingara Aboriginal and Torres Strait Islander Data Sovereignty Collective, and numerous Indigenous Peoples, nations, and communities. The goal is that stewards and other users of Indigenous data will `Be FAIR and CARE.' In this first formal publication of the CARE Principles, we articulate their rationale, describe their relation to the FAIR Principles, and present examples of their application.}, - copyright = {Authors who publish with this journal agree to the following terms: Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access ). All third-party images reproduced on this journal are shared under Educational Fair Use. For more information on Educational Fair Use , please see this useful checklist prepared by Columbia University Libraries . All copyright of third-party content posted here for research purposes belongs to its original owners. Unless otherwise stated all references to characters and comic art presented on this journal are \textcopyright, \textregistered{} or \texttrademark{} of their respective owners. No challenge to any owner's rights is intended or should be inferred.}, - langid = {english}, - keywords = {data governance,data principles,data sovereignty,FAIR principles,Indigenous}, - file = {/Users/renatadiaz/Zotero/storage/6CRHWITZ/Carroll et al. - 2020 - The CARE Principles for Indigenous Data Governance.pdf;/Users/renatadiaz/Zotero/storage/YL4Q5Z4A/dsj-2020-043.html} -} - -@article{chamberlain2014, - title = {How Context Dependent Are Species Interactions?}, - author = {Chamberlain, Scott A. and Bronstein, Judith L. and Rudgers, Jennifer A.}, - year = {2014}, - journal = {Ecology Letters}, - volume = {17}, - number = {7}, - pages = {881--890}, - issn = {1461-0248}, - doi = {10.1111/ele.12279}, - abstract = {The net effects of interspecific species interactions on individuals and populations vary in both sign (-, 0, +) and magnitude (strong to weak). Interaction outcomes are context-dependent when the sign and/or magnitude change as a function of the biotic or abiotic context. While context dependency appears to be common, its distribution in nature is poorly described. Here, we used meta-analysis to quantify variation in species interaction outcomes (competition, mutualism, or predation) for 247 published articles. Contrary to our expectations, variation in the magnitude of effect sizes did not differ among species interactions, and while mutualism was most likely to change sign across contexts (and predation least likely), mutualism did not strongly differ from competition. Both the magnitude and sign of species interactions varied the most along spatial and abiotic gradients, and least as a function of the presence/absence of a third species. However, the degree of context dependency across these context types was not consistent among mutualism, competition and predation studies. Surprisingly, study location and ecosystem type varied in the degree of context dependency, with laboratory studies showing the highest variation in outcomes. We urge that studying context dependency per se, rather than focusing only on mean outcomes, can provide a general method for describing patterns of variation in nature.}, - copyright = {\textcopyright{} 2014 John Wiley \& Sons Ltd/CNRS}, - langid = {english}, - keywords = {Coefficient of variation,community context,conditionality,distributed outcomes,interaction strength,meta-analysis}, - annotation = {\_eprint: https://www.onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12279}, - file = {/Users/renatadiaz/Zotero/storage/62VFT29Q/Chamberlain et al. - 2014 - How context dependent are species interactions.pdf;/Users/renatadiaz/Zotero/storage/7D5NUES8/ele.html} -} - -@article{chao2014, - title = {Rarefaction and Extrapolation with {{Hill}} Numbers: A Framework for Sampling and Estimation in Species Diversity Studies}, - author = {Chao, Anne and Gotelli, Nicholas J and Hsieh, T C and Sander, Elizabeth L and Ma, K H and Colwell, Robert K and Ellison, Aaron M}, - year = {2014}, - journal = {Ecological Monographs}, - volume = {84}, - number = {1}, - pages = {23}, - abstract = {Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness. Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data. Here we extended previous rarefaction and extrapolation models for species richness (Hill number qD, where q {$\frac{1}{4}$} 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number qD, q . 0) and present a unified approach for both individual-based (abundance) data and samplebased (incidence) data. Using this unified sampling framework, we derive both theoretical formulas and analytic estimators for seamless rarefaction and extrapolation based on Hill numbers. Detailed examples are provided for the first three Hill numbers: q {$\frac{1}{4}$} 0 (species richness), q {$\frac{1}{4}$} 1 (the exponential of Shannon's entropy index), and q {$\frac{1}{4}$} 2 (the inverse of Simpson's concentration index). We developed a bootstrap method for constructing confidence intervals around Hill numbers, facilitating the comparison of multiple assemblages of both rarefied and extrapolated samples. The proposed estimators are accurate for both rarefaction and short-range extrapolation. For long-range extrapolation, the performance of the estimators depends on both the value of q and on the extrapolation range. We tested our methods on simulated data generated from species abundance models and on data from large species inventories. We also illustrate the formulas and estimators using empirical data sets from biodiversity surveys of temperate forest spiders and tropical ants.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/LBDWGPRK/Chao et al. - 2014 - Rarefaction and extrapolation with Hill numbers a.pdf} -} - -@article{charlesworth2017, - title = {Population Genetics from 1966 to 2016}, - author = {Charlesworth, B. and Charlesworth, D.}, - year = {2017}, - month = jan, - journal = {Heredity}, - volume = {118}, - number = {1}, - pages = {2--9}, - publisher = {{Nature Publishing Group}}, - issn = {1365-2540}, - doi = {10.1038/hdy.2016.55}, - abstract = {We describe the astonishing changes and progress that have occurred in the field of population genetics over the past 50 years, slightly longer than the time since the first Population Genetics Group (PGG) meeting in January 1968. We review the major questions and controversies that have preoccupied population geneticists during this time (and were often hotly debated at PGG meetings). We show how theoretical and empirical work has combined to generate a highly productive interaction involving successive developments in the ability to characterise variability at the molecular level, to apply mathematical models to the interpretation of the data and to use the results to answer biologically important questions, even in nonmodel organisms. We also describe the changes from a field that was largely dominated by UK and North American biologists to a much more international one (with the PGG meetings having made important contributions to the increased number of population geneticists in several European countries). Although we concentrate on the earlier history of the field, because developments in recent years are more familiar to most contemporary researchers, we end with a brief outline of topics in which new understanding is still actively developing.}, - copyright = {2017 The Author(s)}, - langid = {english}, - keywords = {Evolutionary genetics}, - annotation = {Bandiera\_abtest: a Cc\_license\_type: cc\_y Cg\_type: Nature Research Journals Primary\_atype: Reviews Subject\_term: Evolutionary genetics Subject\_term\_id: evolutionary-genetics}, - file = {/Users/renatadiaz/Zotero/storage/26UIJKA8/Charlesworth and Charlesworth - 2017 - Population genetics from 1966 to 2016.pdf;/Users/renatadiaz/Zotero/storage/BTBLJFAJ/hdy201655.html} -} - -@article{chase2018, - title = {Embracing Scale-Dependence to Achieve a Deeper Understanding of Biodiversity and Its Change across Communities}, - author = {Chase, Jonathan M. and McGill, Brian J. and McGlinn, Daniel J. and May, Felix and Blowes, Shane A. and Xiao, Xiao and Knight, Tiffany M. and Purschke, Oliver and Gotelli, Nicholas J.}, - year = {2018}, - journal = {Ecology Letters}, - volume = {21}, - number = {11}, - pages = {1737--1751}, - issn = {1461-0248}, - doi = {10.1111/ele.13151}, - abstract = {Because biodiversity is multidimensional and scale-dependent, it is challenging to estimate its change. However, it is unclear (1) how much scale-dependence matters for empirical studies, and (2) if it does matter, how exactly we should quantify biodiversity change. To address the first question, we analysed studies with comparisons among multiple assemblages, and found that rarefaction curves frequently crossed, implying reversals in the ranking of species richness across spatial scales. Moreover, the most frequently measured aspect of diversity \textendash{} species richness \textendash{} was poorly correlated with other measures of diversity. Second, we collated studies that included spatial scale in their estimates of biodiversity change in response to ecological drivers and found frequent and strong scale-dependence, including nearly 10\% of studies which showed that biodiversity changes switched directions across scales. Having established the complexity of empirical biodiversity comparisons, we describe a synthesis of methods based on rarefaction curves that allow more explicit analyses of spatial and sampling effects on biodiversity comparisons. We use a case study of nutrient additions in experimental ponds to illustrate how this multi-dimensional and multi-scale perspective informs the responses of biodiversity to ecological drivers.}, - copyright = {\textcopyright{} 2018 John Wiley \& Sons Ltd/CNRS}, - langid = {english}, - keywords = {Evenness,Hill number,rarefaction,scale-dependence,Simpson's index,species richness,species–area relationship}, - file = {/Users/renatadiaz/Zotero/storage/XZN562UG/Chase et al. - 2018 - Embracing scale-dependence to achieve a deeper und.pdf;/Users/renatadiaz/Zotero/storage/HIIEK6P9/ele.html} -} - -@article{chase2019, - title = {Species Richness Change across Spatial Scales}, - author = {Chase, Jonathan M. and McGill, Brian J. and Thompson, Patrick L. and Ant{\~a}o, Laura H. and Bates, Amanda E. and Blowes, Shane A. and Dornelas, Maria and Gonzalez, Andrew and Magurran, Anne E. and Supp, Sarah R. and Winter, Marten and Bjorkman, Anne D. and Bruelheide, Helge and Byrnes, Jarrett E. K. and Cabral, Juliano Sarmento and Elahi, Robin and Gomez, Catalina and Guzman, Hector M. and Isbell, Forest and {Myers-Smith}, Isla H. and Jones, Holly P. and Hines, Jes and Vellend, Mark and Waldock, Conor and O'Connor, Mary}, - year = {2019}, - journal = {Oikos}, - volume = {128}, - number = {8}, - pages = {1079--1091}, - issn = {1600-0706}, - doi = {10.1111/oik.05968}, - abstract = {Humans have elevated global extinction rates and thus lowered global scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in a unidirectional way. Instead, the magnitude of species richness change through time can increase, decrease, reverse, or be unimodal across spatial scales. Using several case studies, we show different forms of scale-dependent richness change through time in the face of anthropogenic pressures. For example, Central American corals show a homogenization pattern, where small scale richness is largely unchanged through time, while larger scale richness change is highly negative. Alternatively, birds in North America showed a differentiation effect, where species richness was again largely unchanged through time at small scales, but was more positive at larger scales. Finally, we collated data from a heterogeneous set of studies of different taxa measured through time from sites ranging from small plots to entire continents, and found highly variable patterns that nevertheless imply complex scale-dependence in several taxa. In summary, understanding how biodiversity is changing in the Anthropocene requires an explicit recognition of the influence of spatial scale, and we conclude with some recommendations for how to better incorporate scale into our estimates of change.}, - langid = {english}, - keywords = {anthropogenic change,biodiversity,change,spatial scale,species richness,time}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/oik.05968}, - file = {/Users/renatadiaz/Zotero/storage/UQYYPB6W/Chase et al. - 2019 - Species richness change across spatial scales.pdf;/Users/renatadiaz/Zotero/storage/2RPYUZMN/oik.html} -} - -@techreport{chen2022, - type = {Preprint}, - title = {Best {{Practices}} for {{Interpretable Machine Learning}} in {{Computational Biology}}}, - author = {Chen, Valerie and Yang, Muyu and Cui, Wenbo and Kim, Joon Sik and Talwalkar, Ameet and Ma, Jian}, - year = {2022}, - month = nov, - institution = {{Bioinformatics}}, - doi = {10.1101/2022.10.28.513978}, - abstract = {Advances in machine learning (ML) have enabled the development of next-generation prediction models for complex computational biology problems. These developments have spurred the use of interpretable machine learning (IML) to unveil fundamental biological insights through data-driven knowledge discovery. However, in general, standards and guidelines for IML usage in computational biology have not been well-characterized, representing a major gap toward fully realizing the potential of IML. Here, we introduce a workflow on the best practices for using IML methods to perform knowledge discovery which covers verification strategies that bridge data, prediction model, and explanation. We outline a workflow incorporating these verification strategies to increase an IML method's accountability, reliability, and generalizability. We contextualize our proposed workflow in a series of widely applicable computational biology problems. Together, we provide an extensive workflow with important principles for the appropriate use of IML in computational biology, paving the way for a better mechanistic understanding of ML models and advancing the ability to discover novel biological phenomena.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/BYXKXD88/Chen et al. - 2022 - Best Practices for Interpretable Machine Learning .pdf} -} - -@article{cheruvelil2018, - title = {Data-{{Intensive Ecological Research Is Catalyzed}} by {{Open Science}} and {{Team Science}}}, - author = {Cheruvelil, Kendra Spence and Soranno, Patricia A}, - year = {2018}, - month = oct, - journal = {BioScience}, - volume = {68}, - number = {10}, - pages = {813--822}, - issn = {0006-3568, 1525-3244}, - doi = {10.1093/biosci/biy097}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/FYASYUEX/Cheruvelil and Soranno - 2018 - Data-Intensive Ecological Research Is Catalyzed by.pdf} -} - -@article{chesson2000, - title = {Mechanisms of {{Maintenance}} of {{Species Diversity}}}, - author = {Chesson, Peter}, - year = {2000}, - journal = {Annual Review of Ecology and Systematics}, - volume = {31}, - number = {1}, - pages = {343--366}, - doi = {10.1146/annurev.ecolsys.31.1.343}, - abstract = {The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence, in which species diversity slowly decays over time, have focused almost exclusively on equalizing mechanisms. These models would be more robust if they also included stabilizing mechanisms, which arise in many and varied ways but need not be adequate for full stability of a system. Models of unstable coexistence invite a broader view of diversity maintenance incorporating species turnover.}, - annotation = {\_eprint: https://doi.org/10.1146/annurev.ecolsys.31.1.343}, - file = {/Users/renatadiaz/Zotero/storage/6NGBAEQF/Chesson - 2000 - Mechanisms of Maintenance of Species Diversity.pdf} -} - -@article{chicco2017, - title = {Ten Quick Tips for Machine Learning in Computational Biology}, - author = {Chicco, Davide}, - year = {2017}, - month = dec, - journal = {BioData Mining}, - volume = {10}, - number = {1}, - pages = {35}, - issn = {1756-0381}, - doi = {10.1186/s13040-017-0155-3}, - abstract = {Machine learning has become a pivotal tool for many projects in computational biology, bioinformatics, and health informatics. Nevertheless, beginners and biomedical researchers often do not have enough experience to run a data mining project effectively, and therefore can follow incorrect practices, that may lead to common mistakes or over-optimistic results. With this review, we present ten quick tips to take advantage of machine learning in any computational biology context, by avoiding some common errors that we observed hundreds of times in multiple bioinformatics projects. We believe our ten suggestions can strongly help any machine learning practitioner to carry on a successful project in computational biology and related sciences.}, - keywords = {Bioinformatics,Biomedical informatics,Computational biology,Computational intelligence,Data mining,Health informatics,Machine learning,Tips}, - file = {/Users/renatadiaz/Zotero/storage/SYFRU2PR/Chicco - 2017 - Ten quick tips for machine learning in computation.pdf;/Users/renatadiaz/Zotero/storage/TLN4W9MN/s13040-017-0155-3.html} -} - -@article{chiu2014, - title = {An Improved Nonparametric Lower Bound of Species Richness via a Modified Good-Turing Frequency Formula}, - author = {Chiu, Chun-Huo and Wang, Yi-Ting and Walther, Bruno A. and Chao, Anne}, - year = {2014}, - month = sep, - journal = {Biometrics}, - volume = {70}, - number = {3}, - pages = {671--682}, - issn = {1541-0420}, - doi = {10.1111/biom.12200}, - abstract = {It is difficult to accurately estimate species richness if there are many almost undetectable species in a hyper-diverse community. Practically, an accurate lower bound for species richness is preferable to an inaccurate point estimator. The traditional nonparametric lower bound developed by Chao (1984, Scandinavian Journal of Statistics 11, 265-270) for individual-based abundance data uses only the information on the rarest species (the numbers of singletons and doubletons) to estimate the number of undetected species in samples. Applying a modified Good-Turing frequency formula, we derive an approximate formula for the first-order bias of this traditional lower bound. The approximate bias is estimated by using additional information (namely, the numbers of tripletons and quadrupletons). This approximate bias can be corrected, and an improved lower bound is thus obtained. The proposed lower bound is nonparametric in the sense that it is universally valid for any species abundance distribution. A similar type of improved lower bound can be derived for incidence data. We test our proposed lower bounds on simulated data sets generated from various species abundance models. Simulation results show that the proposed lower bounds always reduce bias over the traditional lower bounds and improve accuracy (as measured by mean squared error) when the heterogeneity of species abundances is relatively high. We also apply the proposed new lower bounds to real data for illustration and for comparisons with previously developed estimators.}, - langid = {english}, - pmid = {24945937}, - keywords = {Abundance data,Animals,Biometry,Computer Simulation,Data Interpretation; Statistical,Demography,Epidemiologic Methods,Good–Turing frequency formula,Humans,Incidence data,Models; Statistical,Population Dynamics,Sample Size,Species richness,Statistics; Nonparametric} -} - -@article{christensen2018, - title = {Long-Term Community Change through Multiple Rapid Transitions in a Desert Rodent Community}, - author = {Christensen, Erica M. and Harris, David J. and Ernest, S. K. Morgan}, - year = {2018}, - month = jul, - journal = {Ecology}, - volume = {99}, - number = {7}, - pages = {1523--1529}, - issn = {00129658}, - doi = {10.1002/ecy.2373}, - abstract = {While studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-yr span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods, possibly related to climate events, where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.}, - langid = {english}, - keywords = {community composition,community dynamics,desert rodents,extreme climatic events,Latent Dirichlet Allocation,long-term data,temporal dynamics}, - file = {/Users/renatadiaz/Zotero/storage/ABAUHICW/Christensen et al. - 2018 - Long-term community change through multiple rapid .pdf;/Users/renatadiaz/Zotero/storage/FD52FF7Z/Christensen et al. - 2018 - Long-term community change through multiple rapid .pdf;/Users/renatadiaz/Zotero/storage/MKTSFFP6/ecy.html} -} - -@article{christensen2019, - title = {Established Rodent Community Delays Recovery of Dominant Competitor Following Experimental Disturbance}, - author = {Christensen, Erica M. and Simpson, Gavin L. and Ernest, S. K. Morgan}, - year = {2019}, - month = dec, - journal = {Proceedings of the Royal Society B: Biological Sciences}, - volume = {286}, - number = {1917}, - pages = {20192269}, - publisher = {{Royal Society}}, - doi = {10.1098/rspb.2019.2269}, - abstract = {Human activities alter processes that control local biodiversity, causing changes in the abundance and identity of species in ecosystems. However, restoring biodiversity to a previous state is rarely as simple as reintroducing lost species or restoring processes to their pre-disturbance state. Theory suggests that established species can impede shifts in species composition via a variety of mechanisms, including direct interference, pre-empting resources or habitat alteration. These mechanisms can create transitory dynamics that delay convergence to an expected end state. We use an experimental manipulation of a desert rodent community to examine differences in recolonization dynamics of a dominant competitor (kangaroo rats of the genus Dipodomys) when patches were already occupied by an existing rodent community relative to when patches were empty. Recovery of kangaroo rat populations was slow on plots with an established community, taking approximately 2 years, in contrast with rapid recovery on empty plots with no established residents (approx. three months). These results demonstrate that the presence of an established alternate community inhibits recolonization by new species, even those that should be dominant in the community. This has important implications for understanding how biodiversity may change in the future, and what processes may slow or prevent this change.}, - file = {/Users/renatadiaz/Zotero/storage/HNXIQSRM/Christensen et al. - 2019 - Established rodent community delays recovery of do.pdf;/Users/renatadiaz/Zotero/storage/NG9YCEJF/Christensen et al. - 2019 - Established rodent community delays recovery of do.pdf;/Users/renatadiaz/Zotero/storage/2W5IQU7N/rspb.2019.html;/Users/renatadiaz/Zotero/storage/8UJF9ZK2/rspb.2019.html} -} - -@article{christensen2019a, - title = {Portalr: An {{R}} Package for Summarizing and Using the {{Portal Project Data}}}, - author = {Christensen, Erica M. and Yenni, Glenda M. and Ye, Hao and Simonis, Juniper L. and Bledsoe, Ellen K. and Diaz, Renata M. and Taylor, Shawn D. and White, Ethan P. and Ernest, S. K. Morgan}, - year = {2019}, - journal = {Journal of Open Source Software}, - volume = {4}, - number = {33}, - pages = {1098}, - doi = {10.21105/joss.01098} -} - -@article{clark, - title = {General Statistical Scaling Laws for Stability in Ecological Systems}, - author = {Clark, Adam Thomas and Arnoldi, Jean-Francois and Zelnik, Yuval R. and Barabas, Gy{\"o}rgy and Hodapp, Dorothee and Karako{\c c}, Canan and K{\"o}nig, Sara and Radchuk, Viktoriia and Donohue, Ian and Huth, Andreas and Jacquet, Claire and de Mazancourt, Claire and Mentges, Andrea and Nothaa{\ss}, Dorian and Shoemaker, Lauren G. and Taubert, Franziska and Wiegand, Thorsten and Wang, Shaopeng and Chase, Jonathan M. and Loreau, Michel and Harpole, Stanley}, - journal = {Ecology Letters}, - volume = {n/a}, - number = {n/a}, - issn = {1461-0248}, - doi = {10.1111/ele.13760}, - abstract = {Ecological stability refers to a family of concepts used to describe how systems of interacting species vary through time and respond to disturbances. Because observed ecological stability depends on sampling scales and environmental context, it is notoriously difficult to compare measurements across sites and systems. Here, we apply stochastic dynamical systems theory to derive general statistical scaling relationships across time, space, and ecological level of organisation for three fundamental stability aspects: resilience, resistance, and invariance. These relationships can be calibrated using random or representative samples measured at individual scales, and projected to predict average stability at other scales across a wide range of contexts. Moreover deviations between observed vs. extrapolated scaling relationships can reveal information about unobserved heterogeneity across time, space, or species. We anticipate that these methods will be useful for cross-study synthesis of stability data, extrapolating measurements to unobserved scales, and identifying underlying causes and consequences of heterogeneity.}, - copyright = {\textcopyright{} 2021 The Authors. Ecology Letters published by John Wiley \& Sons Ltd.}, - langid = {english}, - keywords = {community,disturbance,diversity,invariability,invariance,population,resilience,resistance,spatial,temporal}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13760}, - file = {/Users/renatadiaz/Zotero/storage/ZUJC22SI/Clark et al. - General statistical scaling laws for stability in .pdf;/Users/renatadiaz/Zotero/storage/CF4J27SW/ele.html} -} - -@article{clauset2009, - title = {Power-{{Law Distributions}} in {{Empirical Data}}}, - author = {Clauset, Aaron and Shalizi, Cosma Rohilla and Newman, M. E. J.}, - year = {2009}, - month = nov, - journal = {SIAM Review}, - volume = {51}, - number = {4}, - pages = {661--703}, - publisher = {{Society for Industrial and Applied Mathematics}}, - issn = {0036-1445}, - doi = {10.1137/070710111}, - abstract = {Power-law distributions occur in many situations of scientific interest and have significant consequences for our understanding of natural and man-made phenomena. Unfortunately, the detection and characterization of power laws is complicated by the large fluctuations that occur in the tail of the distribution\textemdash the part of the distribution representing large but rare events\textemdash and by the difficulty of identifying the range over which power-law behavior holds. Commonly used methods for analyzing power-law data, such as least-squares fitting, can produce substantially inaccurate estimates of parameters for power-law distributions, and even in cases where such methods return accurate answers they are still unsatisfactory because they give no indication of whether the data obey a power law at all. Here we present a principled statistical framework for discerning and quantifying power-law behavior in empirical data. Our approach combines maximum-likelihood fitting methods with goodness-of-fit tests based on the Kolmogorov\textendash Smirnov (KS) statistic and likelihood ratios. We evaluate the effectiveness of the approach with tests on synthetic data and give critical comparisons to previous approaches. We also apply the proposed methods to twenty-four real-world data sets from a range of different disciplines, each of which has been conjectured to follow a power-law distribution. In some cases we find these conjectures to be consistent with the data, while in others the power law is ruled out.}, - keywords = {Condensed Matter - Disordered Systems and Neural Networks,Physics - Data Analysis; Statistics and Probability,Statistics - Applications,Statistics - Methodology}, - file = {/Users/renatadiaz/Zotero/storage/GHHF6B6J/Clauset et al. - 2009 - Power-law distributions in empirical data.pdf;/Users/renatadiaz/Zotero/storage/PNTGEDHF/Clauset et al. - 2009 - Power-Law Distributions in Empirical Data.pdf;/Users/renatadiaz/Zotero/storage/XZ4TU5Q8/Clauset et al. - 2009 - Power-Law Distributions in Empirical Data.pdf;/Users/renatadiaz/Zotero/storage/35LI2IW8/070710111.html;/Users/renatadiaz/Zotero/storage/3ZFNDKF8/070710111.html} -} - -@article{collins2017, - title = {Heterogeneous Changes in Avian Body Size across and within Species}, - author = {Collins, Michael D. and Relyea, George E. and Blustein, Erica C. and Badami, Steven M.}, - year = {2017}, - month = jan, - journal = {Journal of Ornithology}, - volume = {158}, - number = {1}, - pages = {39--52}, - issn = {2193-7206}, - doi = {10.1007/s10336-016-1391-x}, - abstract = {Contemporary climate change has been linked to widespread changes in phenology and in the geographic distribution of species. Based on Bergmann's rule, body sizes of birds have been predicted to decline as global temperatures increase. We examined changes in body size of 20 resident and short-distance migrant passerine species in eastern North America between 1980 and 2012, and how changes in resident species related to annual mean summer and mean winter temperatures. We found that wing length generally increased and that fat-free mass did not change significantly. Fat score, a measure of body condition, declined over time. However, changes in wing length, fat-free mass, and fat score all showed significant variation across species. For resident species, increasing mean summer temperatures were generally associated with shorter wing lengths, but were not related to fat-free mass or fat score. Increasing mean winter temperatures were associated with reduced fat-free mass but not with wing length or fat score. Temperature effects did not vary significantly across species for any of the three measures. Across resident species, the magnitude of body size change over time was not related to the influence of mean winter or mean summer temperatures, and may have been driven by other factors. Our findings contrast with those from a study at a nearby bird banding station, in which widespread decreases in wing length and fat-free mass were observed. Our results demonstrate that populations of the same species can exhibit opposing changes in body size over short geographic distances ({$<$}250~km). We conclude that changes in body size are heterogeneous over short time scales and can vary across and within species over short distances. Continued advances in understanding how body size changes relate to climate change must embrace this inherent complexity and consider alternative hypotheses.}, - langid = {english}, - keywords = {Bergmann’s rule,Body mass,Climate change,Morphology,Passerine,Wing length} -} - -@article{conlisk2010, - title = {Hubbell's Local Abundance Distribution: Insights from a Simple Colonization Rule}, - shorttitle = {Hubbell's Local Abundance Distribution}, - author = {Conlisk, John and Conlisk, Erin and Harte, John}, - year = {2010}, - month = feb, - journal = {Oikos}, - volume = {119}, - number = {2}, - pages = {379--383}, - issn = {00301299, 16000706}, - doi = {10.1111/j.1600-0706.2009.17765.x}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/C49X24HI/Conlisk et al. - 2010 - Hubbell's local abundance distribution insights f.pdf} -} - -@article{conlisk2016, - title = {Colonization Rules and Spatial Distributions in Ecology}, - author = {Conlisk, Erin}, - year = {2016}, - month = dec, - journal = {Ecological Complexity}, - volume = {28}, - pages = {218--221}, - issn = {1476-945X}, - doi = {10.1016/j.ecocom.2016.07.002}, - abstract = {Because they are intuitive and mathematically straight-forward, colonization rules are often used to model spatial patterns in ecology. Colonization rules assign individuals to categories according to the locations of previous colonists. In this note, a compact introduction to colonization rules in ecology is presented with implications for autocorrelation and spatial distributions. I use the colonization rule approach to unify a diverse set of spatial and species diversity analyses, exploring future extensions to incorporate greater realism.}, - langid = {english}, - keywords = {Colonization rule,Hubbell neutral model,Spatial abundance distribution,Spatial clustering,Species abundance distribution}, - file = {/Users/renatadiaz/Zotero/storage/WVWPYEG9/S1476945X16300526.html} -} - -@article{connolly2005, - title = {Community {{Structure}} of {{Corals}} and {{Reef Fishes}} at {{Multiple Scales}}}, - author = {Connolly, Sean R. and Hughes, Terry P. and Bellwood, David R. and Karlson, Ronald H.}, - year = {2005}, - month = aug, - journal = {Science}, - volume = {309}, - number = {5739}, - pages = {1363--1365}, - publisher = {{American Association for the Advancement of Science}}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.1113281}, - abstract = {Distributions of numerical abundance and resource use among species are fundamental aspects of community structure. Here we characterize these patterns for tropical reef fishes and corals across a 10,000-kilometer biodiversity gradient. Numerical abundance and resource-use distributions have similar shapes, but they emerge at markedly different scales. These results are consistent with a controversial null hypothesis regarding community structure, according to which abundance distributions arise from the interplay of multiple stochastic environmental and demographic factors. Our findings underscore the importance of robust conservation strategies that are appropriately scaled to the broad suite of environmental processes that help sustain biodiversity. The local community structure of coral reefs, which reflects differences in the numbers of individuals among species, varies at a larger scale than the partitioning of resources. The local community structure of coral reefs, which reflects differences in the numbers of individuals among species, varies at a larger scale than the partitioning of resources.}, - chapter = {Report}, - copyright = {American Association for the Advancement of Science}, - langid = {english}, - pmid = {16123298}, - file = {/Users/renatadiaz/Zotero/storage/56KSU5R7/Connolly et al. - 2005 - Community Structure of Corals and Reef Fishes at M.pdf;/Users/renatadiaz/Zotero/storage/BDA8KQNS/1363.html} -} - -@article{cooper2019, - title = {Pareto Rules for Malaria Super-Spreaders and Super-Spreading}, - author = {Cooper, Laura and Kang, Su Yun and Bisanzio, Donal and Maxwell, Kilama and {Rodriguez-Barraquer}, Isabel and Greenhouse, Bryan and Drakeley, Chris and Arinaitwe, Emmanuel and G. Staedke, Sarah and Gething, Peter W. and Eckhoff, Philip and Reiner, Robert C. and Hay, Simon I. and Dorsey, Grant and Kamya, Moses R. and Lindsay, Steven W. and Grenfell, Bryan T. and Smith, David L.}, - year = {2019}, - month = sep, - journal = {Nature Communications}, - volume = {10}, - number = {1}, - pages = {3939}, - publisher = {{Nature Publishing Group}}, - issn = {2041-1723}, - doi = {10.1038/s41467-019-11861-y}, - abstract = {Heterogeneity in transmission is a challenge for infectious disease dynamics and control. An 80-20 ``Pareto'' rule has been proposed to describe this heterogeneity whereby 80\% of transmission is accounted for by 20\% of individuals, herein called super-spreaders. It is unclear, however, whether super-spreading can be attributed to certain individuals or whether it is an unpredictable and unavoidable feature of epidemics. Here, we investigate heterogeneous malaria transmission at three sites in Uganda and find that super-spreading is negatively correlated with overall malaria transmission intensity. Mosquito biting among humans is 90-10 at the lowest transmission intensities declining to less than 70-30 at the highest intensities. For super-spreaders, biting ranges from 70-30 down to 60-40. The difference, approximately half the total variance, is due to environmental stochasticity. Super-spreading is thus partly due to super-spreaders, but modest gains are expected from targeting super-spreaders.}, - copyright = {2019 The Author(s)}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/PM7XLHC3/Cooper et al. - 2019 - Pareto rules for malaria super-spreaders and super.pdf;/Users/renatadiaz/Zotero/storage/NI3B5GNH/s41467-019-11861-y.html} -} - -@misc{cosden2022, - title = {Research {{Software Engineers}}: {{Career Entry Points}} and {{Training Gaps}}}, - shorttitle = {Research {{Software Engineers}}}, - author = {Cosden, Ian A. and McHenry, Kenton and Katz, Daniel S.}, - year = {2022}, - month = oct, - number = {arXiv:2210.04275}, - eprint = {2210.04275}, - eprinttype = {arxiv}, - primaryclass = {cs}, - publisher = {{arXiv}}, - abstract = {As software has become more essential to research across disciplines, and as the recognition of this fact has grown, the importance of professionalizing the development and maintenance of this software has also increased. The community of software professionals who work on this software have come together under the title Research Software Engineer (RSE) over the last decade. This has led to the formalization of RSE roles and organized RSE groups in universities, national labs, and industry. This, in turn, has created the need to understand how RSEs come into this profession and into these groups, how to further promote this career path to potential members, as well as the need to understand what training gaps need to be filled for RSEs coming from different entry points. We have categorized three main classifications of entry paths into the RSE profession and identified key elements, both advantages and disadvantages, that should be acknowledged and addressed by the broader research community in order to attract and retain a talented and diverse pool of future RSEs.}, - archiveprefix = {arXiv}, - keywords = {Computer Science - Software Engineering}, - file = {/Users/renatadiaz/Zotero/storage/KKYC2YK6/Cosden et al. - 2022 - Research Software Engineers Career Entry Points a.pdf;/Users/renatadiaz/Zotero/storage/8A2EIL9Z/2210.html} -} - -@article{coyle2013, - title = {Opposing {{Mechanisms Drive Richness Patterns}} of {{Core}} and {{Transient Bird Species}}.}, - author = {Coyle, Jessica R. and Hurlbert, Allen H. and White, Ethan P.}, - year = {2013}, - month = apr, - journal = {The American Naturalist}, - volume = {181}, - number = {4}, - pages = {E83-E90}, - publisher = {{The University of Chicago Press}}, - issn = {0003-0147}, - doi = {10.1086/669903}, - abstract = {Studies of biodiversity typically assume that all species are equivalent. However, some species in a community maintain viable populations in the study area, while others occur only occasionally as transient individuals. Here we show that North American bird communities can reliably be divided into core and transient species groups and that the richness of each group is driven by different processes. The richness of core species is influenced primarily by local environmental conditions, while the richness of transient species is influenced primarily by the heterogeneity of the surrounding landscape. This demonstrates that the well-known effects of the local environment and landscape heterogeneity on overall species richness are the result of two sets of processes operating differentially on core and transient species. Models of species richness should focus on explaining two distinct patterns, those of core and transient species, rather than a single pattern for the community as a whole.}, - keywords = {biodiversity,birds,local environment,mass effects,occupancy,spatial heterogeneity,species richness}, - file = {/Users/renatadiaz/Zotero/storage/4JCCT6F9/Coyle et al. - 2013 - Opposing Mechanisms Drive Richness Patterns of Cor.pdf;/Users/renatadiaz/Zotero/storage/T7WVGAM9/Coyle et al. - 2013 - Opposing Mechanisms Drive Richness Patterns of Cor.pdf} -} - -@article{crossley2020, - title = {No Net Insect Abundance and Diversity Declines across {{US Long Term Ecological Research}} Sites}, - author = {Crossley, Michael S. and Meier, Amanda R. and Baldwin, Emily M. and Berry, Lauren L. and Crenshaw, Leah C. and Hartman, Glen L. and {Lagos-Kutz}, Doris and Nichols, David H. and Patel, Krishna and Varriano, Sofia and Snyder, William E. and Moran, Matthew D.}, - year = {2020}, - month = aug, - journal = {Nature Ecology \& Evolution}, - pages = {1--9}, - publisher = {{Nature Publishing Group}}, - issn = {2397-334X}, - doi = {10.1038/s41559-020-1269-4}, - abstract = {Recent reports of dramatic declines in insect abundance suggest grave consequences for global ecosystems and human society. Most evidence comes from Europe, however, leaving uncertainty about insect population trends worldwide. We used {$>$}5,300 time series for insects and other arthropods, collected over 4\textendash 36 years at monitoring sites representing 68 different natural and managed areas, to search for evidence of declines across the United States. Some taxa and sites showed decreases in abundance and diversity while others increased or were unchanged, yielding net abundance and biodiversity trends generally indistinguishable from zero. This lack of overall increase or decline was consistent across arthropod feeding groups and was similar for heavily disturbed versus relatively natural sites. The apparent robustness of US arthropod populations is reassuring. Yet, this result does not diminish the need for continued monitoring and could mask subtler changes in species composition that nonetheless endanger insect-provided ecosystem services. Analysing {$>$}5,000 population abundance time series for insects and other arthropods from 68 sites within the US Long Term Ecological Research network, the authors find high variation but no overall trend in abundance and diversity among sites and taxa.}, - copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/BF84MMEF/Crossley et al. - 2020 - No net insect abundance and diversity declines acr.pdf;/Users/renatadiaz/Zotero/storage/4H54WGNP/s41559-020-1269-4.html} -} - -@article{curtin2000, - title = {On the Role of Small Mammals in Mediating Climatically Driven Vegetation Change}, - author = {Curtin, C. G. and Kelt, D. A. and Frey, T. C. and Brown, J. H.}, - year = {2000}, - journal = {Ecology Letters}, - volume = {3}, - number = {4}, - pages = {309--317}, - issn = {1461-0248}, - doi = {10.1046/j.1461-0248.2000.00166.x}, - abstract = {Biotic and abiotic processes jointly influence natural systems, yet opportunities to integrate studies of both processes are uncommon. For two decades we have excluded different subsets of the small mammal community from a series of plots near a grassland-desert ecotone in the northern Chihuahuan Desert. These studies spanned a period of historically high winter rainfall, allowing us to distinguish the effects of climate and small mammals on the composition and patch structure of vegetation. Removal of only kangaroo rats (Dipodomys) or of all small mammals led to increased cover of large herbaceous vegetation. The size of vegetative patches increased in all plots but this increase was three times greater where all rodents were removed. Thus, the activity of small mammals that forage under and near shrub canopies appear to significantly inhibit the expansion of existing vegetative patches, and may have a stronger influence on habitat structure than previously recognized.}, - copyright = {Blackwell Science Ltd}, - langid = {english}, - keywords = {Abiotic factors,biotic factors,Chihuahuan Desert,climate change,small mammals}, - annotation = {\_eprint: https://www.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1461-0248.2000.00166.x}, - file = {/Users/renatadiaz/Zotero/storage/E7PCK5V2/Curtin et al. - 2000 - On the role of small mammals in mediating climatic.pdf;/Users/renatadiaz/Zotero/storage/AY24MVZS/j.1461-0248.2000.00166.html;/Users/renatadiaz/Zotero/storage/XJ4UHLE7/j.1461-0248.2000.00166.html} -} - -@article{cusser2020, - title = {Long-Term Research Avoids Spurious and Misleading Trends in Sustainability Attributes of No-Till}, - author = {Cusser, Sarah and Bahlai, Christie and Swinton, Scott M. and Robertson, G. Philip and Haddad, Nick M.}, - year = {2020}, - journal = {Global Change Biology}, - volume = {26}, - number = {6}, - pages = {3715--3725}, - issn = {1365-2486}, - doi = {10.1111/gcb.15080}, - abstract = {Agricultural management recommendations based on short-term studies can produce findings inconsistent with long-term reality. Here, we test the long-term environmental sustainability and profitability of continuous no-till agriculture on yield, soil water availability, and N2O fluxes. Using a moving window approach, we investigate the development and stability of several attributes of continuous no-till as compared to conventional till agriculture over a 29-year period at a site in the upper Midwest, US. Over a decade is needed to detect the consistent effects of no-till. Both crop yield and soil water availability required 15 years or longer to generate patterns consistent with 29-year trends. Only marginal trends for N2O fluxes appeared in this period. Relative profitability analysis suggests that after initial implementation, 86\% of periods between 10 and 29 years recuperated the initial expense of no-till implementation, with the probability of higher relative profit increasing with longevity. Importantly, statistically significant but misleading short-term trends appeared in more than 20\% of the periods examined. Results underscore the importance of decadal and longer studies for revealing consistent dynamics and emergent outcomes of no-till agriculture, shown to be beneficial in the long term.}, - langid = {english}, - keywords = {long-term research,LTER,moving window,N2O fluxes,power analysis,profitability of no-till adoption,soil moisture,soil water availability,sustainable intensification,yield}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15080}, - file = {/Users/renatadiaz/Zotero/storage/YNMHHZ23/Cusser et al. - 2020 - Long-term research avoids spurious and misleading .pdf;/Users/renatadiaz/Zotero/storage/5EY9EK24/gcb.html} -} - -@article{deiner2017, - title = {Environmental {{DNA}} Metabarcoding: {{Transforming}} How We Survey Animal and Plant Communities}, - shorttitle = {Environmental {{DNA}} Metabarcoding}, - author = {Deiner, Kristy and Bik, Holly M. and M{\"a}chler, Elvira and Seymour, Mathew and {Lacoursi{\`e}re-Roussel}, Ana{\"i}s and Altermatt, Florian and Creer, Simon and Bista, Iliana and Lodge, David M. and {de Vere}, Natasha and Pfrender, Michael E. and Bernatchez, Louis}, - year = {2017}, - journal = {Molecular Ecology}, - volume = {26}, - number = {21}, - pages = {5872--5895}, - issn = {1365-294X}, - doi = {10.1111/mec.14350}, - abstract = {The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (``HTS'') platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed ``environmental DNA'' or ``eDNA''). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called ``eDNA metabarcoding'' and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.}, - langid = {english}, - keywords = {bioinformatic pipeline,biomonitoring,citizen science,conservation,ecology,eDNA,invasive species,macro-organism,species richness}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14350}, - file = {/Users/renatadiaz/Zotero/storage/GDEEWFBU/Deiner et al. - 2017 - Environmental DNA metabarcoding Transforming how .pdf;/Users/renatadiaz/Zotero/storage/WCRMDTNW/mec.html} -} - -@article{delong, - title = {Stochasticity Directs Adaptive Evolution toward Nonequilibrium Evolutionary Attractors}, - author = {DeLong, John P. and Cressler, Clayton E.}, - journal = {Ecology}, - volume = {n/a}, - number = {n/a}, - pages = {e3873}, - issn = {1939-9170}, - doi = {10.1002/ecy.3873}, - abstract = {Stochastic processes such as genetic drift may hinder adaptation, but the effect of such stochasticity on evolution via its effect on ecological dynamics is poorly understood. Here we evaluate patterns of adaptation in a population subject to variation in demographic stochasticity. We show that stochasticity can alter population dynamics and lead to evolutionary outcomes that are not predicted by classic eco-evolutionary modeling approaches. We also show, however, that these outcomes are governed by nonequilibrium evolutionary attractors (NEEAs) \textendash{} these are maxima in lifetime reproductive success when stochasticity keeps the ecological system away from the deterministic equilibrium. These NEEAs alter the path of evolution but are not visible through the equilibrium lens that underlies much evolutionary theory. Our results reveal that considering population processes during transient periods can greatly improve our understanding of the path and pace of evolution. This article is protected by copyright. All rights reserved.}, - langid = {english}, - keywords = {eco-evolutionary dynamics,GEM,Gillespie algorithm,maladaptation,stochastic dynamics}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3873}, - file = {/Users/renatadiaz/Zotero/storage/QCLEAW5Z/DeLong and Cressler - Stochasticity directs adaptive evolution toward no.pdf;/Users/renatadiaz/Zotero/storage/86D2P7EM/ecy.html} -} - -@article{desjardins-proulx2017, - title = {Scientific {{Theories}} and {{Artificial Intelligence}}}, - author = {{Desjardins-Proulx}, Philippe and Poisot, Timoth{\'e}e and Gravel, Dominique}, - year = {2017}, - month = oct, - journal = {bioRxiv}, - pages = {161125}, - doi = {10.1101/161125}, - abstract = {{$<$}p{$>$}Artificial Intelligence presents an important paradigm shift for science. Science is traditionally founded on theories and models, most often formalized with mathematical formulas handcrafted by theoretical scientists and refined through experiments. Machine learning, an important branch of modern Artificial Intelligence, focuses on learning from data. This leads to a fundamentally different approach to model-building: we step back and focus on the design of algorithms capable of building models from data, but the models themselves are not designed by humans. This is even more true with deep learning, which requires little engineering by hand and is responsible for many of Artificial Intelligence9s spectacular successes. In contrast to logic systems, knowledge from a deep learning model is difficult to understand, reuse, and may involve up to a billion parameters. On the other hand, probabilistic machine learning techniques such as deep learning offer an opportunity to tackle large complex problems that are out of the reach of traditional theory-making. It is possible that the more intuition-like reasoning performed by deep learning systems is mostly incompatible with the logic formalism of mathematics. Yet recent studies have shown that deep learning can be useful to logic systems and vice versa. Success at unifying different paradigms of Artificial Intelligence from logic to probability theory offers unique opportunities to combine data-driven approaches with traditional theories. These advancements are susceptible to impact significantly biological sciences, where dimensionality is high and limit the investigation of traditional theories.{$<$}/p{$>$}}, - copyright = {\textcopyright{} 2017, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/P678SA2E/Desjardins-Proulx et al. - 2017 - Scientific Theories and Artificial Intelligence.pdf;/Users/renatadiaz/Zotero/storage/DE5KB8XW/161125v2.html} -} - -@article{dewar2008, - title = {Statistical Mechanics Unifies Different Ecological Patterns}, - author = {Dewar, Roderick C. and Port{\'e}, Annabel}, - year = {2008}, - month = apr, - journal = {Journal of Theoretical Biology}, - volume = {251}, - number = {3}, - pages = {389--403}, - issn = {0022-5193}, - doi = {10.1016/j.jtbi.2007.12.007}, - abstract = {Recently there has been growing interest in the use of maximum relative entropy (MaxREnt) as a tool for statistical inference in ecology. In contrast, here we propose MaxREnt as a tool for applying statistical mechanics to ecology. We use MaxREnt to explain and predict species abundance patterns in ecological communities in terms of the most probable behaviour under given environmental constraints, in the same way that statistical mechanics explains and predicts the behaviour of thermodynamic systems. We show that MaxREnt unifies a number of different ecological patterns: (i) at relatively local scales a unimodal biodiversity\textendash productivity relationship is predicted in good agreement with published data on grassland communities, (ii) the predicted relative frequency of rare vs. abundant species is very similar to the empirical lognormal distribution, (iii) both neutral and non-neutral species abundance patterns are explained, (iv) on larger scales a monotonic biodiversity\textendash productivity relationship is predicted in agreement with the species-energy law, (v) energetic equivalence and power law self-thinning behaviour are predicted in resource-rich communities. We identify mathematical similarities between these ecological patterns and the behaviour of thermodynamic systems, and conclude that the explanation of ecological patterns is not unique to ecology but rather reflects the generic statistical behaviour of complex systems with many degrees of freedom under very general types of environmental constraints.}, - langid = {english}, - keywords = {Abundance distribution,Biodiversity,Community ecology,Relative entropy}, - file = {/Users/renatadiaz/Zotero/storage/LXLYAWQF/S0022519307006297.html} -} - -@article{dewsbury2019, - title = {Inclusive {{Teaching}}}, - author = {Dewsbury, Bryan and Brame, Cynthia J.}, - year = {2019}, - month = jun, - journal = {CBE\textemdash Life Sciences Education}, - volume = {18}, - number = {2}, - pages = {fe2}, - publisher = {{American Society for Cell Biology (lse)}}, - doi = {10.1187/cbe.19-01-0021}, - abstract = {Over the past two decades, science, technology, engineering, and mathematics (STEM) faculty have been striving to make their teaching practices more inclusive and welcoming to the variety of students who enter college. However, many STEM faculty, even those at teaching-focused institutions, have been educated in a traditional environment that emphasizes research and may not include classroom teaching. This can produce a deficit in training that leaves many STEM faculty feeling uncertain about inclusive teaching practices and their essential undergirding principles. This essay describes an online, evidence-based teaching guide (https://lse.ascb.org/evidence-based-teaching-guides/inclusive-teaching) intended to help fill this gap, serving as a resource for science faculty as they work to become more inclusive, particular with regard to differences in race, ethnicity, and gender. The guide describes the importance of developing self-awareness and empathy for students as a precursor to considering classroom practices. It also explores the role of classroom climate before turning to pedagogical choices that can support students' sense of belonging, competence, and interest in the course. Finally, the guide suggests that true inclusivity is a community effort and that instructors should leverage local and national networks to maximize student learning and inclusion. Each of these essential points is supported by summaries of and links to articles that can inform these choices. The guide also includes an instructor checklist that offers a concise summary of key points with actionable steps that can guide instructors as they work toward a more inclusive practice. We hope that the guide will provide value for both faculty who are just beginning to consider how to change their teaching practices and faculty seeking to enrich their current efforts.}, - file = {/Users/renatadiaz/Zotero/storage/I6HCL2WL/Dewsbury and Brame - 2019 - Inclusive Teaching.pdf} -} - -@article{dewsbury2020, - title = {Deep Teaching in a College {{STEM}} Classroom}, - author = {Dewsbury, Bryan M.}, - year = {2020}, - month = mar, - journal = {Cultural Studies of Science Education}, - volume = {15}, - number = {1}, - pages = {169--191}, - issn = {1871-1510}, - doi = {10.1007/s11422-018-9891-z}, - abstract = {The retention of underrepresented students remains a significant challenge in the STEM (Science, Technology, Engineering and Math) disciplines. A broad range of studies across several disciplines have shown that conventional approaches to STEM instruction may have been unintentionally exclusive to students whose ethnicities are not traditionally represented in the STEM fields. This `exclusive' classroom atmosphere has emerged as a major reason for the attrition of underrepresented minority students from STEM majors. In this manuscript, I describe a conceptual model called Deep Teaching, describing how pedagogical transformation incorporating practices that are more inclusive can occur. The model marks an evolution from other frameworks advancing inclusive instruction in higher education by advocating for the primacy of Freirean philosophy when thinking about self and student. Using specific examples, I discuss how a sequential approach to understanding ourselves and empathizing with students puts the instructor in a better position to create enduring, positive classroom climates. I also describe considerations necessary for various contexts, and suggestions for continued commitment to inclusive pedagogy in the long-term.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/DWLQAMGR/Dewsbury - 2020 - Deep teaching in a college STEM classroom.pdf} -} - -@article{dexter2012, - title = {Historical Effects on Beta Diversity and Community Assembly in {{Amazonian}} Trees}, - author = {Dexter, Kyle G. and Terborgh, John W. and Cunningham, Clifford W.}, - year = {2012}, - month = may, - journal = {Proceedings of the National Academy of Sciences}, - volume = {109}, - number = {20}, - pages = {7787--7792}, - publisher = {{National Academy of Sciences}}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.1203523109}, - abstract = {We present a unique perspective on the role of historical processes in community assembly by synthesizing analyses of species turnover among communities with environmental data and independent, population genetic-derived estimates of among-community dispersal. We sampled floodplain and terra firme communities of the diverse tree genus Inga (Fabaceae) across a 250-km transect in Amazonian Peru and found patterns of distance-decay in compositional similarity in both habitat types. However, conventional analyses of distance-decay masked a zone of increased species turnover present in the middle of the transect. We estimated past seed dispersal among the same communities by examining geographic plastid DNA variation for eight widespread Inga species and uncovered a population genetic break in the majority of species that is geographically coincident with the zone of increased species turnover. Analyses of these and 12 additional Inga species shared between two communities located on opposite sides of the zone showed that the populations experienced divergence 42,000\textendash 612,000 y ago. Our results suggest that the observed distance decay is the result not of environmental gradients or dispersal limitation coupled with ecological drift\textemdash as conventionally interpreted under neutral ecological theory\textemdash but rather of secondary contact between historically separated communities. Thus, even at this small spatial scale, historical processes seem to significantly impact species' distributions and community assembly. Other documented zones of increased species turnover found in the western Amazon basin or elsewhere may be related to similar historical processes.}, - chapter = {Biological Sciences}, - langid = {english}, - pmid = {22547831}, - keywords = {historical biogeography,phylogeography,tropical trees}, - file = {/Users/renatadiaz/Zotero/storage/XSMBMULS/Dexter et al. - 2012 - Historical effects on beta diversity and community.pdf;/Users/renatadiaz/Zotero/storage/4PCKZCRM/7787.html} -} - -@article{diaz2021, - title = {Empirical Abundance Distributions Are More Uneven than Expected given Their Statistical Baseline}, - author = {Diaz, Renata M. and Ye, Hao and Ernest, S. K. Morgan}, - editor = {Chase, Jonathan}, - year = {2021}, - month = sep, - journal = {Ecology Letters}, - volume = {24}, - number = {9}, - pages = {2025--2039}, - issn = {1461-023X, 1461-0248}, - doi = {10.1111/ele.13820}, - abstract = {Exploring and accounting for the emergent properties of ecosystems as complex systems is a promising horizon in the search for general processes to explain common ecological patterns. For example the ubiquitous hollow-\-curve form of the species abundance distribution is frequently assumed to reflect ecological processes structuring communities, but can also emerge as a statistical phenomenon from the mathematical definition of an abundance distribution. Although the hollow curve may be a statistical artefact, ecological processes may induce subtle deviations between empirical species abundance distributions and their statistically most probable forms. These deviations may reflect biological processes operating on top of mathematical constraints and provide new avenues for advancing ecological theory. Examining \textasciitilde 22,000 communities, we found that empirical SADs are highly uneven and dominated by rare species compared to their statistical baselines. Efforts to detect deviations may be less informative in small communities\textemdash\-those with few species or individuals\textemdash\-because these communities have poorly resolved statistical baselines. The uneven nature of many empirical SADs demonstrates a path forward for leveraging complexity to understand ecological processes governing the distribution of abundance, while the issues posed by small communities illustrate the limitations of using this approach to study ecological patterns in small samples.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/DKBRS3Z6/Diaz et al. - 2021 - Empirical abundance distributions are more uneven .pdf} -} - -@techreport{diaz2021a, - type = {Preprint}, - title = {Maintenance of Community Function through Compensation Breaks down over Time in a Desert Rodent Community}, - author = {Diaz, Renata M. and Ernest, S. K. Morgan}, - year = {2021}, - month = oct, - institution = {{bioRxiv}}, - doi = {10.1101/2021.10.01.462799}, - abstract = {Abstract Understanding the ecological processes that maintain community function in systems experiencing species loss, and how these processes change over time, is key to understanding the relationship between community structure and function and predicting how communities may respond to perturbations in the Anthropocene. Using a 30-year experiment on desert rodents, we show that the impact of species loss on community-level energy use has changed dramatically over time, due to changes in both species composition and in the degree of functional redundancy among the same set of species. Although strong compensation, initially driven by the dispersal of functionally redundant species to the local community, occurred in this system from 1996-2010, since 2010, compensation has broken down due to decreasing functional overlap within the same set of species. Simultaneously, long-term changes in sitewide community composition due to niche complementarity have decoupled the dynamics of compensation from the overall impact of species loss on community-level energy use. These results highlight the importance of explicitly long-term, metacommunity, and eco-evolutionary perspectives on compensatory dynamics, zero-sum constraints, and the link between species-level fluctuations and community function in a changing world. Original submission This submission analyzes long-term data on rodent community abundance and energy use from the Portal Project. Sections of this timeseries have been analyzed in numerous other publications, but this is the first to analyze data from 2007-2020 on compensation on experimental and control plots. No prior publication This submission is posted as a preprint on bioRxiv at [bioRxiv]. Animal welfare Rodent censuses were conducted with IACUC approval, most recently under protocol 201808839\_01 at the University of Florida. Open research All data and code to reproduce these analyses are archived on Zenodo at https://doi.org/10.5281/zenodo.5544362 and https://doi.org/10.5281/zenodo.5539881 . Analytic methods All analyses were conducted in R version 4.0.3.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/36HZVLZ5/2021.10.01.462799v1.full.pdf} -} - -@article{diaz2021b, - title = {Empirical Abundance Distributions Are More Uneven than Expected given Their Statistical Baseline}, - author = {Diaz, Renata M. and Ye, Hao and Ernest, S. K. Morgan}, - year = {2021}, - journal = {Ecology Letters}, - volume = {24}, - number = {9}, - pages = {2025--2039}, - issn = {1461-0248}, - doi = {10.1111/ele.13820}, - abstract = {Exploring and accounting for the emergent properties of ecosystems as complex systems is a promising horizon in the search for general processes to explain common ecological patterns. For example the ubiquitous hollow-curve form of the species abundance distribution is frequently assumed to reflect ecological processes structuring communities, but can also emerge as a statistical phenomenon from the mathematical definition of an abundance distribution. Although the hollow curve may be a statistical artefact, ecological processes may induce subtle deviations between empirical species abundance distributions and their statistically most probable forms. These deviations may reflect biological processes operating on top of mathematical constraints and provide new avenues for advancing ecological theory. Examining 22,000 communities, we found that empirical SADs are highly uneven and dominated by rare species compared to their statistical baselines. Efforts to detect deviations may be less informative in small communities\textemdash those with few species or individuals\textemdash because these communities have poorly resolved statistical baselines. The uneven nature of many empirical SADs demonstrates a path forward for leveraging complexity to understand ecological processes governing the distribution of abundance, while the issues posed by small communities illustrate the limitations of using this approach to study ecological patterns in small samples.}, - langid = {english}, - keywords = {combinatorics,constraints,feasible set,macroecology,species abundance distributions}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13820}, - file = {/Users/renatadiaz/Zotero/storage/4QYGK4WX/Diaz et al. - 2021 - Empirical abundance distributions are more uneven .pdf;/Users/renatadiaz/Zotero/storage/J6L6HUE4/Diaz et al. - Empirical abundance distributions are more uneven .pdf;/Users/renatadiaz/Zotero/storage/IHGQFPXJ/ele.html;/Users/renatadiaz/Zotero/storage/WJM9W6XI/ele.html} -} - -@misc{diaz2021c, - title = {Diazrenata/Feasiblesads: Feasiblesads}, - shorttitle = {Diazrenata/Feasiblesads}, - author = {Diaz, Renata and Ye, Hao}, - year = {2021}, - month = apr, - doi = {10.5281/zenodo.4710750}, - abstract = {Stable version used for all sampling in diazrenata/scadsanalysis.}, - howpublished = {Zenodo}, - file = {/Users/renatadiaz/Zotero/storage/RPY2554Y/4710750.html} -} - -@misc{diaz2021d, - title = {{{https://github.com/diazrenata/BBSsize}}}, - shorttitle = {{{https://github.com/diazrenata/BBSsize}}}, - author = {Diaz, Renata}, - year = {2021} -} - -@misc{diaz2021e, - title = {{{https://github.com/diazrenata/cvlt}}}, - shorttitle = {{{https://github.com/diazrenata/cvlt}}}, - author = {Diaz, Renata}, - year = {2021} -} - -@article{diaz2022, - title = {Maintenance of Community Function through Compensation Breaks down over Time in a Desert Rodent Community}, - author = {Diaz, Renata M. and Ernest, S. K. Morgan}, - year = {2022}, - journal = {Ecology}, - volume = {n/a}, - number = {n/a}, - pages = {e3709}, - issn = {1939-9170}, - doi = {10.1002/ecy.3709}, - abstract = {Understanding the ecological processes that maintain community function in systems experiencing species loss, and how these processes change over time, is key to understanding the relationship between community structure and function and predicting how communities may respond to perturbations in the Anthropocene. Using a 30-year experiment on desert rodents, we show that the impact of species loss on community-level energy use has changed repeatedly and dramatically over time, due to 1) the addition of new species to the community, and 2) a reduction in functional redundancy among the same set of species. Although strong compensation, initially driven by the dispersal of functionally redundant species to the local community, occurred in this system from 1997-2010, since 2010, compensation has broken down due to decreasing functional overlap within the same set of species. Simultaneously, long-term changes in sitewide community composition due to niche complementarity have decoupled the dynamics of compensation from the overall impact of species loss on community-level energy use. Shifting, context-dependent compensatory dynamics, such as those demonstrated here, highlight the importance of explicitly long-term, metacommunity, and eco-evolutionary perspectives on the link between species-level fluctuations and community function in a changing world.}, - langid = {english}, - keywords = {community function,compensation,environmental fluctuations,functional redundancy,zero-sum dynamic}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3709}, - file = {/Users/renatadiaz/Zotero/storage/PFWLGGSC/Diaz and Ernest - Maintenance of community function through compensa.pdf;/Users/renatadiaz/Zotero/storage/5DMGYYVY/ecy.html} -} - -@article{diaz2022a, - title = {Maintenance of Community Function through Compensation Breaks down over Time in a Desert Rodent Community}, - author = {Diaz, Renata M. and Ernest, S. K. Morgan}, - year = {2022}, - journal = {Ecology}, - volume = {103}, - number = {7}, - pages = {e3709}, - issn = {1939-9170}, - doi = {10.1002/ecy.3709}, - abstract = {Understanding the ecological processes that maintain community function in systems experiencing species loss, and how these processes change over time, is key to understanding the relationship between community structure and function and predicting how communities may respond to perturbations in the Anthropocene. Using a 30-year experiment on desert rodents, we show that the impact of species loss on community-level energy use has changed repeatedly and dramatically over time, due to (1) the addition of new species to the community, and (2) a reduction in functional redundancy among the same set of species. Although strong compensation, initially driven by the dispersal of functionally redundant species to the local community, occurred in this system from 1997 to 2010, since 2010, compensation has broken down due to decreasing functional overlap within the same set of species. Simultaneously, long-term changes in sitewide community composition due to niche complementarity have decoupled the dynamics of compensation from the overall impact of species loss on community-level energy use. Shifting, context-dependent compensatory dynamics, such as those demonstrated here, highlight the importance of explicitly long-term, metacommunity, and eco-evolutionary perspectives on the link between species-level fluctuations and community function in a changing world.}, - langid = {english}, - keywords = {community function,compensation,environmental fluctuations,functional redundancy,zero-sum dynamic}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3709}, - file = {/Users/renatadiaz/Zotero/storage/NNACG24D/Diaz and Ernest - 2022 - Maintenance of community function through compensa.pdf;/Users/renatadiaz/Zotero/storage/8EDH7JC8/ecy.html} -} - -@misc{diaz2022b, - title = {Temporal Changes in the Individual Size Distribution Decouple Long-Term Trends in Abundance, Biomass, and Energy Use of {{North American}} Breeding Bird Communities}, - author = {Diaz, Renata M. and Ernest, S. K. Morgan}, - year = {2022}, - month = nov, - pages = {2022.11.08.515659}, - publisher = {{bioRxiv}}, - doi = {10.1101/2022.11.08.515659}, - abstract = {Aim A core objective of contemporary biodiversity science is to understand long-term trends in the structure and function of ecological communities. Different currencies of ecological function \textendash{} specifically, total abundance, total standing biomass, and total metabolic flux \textendash{} are naturally linked, but may become decoupled if the underlying size structure of a system changes. Here, we seek to establish how changes in community size composition modulate long-term relationships between different currencies of ecological function for North American birds. Location North America, north of Mexico. Time period 1988-2018. Major taxa studied Breeding birds. Methods We used species' traits and allometric scaling to estimate individual size measurements and basal metabolic rate for birds observed in the North American Breeding Bird Survey. We compared the long-term trajectories for community-wide standing biomass and energy use to the long-term trends driven by changes in individual abundance alone. Finally, we used dissimilarity metrics to evaluate the link between changes in species and size composition and changes in the relationship between abundance- and size-driven dynamics. Results For a substantial minority of communities, shifts in community size composition have decoupled the long-term dynamics of biomass, energy use, and individual abundance. While trends in abundance were dominated by decreases, trends in biomass were evenly divided between decreases and increases, and trends in energy use featured more increases than expected given changes in abundance alone. Communities with decoupled dynamics showed greater increases in community-wide mean body size than other communities, but did not differ from other communities in overall turnover in species or size composition. Main conclusions Size- and abundance-based currencies of ecological function are linked, but not necessarily equivalent. For North American breeding birds, shifts in species composition favoring larger-bodied species may have partially offset declines in standing biomass driven by losses of individuals over the past 30 years.}, - chapter = {New Results}, - copyright = {\textcopyright{} 2022, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/9JH3VJ5K/Diaz and Ernest - 2022 - Temporal changes in the individual size distributi.pdf;/Users/renatadiaz/Zotero/storage/MFR65H6Y/2022.11.08.html} -} - -@article{dirzo2014, - title = {Defaunation in the {{Anthropocene}}}, - author = {Dirzo, Rodolfo and Young, Hillary S. and Galetti, Mauro and Ceballos, Gerardo and Isaac, Nick J. B. and Collen, Ben}, - year = {2014}, - month = jul, - journal = {Science}, - volume = {345}, - number = {6195}, - pages = {401--406}, - publisher = {{American Association for the Advancement of Science}}, - doi = {10.1126/science.1251817}, - file = {/Users/renatadiaz/Zotero/storage/5FN4RUIE/Dirzo et al. - 2014 - Defaunation in the Anthropocene.pdf;/Users/renatadiaz/Zotero/storage/TRP6V5QH/Dirzo et al. - 2014 - Defaunation in the Anthropocene.pdf} -} - -@article{djawdan1988, - title = {Maximal {{Running Speeds}} of {{Bipedal}} and {{Quadrupedal Rodents}}}, - author = {Djawdan, Minou and Garland, Jr., Theodore}, - year = {1988}, - month = nov, - journal = {Journal of Mammalogy}, - volume = {69}, - number = {4}, - pages = {765--772}, - issn = {0022-2372}, - doi = {10.2307/1381631}, - abstract = {Maximal running speeds of both bipedal (Dipodomys, Microdipodops) and quadrupedal (Chaetodipus, Perognathus) heteromyid rodents, and some sympatric nocturnal cricetids and diurnal sciurids, were measured in the laboratory (17 species, 131 individuals) and in the field (eight species, 138 individuals). We found significant, repeatable differences among individuals within species. Significant differences also were found among species: Perognathus longi-membris (8.9 g, 9.9 km/h) and Onychomys torridus (19.3 g, 10.3 km/h) were relatively slow; Microdipodops megacephalus (12.3 g, 10.9 km/h) and Peromyscus crinitus (13.7 g, 11.4 km/h) were somewhat faster; Chaetodipus baileyi (39.1 g, 12.4 km/h), Perognathus parvus (24.4 g, 12.5 km/h), Chaetodipus fallax (18.0 g, 12.8 km/h), Peromyscus eremicus (19.8 g, 13.1 km/h), and Peromyscus maniculatus (18.2 g, 13.4 km/h) attained similar speeds; Peromyscus truei (19.3 g, 14.3 km/h) was faster still; Neotoma lepida (110.6 g, 17.1 km/h) and three squirrel species were the fastest tested in the laboratory. Kangaroo rats (Dipodomys) did not exert themselves maximally in the laboratory, but attained speeds significantly higher than pocket mice (Chaetodipus, Perognathus) or other sympatric rodents in the field. In addition, Dipodomys displayed erratic escape behavior (zig-zagging) when pursued in the field significantly more frequently than Chaetodipus or Perognathus. Higher sprint speeds and erratic escape behavior may allow kangaroo rats to escape from some predators (e.g., raptors, canids), and hence exploit open microhabitats (of presumed higher predation risk) to a greater extent than slower sympatric rodents.}, - file = {/Users/renatadiaz/Zotero/storage/6TWW6WC7/Djawdan and Garland - 1988 - Maximal Running Speeds of Bipedal and Quadrupedal .pdf;/Users/renatadiaz/Zotero/storage/C9P6J9GZ/884085.html} -} - -@article{dornelas2011, - title = {Abundance and Dominance Become Less Predictable as Species Richness Decreases}, - author = {Dornelas, Maria and Phillip, Dawn A. T. and Magurran, Anne E.}, - year = {2011}, - journal = {Global Ecology and Biogeography}, - volume = {20}, - number = {6}, - pages = {832--841}, - issn = {1466-8238}, - doi = {10.1111/j.1466-8238.2010.00640.x}, - abstract = {Aim To test the hypothesis that communities with higher diversity have more predictable properties by examining patterns of community structure along a species richness gradient. Location Trinidad and Tobago (11\textdegree 00 N, 61\textdegree 00 W), on the South American continental shelf, opposite the Orinoco River delta, north-east Venezuela. Methods We used quantile regressions to investigate how three total abundance, absolute and relative dominance measures \textendash{} numerical abundance, biomass and energy use, respectively \textendash{} change across a species richness gradient. We investigated which allocation rule best mimics community assembly in this species richness gradient by examining the abundance of the dominant species and comparing it with predictions of niche apportionment models. Results All measures of total abundance increase on average across the gradient, but the upper limit remains constant. On average, absolute dominance is constant, but the distance between the upper and lower limits decreases along the gradient. Relative dominance decreases with species richness. Observed dominance patterns are best described by Tokeshi's random fraction model. Main conclusions Our results show that both total abundance and absolute dominance become increasingly variable as biodiversity decreases. Consequently, our study suggests that ecosystem properties are less predictable when biodiversity is lower.}, - langid = {english}, - keywords = {Aquatic biomass,community structure,dominant species,energy use,freshwater fish,niche model,resources,species richness,total abundance,Trinidad and Tobago}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1466-8238.2010.00640.x}, - file = {/Users/renatadiaz/Zotero/storage/DSCFWQ6R/Dornelas et al. - 2011 - Abundance and dominance become less predictable as.pdf;/Users/renatadiaz/Zotero/storage/J49SY7FB/j.1466-8238.2010.00640.html} -} - -@article{dornelas2014, - title = {Assemblage {{Time Series Reveal Biodiversity Change}} but {{Not Systematic Loss}}}, - author = {Dornelas, M. and Gotelli, N. J. and McGill, B. and Shimadzu, H. and Moyes, F. and Sievers, C. and Magurran, A. E.}, - year = {2014}, - month = apr, - journal = {Science}, - volume = {344}, - number = {6181}, - pages = {296--299}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.1248484}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/4L3Y25SD/Dornelas et al. - 2014 - Assemblage Time Series Reveal Biodiversity Change .pdf;/Users/renatadiaz/Zotero/storage/N6J43YHB/Dornelas et al. - 2014 - Assemblage Time Series Reveal Biodiversity Change .pdf;/Users/renatadiaz/Zotero/storage/PG24FXLM/Dornelas et al. - 2014 - Assemblage Time Series Reveal Biodiversity Change .pdf} -} - -@article{dornelas2019, - title = {A Balance of Winners and Losers in the {{Anthropocene}}}, - author = {Dornelas, Maria and Gotelli, Nicholas J. and Shimadzu, Hideyasu and Moyes, Faye and Magurran, Anne E. and McGill, Brian J.}, - year = {2019}, - journal = {Ecology Letters}, - volume = {0}, - number = {0}, - issn = {1461-0248}, - doi = {10.1111/ele.13242}, - abstract = {Scientists disagree about the nature of biodiversity change. While there is evidence for widespread declines from population surveys, assemblage surveys reveal a mix of declines and increases. These conflicting conclusions may be caused by the use of different metrics: assemblage metrics may average out drastic changes in individual populations. Alternatively, differences may arise from data sources: populations monitored individually, versus whole-assemblage monitoring. To test these hypotheses, we estimated population change metrics using assemblage data. For a set of 23 241 populations, 16 009 species, in 158 assemblages, we detected significantly accelerating extinction and colonisation rates, with both rates being approximately balanced. Most populations (85\%) did not show significant trends in abundance, and those that did were balanced between winners (8\%) and losers (7\%). Thus, population metrics estimated with assemblage data are commensurate with assemblage metrics and reveal sustained and increasing species turnover.}, - langid = {english}, - keywords = {Anthropogenic,biodiversity,colonisation,extinction,population change}, - file = {/Users/renatadiaz/Zotero/storage/22NLPTUU/Dornelas et al. - 2019 - A balance of winners and losers in the Anthropocen.pdf;/Users/renatadiaz/Zotero/storage/D3ZA4GQ2/Dornelas et al. - 2019 - A balance of winners and losers in the Anthropocen.pdf;/Users/renatadiaz/Zotero/storage/TSZ7KS3S/Dornelas et al. - A balance of winners and losers in the Anthropocen.pdf;/Users/renatadiaz/Zotero/storage/745IPMPQ/ele.html;/Users/renatadiaz/Zotero/storage/DRJN7NLR/ele.html;/Users/renatadiaz/Zotero/storage/E4UNBJBI/ele.html} -} - -@article{dragulescu2001, - title = {Exponential and Power-Law Probability Distributions of Wealth and Income in the {{United Kingdom}} and the {{United States}}}, - author = {Dr{\u a}gulescu, Adrian and Yakovenko, Victor M.}, - year = {2001}, - month = oct, - journal = {Physica A: Statistical Mechanics and its Applications}, - volume = {299}, - number = {1-2}, - pages = {213--221}, - issn = {03784371}, - doi = {10.1016/S0378-4371(01)00298-9}, - abstract = {We present the data on wealth and income distributions in the United Kingdom, as well as on the income distributions in the individual states of the USA. In all of these data, we \"ynd that the great majority of population is described by an exponential distribution, whereas the high-end tail follows a power law. The distributions are characterized by a dimensional scale analogous to temperature. The values of temperature are determined for the UK and the USA, as well as for the individual states of the USA. c 2001 Elsevier Science B.V. All rights reserved.}, - langid = {english}, - keywords = {Boltzmann,Econophysics,Gibbs,Income,Pareto,Wealth}, - file = {/Users/renatadiaz/Zotero/storage/4MA9QCKV/Drăgulescu and Yakovenko - 2001 - Exponential and power-law probability distribution.pdf;/Users/renatadiaz/Zotero/storage/YUT7NI27/Drăgulescu and Yakovenko - 2001 - Exponential and power-law probability distribution.pdf} -} - -@article{dubiner2022, - title = {Widespread Recent Changes in Morphology of {{Old World}} Birds, Global Warming the Immediate Suspect}, - author = {Dubiner, Shahar and Meiri, Shai}, - year = {2022}, - journal = {Global Ecology and Biogeography}, - volume = {31}, - number = {4}, - pages = {791--801}, - issn = {1466-8238}, - doi = {10.1111/geb.13474}, - abstract = {Aim A decline in body size has been proposed as a universal response to global warming, but this is often questioned. We describe and characterize recent morphological changes in the avifauna of Israel as a whole and test several hypotheses regarding their cause. Location Israel. Time period 1950\textendash 2020. Major taxa studied Aves. Methods We analysed the morphology of 7,981 museum specimens. For each of the 106 species, we calculated the rate of change in mass, head and body length, wing length and approximate relative surface area, both over time and as a function of temperature anomaly (the difference between temperatures in a given year and the interannual average). We used phylogenetic generalized linear mixed models (PGLMMs) to determine trends and their relationship to the ecology of species. Results Over the last 70 years there have been consistent changes through time in mass, length and surface area-to-volume ratio. Mass decreased by 18.3\%, length increased by 5.1\%, and surface area-to-volume ratio increased by 28.9\%. The increase in the ratio of surface area to volume through time corresponds to a 12.2\% increase per degree Celsius of warming. In contrast, changes in wing length were few and inconsistent. Most species changed in either mass or length, but seldom in both. The effect of rising temperature on morphology was roughly an order of magnitude stronger than the effect of a comparable geographical difference in habitat temperature. Changes were modulated by migratory habits but not explained by human commensalism or diet. Main conclusions A decrease in mass and increase in length are widespread, both leading to higher relative surface area. Results conform with predicted responses to global warming, but not with any of our other tested hypotheses. If warming is the driver of these changes, the diverging responses observed between different species might represent different solutions to solve a common problem.}, - langid = {english}, - keywords = {birds,body condition,body size,climate change,global warming,heat loss,migration,morphology,museum specimens}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.13474}, - file = {/Users/renatadiaz/Zotero/storage/LY7APMTK/Dubiner and Meiri - 2022 - Widespread recent changes in morphology of Old Wor.pdf;/Users/renatadiaz/Zotero/storage/CT9FVW2R/geb.html} -} - -@book{dunning2008, - title = {{{CRC}} Handbook of Avian Body Masses}, - author = {Dunning, John B.}, - year = {2008}, - journal = {CRC handbook of avian body masses}, - edition = {2nd ed.}, - publisher = {{CRC Press}}, - address = {{Boca Raton}}, - isbn = {978-1-4200-6445-2}, - langid = {english}, - keywords = {Anatomy \& Physiology,Birds,Body size,Electronic books,Life Sciences,SCIENCE,Size,Tables} -} - -@article{eckrich2018, - title = {Functional and Numerical Responses of Shrews to Competition Vary with Mouse Density}, - author = {Eckrich, Carolyn A. and Flaherty, Elizabeth A. and {Ben-David}, Merav}, - year = {2018}, - month = jan, - journal = {Plos One}, - volume = {13}, - number = {1}, - pages = {e0189471}, - publisher = {{Public Library Science}}, - address = {{San Francisco}}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0189471}, - abstract = {For decades, ecologists have debated the importance of biotic interactions (e.g., competition) and abiotic factors in regulating populations. Competition can influence patterns of distribution, abundance, and resource use in many systems but remains difficult to measure. We quantified competition between two sympatric small mammals, Keen's mice (Peromyscus keen) and dusky shrews (Sorex monticolus), in four habitat types on Prince of Wales Island in Southeast Alaska. We related shrew density to that of mice using standardized regression models while accounting for habitat variables in each year from 2010-2012, during which mice populations peaked (2011) and then crashed (2012). Additionally, we measured dietary overlap and segregation using stable isotope analysis and kernel utilization densities and estimated the change in whole community energy consumption among years. We observed an increase in densities of dusky shrews after mice populations crashed in 2012 as expected under competitive release. In addition, competition coefficients revealed that the influence of Keen's mice was dependent on their density. Also in 2012, shrew diets shifted, indicating that they were able to exploit resources previously used by mice. Nonetheless, increases in shrew numbers only partially compensated for the community energy consumption because, as insectivores, they are unlikely to utilize all food types consumed by their competitors. In pre-commercially thinned stands, which exhibit higher diversity of resources compared to other habitat types, shrew populations were less affected by changes in mice densities. These spatially and temporally variable interactions between unlikely competitors, observed in a relatively simple, high-latitude island ecosystem, highlight the difficulty in assessing the role of biotic factors in structuring communities.}, - langid = {english}, - keywords = {coefficients,coexistence,compensation,demography,niche,population-dynamics,predation,seasonal-changes,small rodents,sorex-monticolus}, - annotation = {WOS:000419185200012}, - file = {/Users/renatadiaz/Zotero/storage/7D4ZU74W/Eckrich et al. - 2018 - Functional and numerical responses of shrews to co.pdf} -} - -@article{ellis2018, - title = {Indirect Effects of a Large Mammalian Herbivore on Small Mammal Populations: {{Context-dependent}} Variation across Habitat Types, Mammal Species, and Seasons}, - shorttitle = {Indirect Effects of a Large Mammalian Herbivore on Small Mammal Populations}, - author = {Ellis, Taylor D. and Cushman, J. Hall}, - year = {2018}, - journal = {Ecology and Evolution}, - volume = {8}, - number = {23}, - pages = {12115--12125}, - issn = {2045-7758}, - doi = {10.1002/ece3.4670}, - abstract = {Multiple consumer species frequently co-occur in the same landscape and, through effects on surrounding environments, can interact in direct and indirect ways. These interactions can vary in occurrence and importance, and focusing on this variation is critical for understanding the dynamics of interactions among consumers. Large mammalian herbivores are important engineers of ecosystems worldwide, have substantial impacts on vegetation, and can indirectly affect small-mammal populations. However, the degree to which such indirect effects vary within the same system has received minimal attention. We used a 16-year-old exclosure experiment, stratified across a heterogeneous landscape, to evaluate the importance of context-dependent interactions between tule elk (Cervus canadensis nannodes) and small mammals (deer mice [Peromyscus maniculatus], meadow voles [Microtus californicus], and harvest mice [Reithrodontymys megalotis]) in a coastal grassland in California. Effects of elk on voles varied among habitats and seasons: In open grasslands, elk reduced vole numbers during fall 2013 but not summer 2014; in Lupinus-dominated grasslands, elk reduced vole numbers during summer 2014 but not fall 2013; and in Baccharis-dominated grasslands, elk had no effect on vole numbers in either season. Effects of elk on the two mice species also varied among habitats and seasons, but often in different ways from voles and each other. In fall 2013, elk decreased mice abundances in Lupinus-dominated grasslands, but not in Baccharis-dominated or open grasslands. In summer 2014, elk decreased the abundance of harvest mice consistently across habitat types. In contrast, elk increased deer-mice numbers in open grasslands but not other habitats. Within the same heterogenous study system, the influence of elk on small mammals was strongly context-dependent, varying among habitats, mammal species, and seasons. We hypothesize that such variability is common in nature and that failure to consider it may yield inaccurate findings and limit our understanding of interactions among co-occurring consumers.}, - copyright = {\textcopyright{} 2018 The Authors. Ecology and Evolution published by John Wiley \& Sons Ltd.}, - langid = {english}, - keywords = {consumers,context-dependent interactions,elk,grasslands,grazers,herbivores,indirect interactions,rodents,ungulates}, - annotation = {\_eprint: https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4670}, - file = {/Users/renatadiaz/Zotero/storage/K2DPSTUP/Ellis and Cushman - 2018 - Indirect effects of a large mammalian herbivore on.pdf;/Users/renatadiaz/Zotero/storage/XERWHD9Z/ece3.html} -} - -@article{elmberg2020, - title = {Population Change in Breeding Boreal Waterbirds in a 25-Year Perspective: {{What}} Characterises Winners and Losers?}, - shorttitle = {Population Change in Breeding Boreal Waterbirds in a 25-Year Perspective}, - author = {Elmberg, Johan and Arzel, Celine and Gunnarsson, Gunnar and Holopainen, Sari and Nummi, Petri and P{\"o}ys{\"a}, Hannu and Sj{\"o}berg, Kjell}, - year = {2020}, - journal = {Freshwater Biology}, - volume = {65}, - number = {2}, - pages = {167--177}, - issn = {1365-2427}, - doi = {10.1111/fwb.13411}, - abstract = {Understanding drivers of variation and trends in biodiversity change is a general scientific challenge, but also crucial for conservation and management. Previous research shows that patterns of increase and decrease are not always consistent at different spatial scales, calling for approaches combining the latter. We here explore the idea that functional traits of species may help explaining divergent population trends. Complementing a previous community level study, we here analyse data about breeding waterbirds on 58 wetlands in boreal Fennoscandia, covering gradients in latitude as well as trophic status. We used linear mixed models to address how change in local abundance over 25 years in 25 waterbird species are associated with life history traits, diet, distribution, breeding phenology, and habitat affinity. Mean abundance increased in 10 species from 1990/1991 to 2016, whereas it decreased in 15 species. Local population increases were associated with species that are early breeders and have small clutches, an affinity for luxurious wetlands, an herbivorous diet, and a wide breeding range rather than a southern distribution. Local decreases, by contrast, were associated with species having large clutches and invertivorous diet, as well as being late breeders and less confined to luxurious wetlands. The three species occurring on the highest number of wetlands all decreased in mean abundance. The fact that early breeders have done better than late fits well with previous research about adaptability to climate change, that is, response to earlier springs. We found only limited support for the idea that life history traits are good predictors of wetland level population change. Instead, diet turned out to be a strong candidate for an important driver of population change, as supported by a general decrease of invertivores and a concomitant increase of large herbivores. In a wider perspective, future research needs to address whether population growth of large-bodied aquatic herbivores affects abundance of co-occurring invertivorous species, and if so, if this is due to habitat alteration, or to interference or exploitative competition.}, - copyright = {\textcopyright{} 2019 John Wiley \& Sons Ltd.}, - langid = {english}, - keywords = {breeding phenology,diet,distribution,life history,waterfowl}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fwb.13411}, - file = {/Users/renatadiaz/Zotero/storage/NQ9RE9FG/fwb.html} -} - -@article{emery2021, - title = {Data {{Science}} in {{Undergraduate Life Science Education}}: {{A Need}} for {{Instructor Skills Training}}}, - shorttitle = {Data {{Science}} in {{Undergraduate Life Science Education}}}, - author = {Emery, Nathan C and Crispo, Erika and Supp, Sarah R and Farrell, Kaitlin J and Kerkhoff, Andrew J and Bledsoe, Ellen K and O'Donnell, Kelly L and McCall, Andrew C and {Aiello-Lammens}, Matthew E}, - year = {2021}, - month = oct, - journal = {BioScience}, - number = {biab107}, - issn = {0006-3568}, - doi = {10.1093/biosci/biab107}, - abstract = {There is a clear demand for quantitative literacy in the life sciences, necessitating competent instructors in higher education. However, not all instructors are versed in data science skills or research-based teaching practices. We surveyed biological and environmental science instructors (n = 106) about the teaching of data science in higher education, identifying instructor needs and illuminating barriers to instruction. Our results indicate that instructors use, teach, and view data management, analysis, and visualization as important data science skills. Coding, modeling, and reproducibility were less valued by the instructors, although this differed according to institution type and career stage. The greatest barriers were instructor and student background and space in the curriculum. The instructors were most interested in training on how to teach coding and data analysis. Our study provides an important window into how data science is taught in higher education biology programs and how we can best move forward to empower instructors across disciplines.}, - file = {/Users/renatadiaz/Zotero/storage/MVGPITSQ/Emery et al. - 2021 - Data Science in Undergraduate Life Science Educati.pdf;/Users/renatadiaz/Zotero/storage/85WGK6B7/6403634.html} -} - -@article{emery2021a, - title = {Cultivating Inclusive Instructional and Research Environments in Ecology and Evolutionary Science}, - author = {Emery, Nathan C. and Bledsoe, Ellen K. and Hasley, Andrew O. and Eaton, Carrie Diaz}, - year = {2021}, - journal = {Ecology and Evolution}, - volume = {11}, - number = {4}, - pages = {1480--1491}, - issn = {2045-7758}, - doi = {10.1002/ece3.7062}, - abstract = {As we strive to lift up a diversity of voices in science, it is important for ecologists, evolutionary scientists, and educators to foster inclusive environments in their research and teaching. Academics in science often lack exposure to research on best practices in diversity, equity, and inclusion and may not know where to start to make scientific environments more welcoming and inclusive. We propose that by approaching research and teaching with empathy, flexibility, and a growth mind-set, scientists can be more supportive and inclusive of their colleagues and students. This paper provides guidance, explores strategies, and directs scientists to resources to better cultivate an inclusive environment in three common settings: the classroom, the research laboratory, and the field. As ecologists and evolutionary scientists, we have an opportunity to adapt our teaching and research practices in order to foster an inclusive educational ecosystem for students and colleagues alike.}, - langid = {english}, - keywords = {diversity,equity,Inclusivity,research,teaching}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.7062}, - file = {/Users/renatadiaz/Zotero/storage/ZKD758ED/Emery et al. - 2021 - Cultivating inclusive instructional and research e.pdf;/Users/renatadiaz/Zotero/storage/GP9JTHIH/ece3.html} -} - -@article{emery2021b, - title = {Cultivating Inclusive Instructional and Research Environments in Ecology and Evolutionary Science}, - author = {Emery, Nathan C. and Bledsoe, Ellen K. and Hasley, Andrew O. and Eaton, Carrie Diaz}, - year = {2021}, - journal = {Ecology and Evolution}, - volume = {11}, - number = {4}, - pages = {1480--1491}, - issn = {2045-7758}, - doi = {10.1002/ece3.7062}, - abstract = {As we strive to lift up a diversity of voices in science, it is important for ecologists, evolutionary scientists, and educators to foster inclusive environments in their research and teaching. Academics in science often lack exposure to research on best practices in diversity, equity, and inclusion and may not know where to start to make scientific environments more welcoming and inclusive. We propose that by approaching research and teaching with empathy, flexibility, and a growth mind-set, scientists can be more supportive and inclusive of their colleagues and students. This paper provides guidance, explores strategies, and directs scientists to resources to better cultivate an inclusive environment in three common settings: the classroom, the research laboratory, and the field. As ecologists and evolutionary scientists, we have an opportunity to adapt our teaching and research practices in order to foster an inclusive educational ecosystem for students and colleagues alike.}, - langid = {english}, - keywords = {diversity,equity,Inclusivity,research,teaching}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.7062}, - file = {/Users/renatadiaz/Zotero/storage/CUFFHMWV/Emery et al. - 2021 - Cultivating inclusive instructional and research e.pdf;/Users/renatadiaz/Zotero/storage/9ZUAKLUY/ece3.html} -} - -@article{ernest2000, - title = {Rodents, Plants, and Precipitation: Spatial and Temporal Dynamics of Consumers and Resources}, - shorttitle = {Rodents, Plants, and Precipitation}, - author = {Ernest, S. K. Morgan and Brown, James H. and Parmenter, Robert R.}, - year = {2000}, - month = mar, - journal = {Oikos}, - volume = {88}, - number = {3}, - pages = {470--482}, - issn = {00301299}, - doi = {10.1034/j.1600-0706.2000.880302.x}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/9IETP7ZX/Ernest et al. - 2000 - Rodents, plants, and precipitation spatial and te.pdf;/Users/renatadiaz/Zotero/storage/XNFDQG2P/Ernest et al. - 2000 - Rodents, plants, and precipitation spatial and te.pdf} -} - -@article{ernest2001, - title = {Homeostasis and {{Compensation}}: {{The Role}} of {{Species}} and {{Resources}} in {{Ecosystem Stability}}}, - shorttitle = {Homeostasis and {{Compensation}}}, - author = {Ernest, S. K. Morgan and Brown, James H.}, - year = {2001}, - journal = {Ecology}, - volume = {82}, - number = {8}, - pages = {2118--2132}, - publisher = {{Ecological Society of America}}, - issn = {0012-9658}, - doi = {10.2307/2680220}, - abstract = {A synthesis of community and ecosystem ecology should yield insights into the role of species in ecosystem function. Concepts from these subdisciplines of ecology, specifically species compensation and ecosystem homeostasis, can be linked by analyzing the effect of changes in the abundance of species on ecosystem processes. Compensatory changes in species populations in response to environmental fluctuations can maintain an approximate steady state between rates of resource supply and resource consumption. We predict that ecosystem-level properties, such as species richness, total population, biomass, and energy use, will exhibit less variability in response to environmental change than will species composition. We tested this prediction using long-term data of a desert rodent community responding to natural environmental fluctuations and of a plant community responding to experimental manipulations. For the rodents, species composition was twice as variable as the ecosystem properties. This result was the same for both the analysis of variability around the 22-yr average and the analysis of variability from one time period to the next. For the plant communities, species composition was more variable among treatments in most years than stem count or species richness. Using the variance ratio proposed by J. L. Klug et al. we detected negative covariances in the rodent community, confirming the presence of compensatory dynamics.}, - file = {/Users/renatadiaz/Zotero/storage/6CELFM2Q/Ernest and Brown - 2001 - Homeostasis and Compensation The Role of Species .pdf} -} - -@article{ernest2001a, - title = {Delayed {{Compensation}} for {{Missing Keystone Species}} by {{Colonization}}}, - author = {Ernest, S. K. Morgan and Brown, James H.}, - year = {2001}, - month = apr, - journal = {Science}, - volume = {292}, - number = {5514}, - pages = {101--104}, - publisher = {{American Association for the Advancement of Science}}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.292.5514.101}, - abstract = {Because individual species can play key roles, the loss of species through extinction or their gain through colonization can cause major changes in ecosystems. For almost 20 years after kangaroo rats were experimentally removed from a Chihuahuan desert ecosystem in the United States, other rodent species were unable to compensate and use the available resources. This changed abruptly in 1995, when an alien species of pocket mouse colonized the ecosystem, used most of the available resources, and compensated almost completely for the missing kangaroo rats. These results demonstrate the importance of individual species and of colonization and extinction events in the structure and dynamics of ecosystems.}, - chapter = {Report}, - langid = {english}, - pmid = {11292873}, - file = {/Users/renatadiaz/Zotero/storage/IGBYPU4W/Ernest and Brown - 2001 - Delayed Compensation for Missing Keystone Species .pdf;/Users/renatadiaz/Zotero/storage/S6VMRCIY/Ernest and Brown - 2001 - Delayed Compensation for Missing Keystone Species .pdf;/Users/renatadiaz/Zotero/storage/I22TQVPY/101.html;/Users/renatadiaz/Zotero/storage/QDIU2VC6/tab-pdf.html} -} - -@article{ernest2005, - title = {Body Size, Energy Use, and Community Structure of Small Mammals}, - author = {Ernest, S. K. Morgan}, - year = {2005}, - month = jun, - journal = {Ecology}, - volume = {86}, - number = {6}, - pages = {1407--1413}, - issn = {0012-9658}, - doi = {10.1890/03-3179}, - abstract = {Body size has long been hypothesized to play a major role in community structure and dynamics. Two general hypotheses exist for how resources are distributed among body sizes: (1) resources are equally available and uniformly utilized across body sizes and (2) resources are differentially available to organisms of different body sizes, resulting in a nonuniform or modal distribution. It has also been predicted that the distribution of body sizes of species in a community should reflect the underlying availability of resources, with the emergence of aggregations of species around specific body sizes. I examined the relationship between energy utilization, body size, and community structure in nine small-mammal communities in North America. In all communities, energy use across body sizes was significantly different from uniform. In contrast, none of the nine species-level body size distributions were significantly different from uniform. Cross-site comparisons showed that, while the species-level body size distribution did not vary significantly among sites, the utilization of energy across body sizes did. These results suggest that uniform energy utilization does not occur in small-mammal communities and that the species-level body size distribution of a community is not determined by resource utilization.}, - langid = {english}, - keywords = {body size distribution,body size–energy distribution,community structure,energetic equivalence rule,macroecology,small mammals}, - file = {/Users/renatadiaz/Zotero/storage/V69KYP2D/Ernest - 2005 - Body Size, Energy Use, and Community Structure of .pdf;/Users/renatadiaz/Zotero/storage/VQD3VYAB/Ernest - 2005 - BODY SIZE, ENERGY USE, AND COMMUNITY STRUCTURE OF .pdf;/Users/renatadiaz/Zotero/storage/5MGC88UU/03-3179.html} -} - -@article{ernest2008, - title = {Zero {{Sum}}, the {{Niche}}, and {{Metacommunities}}: {{Long}}-{{Term Dynamics}} of {{Community Assembly}}}, - shorttitle = {Zero {{Sum}}, the {{Niche}}, and {{Metacommunities}}}, - author = {Ernest, S.~K.~Morgan and Brown, James~H. and Thibault, Katherine~M. and White, Ethan~P. and Goheen, Jacob~R.}, - year = {2008}, - month = dec, - journal = {The American Naturalist}, - volume = {172}, - number = {6}, - pages = {E257-E269}, - issn = {0003-0147, 1537-5323}, - doi = {10.1086/592402}, - abstract = {Recent models of community assembly, structure, and dynamics have incorporated, to varying degrees, three mechanistic processes: resource limitation and interspecific competition, niche requirements of species, and exchanges between a local community and a regional species pool. Synthesizing 30 years of data from an intensively studied desert rodent community, we show that all of these processes, separately and in combination, have influenced the structural organization of this community and affected its dynamical response to both natural environmental changes and experimental perturbations. In addition, our analyses suggest that zero-sum constraints, niche differences, and metacommunity processes are inextricably linked in the ways that they affect the structure and dynamics of this system. Explicit consideration of the interaction of these processes should yield a deeper understanding of the assembly and dynamics of other ecological communities. This synthesis highlights the role that long-term data, especially when coupled with experimental manipulations, can play in assessing the fundamental processes that govern the structure and function of ecological communities.}, - langid = {english}, - keywords = {body-size,Chihuahuan Desert,community dynamics,compensatory dynamics,desert rodent community,environmental heterogeneity,food addition,indirect facilitation,interspecific competition,neutral theory,regulates species richness,resource limitation,species sorting,theoretical biology,trade-offs}, - file = {/Users/renatadiaz/Zotero/storage/83QMEE3H/Ernest et al. - 2008 - Zero Sum, the Niche, and Metacommunities Long‐Ter.pdf;/Users/renatadiaz/Zotero/storage/VSW9946P/Ernest et al. - 2008 - Zero Sum, the Niche, and Metacommunities Long-Ter.pdf;/Users/renatadiaz/Zotero/storage/XSL48E93/Ernest et al. - 2008 - Zero Sum, the Niche, and Metacommunities Long‐Ter.pdf} -} - -@article{ernest2009, - title = {Long-Term Monitoring and Experimental Manipulation of a {{Chihuahuan Desert}} Ecosystem near {{Portal}}, {{Arizona}}, {{USA}}}, - author = {Ernest, S. K. Morgan and Valone, Thomas J. and Brown, James H.}, - year = {2009}, - journal = {Ecology}, - volume = {90}, - number = {6}, - pages = {1708--1708}, - issn = {1939-9170}, - doi = {10.1890/08-1222.1}, - abstract = {Desert ecosystems have long served as model systems in the study of ecological concepts (e.g., competition, resource pulses, top-down/bottom-up dynamics). However, the inherent variability of resource availability in deserts, and hence consumer dynamics, can also make them challenging ecosystems to understand. Study of a Chihuahuan desert ecosystem near Portal, Arizona, USA, began in 1977. At this site, 24 experimental plots were established in 1977 and divided among controls and experimental manipulations. Experimental manipulations over the years include removal of all or some rodent species, all or some ants, seed additions, and various alterations of the annual plant community. While some of these manipulations were discontinued early on, others (i.e., ant and rodent manipulations) have been maintained throughout the study. Monitoring of the composition and abundances of ants, plants, and rodents has occurred continuously on all 24 plots. From 1977 to 2002, individual-level data on rodents (i.e., species, sex, size, reproductive condition) were collected monthly for each plot. From 1983 to 2002, the species-level abundances of plants were sampled on permanent quadrats. From 1977 to 2002, the species-level abundance of ant colonies was recorded for each plot, and from 1988 to 2002 additional information on ant abundances were recorded. Finally, from 1980 to 2002 we recorded precipitation at the study site. These data have been used in a variety of publications documenting the effects of the experimental manipulations as well as the response of populations and communities to long-term changes in climate and habitat. Sampling is ongoing and this database will be periodically updated. The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at {$\langle$}http://esapubs.org/archive{$\rangle$}. (The accession number for each Data Paper is given directly beneath the title.)}, - copyright = {\textcopyright{} 2009 by the Ecological Society of America}, - langid = {english}, - keywords = {ants,Chihuahuan Desert,LTREB data,plants,rodents}, - file = {/Users/renatadiaz/Zotero/storage/2RCIEGFT/Ernest et al. - 2009 - Long-term monitoring and experimental manipulation.pdf;/Users/renatadiaz/Zotero/storage/46LYU7IJ/08-1222.html} -} - -@article{ernest2009a, - title = {Changes in a Tropical Forest Support Metabolic Zero-Sum Dynamics}, - author = {Ernest, S. K. Morgan and White, Ethan P. and Brown, James H.}, - year = {2009}, - journal = {Ecology Letters}, - volume = {12}, - number = {6}, - pages = {507--515}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2009.01305.x}, - abstract = {Major shifts in many ecosystem-level properties of tropical forests have been observed, but the processes driving these changes are poorly understood. The forest on Barro Colorado Island (BCI) exhibited a 20\% decrease in the number of trees and a 10\% increase in average diameter. Using a metabolism-based zero-sum framework, we show that increases in per capita resource use at BCI, caused by increased tree size and increased temperature, compensated for the observed declines in abundance. This trade-off between abundance and average resource use resulted in no net change in the rate resources are fluxed by the forest. Observed changes in the forest are not consistent with other hypotheses, including changes in overall resource availability and existing self-thinning models. The framework successfully predicts interrelated changes in size, abundance and temperature, indicating its utility for understanding changes in the structure and dynamics of ecosystems.}, - copyright = {\textcopyright{} 2009 Blackwell Publishing Ltd/CNRS}, - langid = {english}, - keywords = {Community ecology,metabolic ecology,neutral theory,tropical forests,zero-sum dynamics}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2009.01305.x}, - file = {/Users/renatadiaz/Zotero/storage/U3BVI3KB/Ernest et al. - 2009 - Changes in a tropical forest support metabolic zer.pdf;/Users/renatadiaz/Zotero/storage/VX97KK5A/Ernest et al. - 2009 - Changes in a tropical forest support metabolic zer.pdf;/Users/renatadiaz/Zotero/storage/ZYZVJB59/Ernest et al. - 2009 - Changes in a tropical forest support metabolic zer.pdf;/Users/renatadiaz/Zotero/storage/77A9B3QL/j.1461-0248.2009.01305.html;/Users/renatadiaz/Zotero/storage/R3E2RQG9/j.1461-0248.2009.01305.html} -} - -@inbook{ernest2013, - title = {Using {{Size Distributions}} to {{Understand}} the {{Role}} of {{Body Size}} in {{Mammalian Community Assembly}}}, - booktitle = {Animal {{Body Size}}: {{Linking Pattern}} and {{Process}} across {{Space}}, {{Time}}, and {{Taxonomic Group}}}, - author = {Ernest, S.K. Morgan}, - year = {2013}, - publisher = {{University of Chicago Press}}, - doi = {10.7208/chicago/9780226012285.001.0001}, - collaborator = {Smith, Felisa A. and Lyons, S. Kathleen}, - isbn = {978-0-226-01214-8 978-0-226-01228-5}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/ZMQBW8WR/Smith and Lyons - 2013 - Animal Body Size Linking Pattern and Process acro.pdf} -} - -@article{ernest2020, - title = {The {{Portal Project}}: A Long-Term Study of a {{Chihuahuan}} Desert Ecosystem}, - author = {Ernest, S. K. Morgan and Yenni, Glenda M. and Allington, Ginger and Bledsoe, Ellen K. and Christensen, Erica M. and Diaz, Renata M. and Geluso, Keith and Goheen, Jacob R. and Guo, Qinfeng and Heske, Edward and Kelt, Douglas and Meiners, Joan M. and Munger, Jim and Restrepo, Carla and Samson, Douglas A. and Schutzenhofer, Michele R. and Skupski, Marian and Supp, Sarah R. and Thibault, Kate and Taylor, Shawn and White, Ethan and Ye, Hao and Davidson, Diane W. and Brown, James H. and Valone, Thomas J.}, - year = {2020}, - month = jan, - journal = {bioRxiv}, - pages = {332783}, - doi = {10.1101/332783}, - abstract = {This is a data paper for the Portal Project, a long-term ecological study of rodents, plants, and ants located in southeastern Arizona, U.S.A. This paper contains an overview of methods and information about the structure of the data files and the relational structure among the files. This is a living data paper and will be updated with new information as major changes or additions are made to the data. All data - along with more detailed data collection protocols and site information - is archived at: https://doi.org/10.5281/zenodo.1215988.Competing Interest StatementThe authors have declared no competing interest.} -} - -@article{etienne2005, - title = {A Dispersal-Limited Sampling Theory for Species and Alleles}, - author = {Etienne, Rampal S. and Alonso, David}, - year = {2005}, - journal = {Ecology Letters}, - volume = {8}, - number = {11}, - pages = {1147--1156}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2005.00817.x}, - abstract = {The importance of dispersal for biodiversity has long been recognized. However, it was never advertised as vigorously as Stephen Hubbell did in the context of his neutral community theory. After his book appeared in 2001, several scientists have sought and found analytical expressions for the effect of dispersal limitation on community composition, still in the neutral context. This has been done along two relatively independent lines of research that have a different mathematical approach and focus on different, yet related, types of results. Here, we study both types in a new framework that makes use of the sampling nature of the theory. We present sampling distributions that contain binomial or hypergeometric sampling on the one hand, and dispersal limitation on the other, and thus views dispersal limitation as ubiquitous as sampling effects. Further, we express the results of one line of research in terms of the other and vice versa, using the concept of subsamples. A consequence of our findings is that metacommunity size does not independently affect the outcome of neutral models in contrast to a previous assertion (Ecol. Lett., 7, 2004, p. 904) based on an incorrect formula (Phys. Rev. E, 68, 2003, p. 061902, eqns 11\textendash 14). Our framework provides the basis for development of a dispersal-limited non-neutral community theory and applies in population genetics as well, where alleles and mutation play the roles of species and speciation respectively.}, - langid = {english}, - keywords = {Binomial sampling,biodiversity,community,dispersal-limited sampling,Ewens sampling formula,hypergeometric sampling,neutral model,random sampling}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2005.00817.x}, - file = {/Users/renatadiaz/Zotero/storage/5GJJPUDY/Etienne and Alonso - 2005 - A dispersal-limited sampling theory for species an.pdf;/Users/renatadiaz/Zotero/storage/JR3V6GUE/j.1461-0248.2005.00817.html} -} - -@article{etienne2019, - title = {A {{Minimal Model}} for the {{Latitudinal Diversity Gradient Suggests}} a {{Dominant Role}} for {{Ecological Limits}}}, - author = {Etienne, Rampal S. and Cabral, Juliano Sarmento and Hagen, Oskar and Hartig, Florian and Hurlbert, Allen H. and Pellissier, Lo{\"i}c and Pontarp, Mikael and Storch, David}, - year = {2019}, - month = jul, - journal = {The American Naturalist}, - volume = {194}, - number = {5}, - pages = {E122-E133}, - publisher = {{The University of Chicago Press}}, - issn = {0003-0147}, - doi = {10.1086/705243}, - abstract = {The latitudinal diversity gradient (LDG) is one of Earth's most iconic biodiversity patterns and still one of the most debated. Explanations for the LDG are often categorized into three broad pathways in which the diversity gradient is created by (1) differential diversification rates, (2) differential carrying capacities (ecological limits), or (3) differential time to accumulate species across latitude. Support for these pathways has, however, been mostly verbally expressed. Here, we present a minimal model to clarify the essential assumptions of the three pathways and explore the sensitivity of diversity dynamics to these pathways. We find that an LDG arises most easily from a gradient in ecological limits compared with a gradient in the time for species accumulation or diversification rate in most modeled scenarios. Differential diversification rates create a stronger LDG than ecological limits only when speciation and dispersal rates are low, but then the predicted LDG seems weaker than the observed LDG. Moreover, range dynamics may reduce an LDG created by a gradient in diversification rates or time for species accumulation, but they cannot reduce an LDG induced by differential ecological limits. We conclude that our simple model provides a null prediction for the effectiveness of the three LDG pathways and can thus aid discussions about the causal mechanisms underlying the LDG or motivate more complex models to confirm or falsify our findings.}, - file = {/Users/renatadiaz/Zotero/storage/38SZP8K7/Etienne et al. - 2019 - A Minimal Model for the Latitudinal Diversity Grad.pdf} -} - -@article{euler1862, - title = {Sex Litterae Ad {{Nicolaum Bernoullium II}}, {{Basileensem J}}. {{U}}. {{D}}. Datae 1742 Ad 1745}, - author = {Euler, Leonhard}, - year = {1862}, - month = jan, - journal = {{$<$}p{$>$}Opera Postuma{$<$}/p{$>$}}, - pages = {519--549}, - file = {/Users/renatadiaz/Zotero/storage/YX95NNV8/820.html} -} - -@article{evanno2009, - title = {Parallel Changes in Genetic Diversity and Species Diversity Following a Natural Disturbance}, - author = {Evanno, Guillaume and CasTELla, Emmanuel and Antoine, C{\'e}line and Paillat, Gabrielle and Goudet, J{\'e}r{\^o}me}, - year = {2009}, - journal = {Molecular Ecology}, - volume = {18}, - number = {6}, - pages = {1137--1144}, - issn = {1365-294X}, - doi = {10.1111/j.1365-294X.2009.04102.x}, - abstract = {We examined the spatial and temporal variation of species diversity and genetic diversity in a metacommunity comprising 16 species of freshwater gastropods. We monitored species abundance at five localities of the Ain river floodplain in southeastern France, over a period of four years. Using 190 AFLP loci, we monitored the genetic diversity of Radix balthica, one of the most abundant gastropod species of the metacommunity, twice during that period. An exceptionally intense drought occurred during the last two years and differentially affected the study sites. This allowed us to test the effect of natural disturbances on changes in both genetic and species diversity. Overall, local (alpha) diversity declined as reflected by lower values of gene diversity HS and evenness. In parallel, the among-sites (beta) diversity increased at both the genetic (FST) and species (FSTC) levels. These results suggest that disturbances can lead to similar changes in genetic and community structure through the combined effects of selective and neutral processes.}, - langid = {english}, - keywords = {beta diversity,biodiversity,disturbance,floodplain,gastropods,genetic structure}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2009.04102.x}, - file = {/Users/renatadiaz/Zotero/storage/AIV4N75D/Evanno et al. - 2009 - Parallel changes in genetic diversity and species .pdf;/Users/renatadiaz/Zotero/storage/LJR3TNWD/Evanno et al. - 2009 - Parallel changes in genetic diversity and species .pdf;/Users/renatadiaz/Zotero/storage/XF8FTWH7/j.1365-294X.2009.04102.html;/Users/renatadiaz/Zotero/storage/XHZD97NU/j.1365-294X.2009.04102.html} -} - -@article{farrell2018, - title = {Power, Pitfalls, and Potential for Integrating Computational Literacy into Undergraduate Ecology Courses}, - author = {Farrell, Kaitlin J. and Carey, Cayelan C.}, - year = {2018}, - journal = {Ecology and Evolution}, - volume = {8}, - number = {16}, - pages = {7744--7751}, - issn = {2045-7758}, - doi = {10.1002/ece3.4363}, - abstract = {Environmental research requires understanding nonlinear ecological dynamics that interact across multiple spatial and temporal scales. The analysis of long-term and high-frequency sensor data combined with simulation modeling enables interpretation of complex ecological phenomena, and the computational skills needed to conduct these analyses are increasingly being integrated into graduate student training programs in ecology. Despite its importance, however, computational literacy\textemdash that is, the ability to harness the power of computer technologies to accomplish tasks\textemdash is rarely taught in undergraduate ecology classrooms, representing a major gap in training students to tackle complex environmental challenges. Through our experience developing undergraduate curricula in long-term and high-frequency data analysis and simulation modeling for two environmental science pedagogical initiatives, Project EDDIE (Environmental Data-Driven Inquiry and Exploration) and Macrosystems EDDIE, we have found that students often feel intimidated by computational tasks, which is compounded by the lack of familiarity with software (e.g., R) and the steep learning curves associated with script-based analytical tools. The use of prepackaged, flexible modules that introduce programming as a mechanism to explore environmental datasets and teach inquiry-based ecology, such as those developed for Project EDDIE and Macrosystems EDDIE, can significantly increase students' experience and comfort levels with advanced computational tools. These types of modules in turn provide great potential for empowering students with the computational literacy needed to ask ecological questions and test hypotheses on their own. As continental-scale sensor observatory networks rapidly expand the availability of long-term and high-frequency data, students with the skills to manipulate, visualize, and interpret such data will be well-prepared for diverse careers in data science, and will help advance the future of open, reproducible science in ecology.}, - langid = {english}, - keywords = {active learning,big data,computer programming,data science,education,R software,sensor data,teaching modules}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4363}, - file = {/Users/renatadiaz/Zotero/storage/2M88BANR/Farrell and Carey - 2018 - Power, pitfalls, and potential for integrating com.pdf;/Users/renatadiaz/Zotero/storage/66GQIGE2/ece3.html} -} - -@article{favretti2018, - title = {Remarks on the {{Maximum Entropy Principle}} with {{Application}} to the {{Maximum Entropy Theory}} of {{Ecology}}}, - author = {Favretti, Marco}, - year = {2018}, - month = jan, - journal = {Entropy}, - volume = {20}, - number = {1}, - pages = {11}, - publisher = {{Multidisciplinary Digital Publishing Institute}}, - doi = {10.3390/e20010011}, - abstract = {In the first part of the paper we work out the consequences of the fact that Jaynes' Maximum Entropy Principle, when translated in mathematical terms, is a constrained extremum problem for an entropy function H ( p ) expressing the uncertainty associated with the probability distribution p. Consequently, if two observers use different independent variables p or g ( p ) , the associated entropy functions have to be defined accordingly and they are different in the general case. In the second part we apply our findings to an analysis of the foundations of the Maximum Entropy Theory of Ecology (M.E.T.E.) a purely statistical model of an ecological community. Since the theory has received considerable attention by the scientific community, we hope to give a useful contribution to the same community by showing that the procedure of application of MEP, in the light of the theory developed in the first part, suffers from some incongruences. We exhibit an alternative formulation which is free from these limitations and that gives different results.}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - langid = {english}, - keywords = {Boltzmann counting,Maximum Entropy principle,Maximum Entropy Theory of Ecology,Shannon entropy}, - file = {/Users/renatadiaz/Zotero/storage/4U3JFEAS/Favretti - 2018 - Remarks on the Maximum Entropy Principle with Appl.pdf;/Users/renatadiaz/Zotero/storage/W2TCMXJF/Favretti - 2018 - Remarks on the Maximum Entropy Principle with Appl.pdf;/Users/renatadiaz/Zotero/storage/45BRYHIK/11.html;/Users/renatadiaz/Zotero/storage/LX6SRPLP/11.html} -} - -@article{fetzer2015, - title = {The Extent of Functional Redundancy Changes as Species' Roles Shift in Different Environments}, - author = {Fetzer, Ingo and Johst, Karin and Sch{\"a}we, Robert and Banitz, Thomas and Harms, Hauke and Chatzinotas, Antonis}, - year = {2015}, - month = dec, - journal = {Proceedings of the National Academy of Sciences}, - volume = {112}, - number = {48}, - pages = {14888--14893}, - publisher = {{National Academy of Sciences}}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.1505587112}, - abstract = {Assessing the ecological impacts of environmental change requires knowledge of the relationship between biodiversity and ecosystem functioning. The exact nature of this relationship can differ considerably between ecosystems, with consequences for the efficacy of species diversity as a buffer against environmental change. Using a microbial model system, we show that the relationship can vary depending on environmental conditions. Shapes suggesting functional redundancy in one environment can change, suggesting functional differences in another environment. We find that this change is due to shifting species roles and interactions. Species that are functionally redundant in one environment may become pivotal in another. Thus, caution is advised in drawing conclusions about functional redundancy based on a single environmental situation. It also implies that species richness is important because it provides a pool of species with potentially relevant traits. These species may turn out to be essential performers or partners in new interspecific interactions after environmental change. Therefore, our results challenge the generality of functional redundancy.}, - chapter = {Biological Sciences}, - langid = {english}, - pmid = {26578806}, - keywords = {biodiversity-ecosystem functioning,environmental change,functional redundancy,microbial model system,species interactions}, - file = {/Users/renatadiaz/Zotero/storage/4I7Q6QXI/Fetzer et al. - 2015 - The extent of functional redundancy changes as spe.pdf;/Users/renatadiaz/Zotero/storage/4ZD22VMJ/Fetzer et al. - 2015 - The extent of functional redundancy changes as spe.pdf;/Users/renatadiaz/Zotero/storage/2ETI28ZS/14888.html;/Users/renatadiaz/Zotero/storage/JLBVNJJL/14888.html} -} - -@article{filazzola, - title = {A Call for Clean Code to Effectively Communicate Science}, - author = {Filazzola, Alessandro and Lortie, Cj}, - journal = {Methods in Ecology and Evolution}, - volume = {n/a}, - number = {n/a}, - issn = {2041-210X}, - doi = {10.1111/2041-210X.13961}, - abstract = {Effective coding is fundamental to the study of biology. Computation underpins most research, and reproducible science can be promoted through clean coding practices. Clean coding is crafting code design, syntax and nomenclature in a manner that maximizes the potential to communicate its intent with other scientists. However, computational biologists are not software engineers, and many of our coding practices have developed ad hoc without formal training, often creating difficult-to-read code for others. Hard-to-understand code can thus be limiting our efficiency and ability to communicate as scientists with one another. The purpose of this paper is to provide a primer on some of the practices associated with crafting clean code by synthesizing a transformative text in software engineering along with recent articles on coding practices in computational biology. We review past recommendations to provide a series of best practices that transform coding into a human-accessible form of communication. Three common themes shared in this synthesis are the following: (a) code has value and you are responsible for its organization to enable clear communication, (b) use a formatting style to guide writing code that is easily understandable and consistent and (c) apply abstraction to emphasize important elements and declutter. While many of the provided practices and recommendations were developed with computational biologists in mind, we believe there is wider applicability to any biologist undertaking work in data management or statistical analyses. Clean code is thus a crucial step forward in resolving some of the crisis in reproducibility for science.}, - langid = {english}, - keywords = {open science,principles,programming,replication,reproducibility,science communication,transparency}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13961}, - file = {/Users/renatadiaz/Zotero/storage/PF5J6B6X/Filazzola and Lortie - A call for clean code to effectively communicate s.pdf;/Users/renatadiaz/Zotero/storage/ZDUHKLQU/2041-210X.html} -} - -@article{fischer2001, - title = {Compensatory {{Dynamics}} in {{Zooplankton Community Responses}} to {{Acidification}}: {{Measurement}} and {{Mechanisms}}}, - shorttitle = {Compensatory {{Dynamics}} in {{Zooplankton Community Responses}} to {{Acidification}}}, - author = {Fischer, Janet M. and Frost, Thomas M. and Ives, Anthony R.}, - year = {2001}, - journal = {Ecological Applications}, - volume = {11}, - number = {4}, - pages = {1060--1072}, - issn = {1939-5582}, - doi = {10.1890/1051-0761(2001)011[1060:CDIZCR]2.0.CO;2}, - abstract = {Previous studies indicate substantial variation in ecological responses to perturbation. In some cases, ecosystems are resilient to perturbation due to compensatory dynamics in which losses of sensitive species are offset by population increases of species that perform similar ecological functions. Here, we report a detailed evaluation of compensatory dynamics in zooplankton community responses to the experimental acidification of Little Rock Lake, Wisconsin, USA. We used a variance ratio to quantify compensatory dynamics in functional groups of zooplankton containing species that use similar resources and are vulnerable to the same predators. We also used first-order autoregressive models to explore mechanisms driving the dynamics of each functional group. Our results indicate that responses of functional groups to acidification can be highly variable. Herbivorous copepods and medium-sized herbivorous cladocerans exhibited significant compensatory dynamics in response to acidification, whereas other functional groups exhibited independent or synchronous dynamics. First-order autoregressive models indicated that groups exhibiting compensatory dynamics contained both acid-tolerant and acid-sensitive species that competed. In contrast, groups that contained only acid-sensitive or acid-tolerant species exhibited more independent or synchronous dynamics. Overall, our study highlights the combined roles of sensitivity to environmental perturbation and species interactions in determining the extent of compensatory dynamics in zooplankton functional group responses to acidification.}, - copyright = {\textcopyright{} 2001 by the Ecological Society of America}, - langid = {english}, - keywords = {acidification,community ecology,compensatory dynamics,functional compensation,functional redundancy,zooplankton}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/1051-0761\%282001\%29011\%5B1060\%3ACDIZCR\%5D2.0.CO\%3B2}, - file = {/Users/renatadiaz/Zotero/storage/K8VDKGR6/1051-0761(2001)011[1060CDIZCR]2.0.html} -} - -@article{fischer2021, - title = {Compensatory {{Dynamics}} in {{Zooplankton Community Responses}} to {{Acidification}}: {{Measurement}} and {{Mechanisms}}}, - author = {Fischer, Janet M and Frost, Thomas M and Ives, Anthony R}, - year = {2021}, - pages = {14}, - abstract = {Previous studies indicate substantial variation in ecological responses to perturbation. In some cases, ecosystems are resilient to perturbation due to compensatory dynamics in which losses of sensitive species are offset by population increases of species that perform similar ecological functions. Here, we report a detailed evaluation of compensatory dynamics in zooplankton community responses to the experimental acidification of Little Rock Lake, Wisconsin, USA. We used a variance ratio to quantify compensatory dynamics in functional groups of zooplankton containing species that use similar resources and are vulnerable to the same predators. We also used first-order autoregressive models to explore mechanisms driving the dynamics of each functional group. Our results indicate that responses of functional groups to acidification can be highly variable. Herbivorous copepods and medium-sized herbivorous cladocerans exhibited significant compensatory dynamics in response to acidification, whereas other functional groups exhibited independent or synchronous dynamics. First-order autoregressive models indicated that groups exhibiting compensatory dynamics contained both acid-tolerant and acid-sensitive species that competed. In contrast, groups that contained only acid-sensitive or acid-tolerant species exhibited more independent or synchronous dynamics. Overall, our study highlights the combined roles of sensitivity to environmental perturbation and species interactions in determining the extent of compensatory dynamics in zooplankton functional group responses to acidification.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/T3YLCIV2/Fischer et al. - 2021 - Compensatory Dynamics in Zooplankton Community Res.pdf;/Users/renatadiaz/Zotero/storage/XTX8EJKK/Fischer et al. - 2021 - Compensatory Dynamics in Zooplankton Community Res.pdf} -} - -@article{fisher1943, - title = {The {{Relation Between}} the {{Number}} of {{Species}} and the {{Number}} of {{Individuals}} in a {{Random Sample}} of an {{Animal Population}}}, - author = {Fisher, R. A. and Corbet, A. Steven and Williams, C. B.}, - year = {1943}, - journal = {Journal of Animal Ecology}, - volume = {12}, - number = {1}, - pages = {42--58}, - publisher = {{[Wiley, British Ecological Society]}}, - issn = {0021-8790}, - doi = {10.2307/1411}, - abstract = {Part 1. It is shown that in a large collection of Lepidoptera captured in Malaya the frequency of the number of species represented by different numbers of individuals fitted somewhat closely to a hyperbola type of curve, so long as only the rarer species were considered. The data for the commoner species was not so strictly `randomized', but the whole series could be closely fitted by a series of the logarithmic type as described by Fisher in Part 3. Other data for random collections of insects in the field were also shown to fit fairly well to this series. Part 2. Extensive data on the capture of about 1500 Macrolepidoptera of about 240 species in a light-trap at Harpenden is analysed in relation to Fisher's mathematical theory and is shown to fit extremely closely to the calculations. The calculations are applied first to the frequency of occurrence of species represented by different numbers of individuals--and secondly to the number of species in samples of different sizes from the same population. The parameter ` alpha ', which it is suggested should be called the `index of diversity', is shown to have a regular seasonal change in the case of the Macrolepidoptera in the trap. In addition, samples from two traps which overlooked somewhat different vegetation are shown to have ` alpha ' values which are significantly different. It is shown that, provided the samples are not small, ` alpha ' is the increase in the number of species obtained by increasing the size of a sample by e (2.718). A diagram is given (Fig. 8) from which any one of the values, total number of species, total number of individuals and index of diversity (alpha), can be obtained approximately if the other two are known. The standard error of alpha is also indicated on the same diagram. Part 3. A theoretical distribution is developed which appears to be suitable for the frequencies with which different species occur in a random collection, in the common case in which many species are so rare that their chance of inclusion is small. The relationships of the new distribution with the negative binomial and the Poisson series are established. Numerical processes are exhibited for fitting the series to observations containing given numbers of species and individuals, and for estimating the parameter alpha representing the richness in species of the material sampled; secondly, for calculating the standard error of alpha, and thirdly, for testing whether the series exhibits a significant deviation from the limiting form used. Special tables are presented for facilitating these calculations.}, - file = {/Users/renatadiaz/Zotero/storage/ENHUGFR8/Fisher et al. - 1943 - The Relation Between the Number of Species and the.pdf} -} - -@article{fisher2010, - title = {Dynamic Macroecology on Ecological Time-Scales}, - author = {Fisher, Jonathan A. D. and Frank, Kenneth T. and Leggett, William C.}, - year = {2010}, - journal = {Global Ecology and Biogeography}, - volume = {19}, - number = {1}, - pages = {1--15}, - issn = {1466-8238}, - doi = {10.1111/j.1466-8238.2009.00482.x}, - abstract = {Aim The discipline of macroecology is increasingly being regarded as an effective vehicle for the evaluation of recent population- to ecosystem-level responses to widespread human and environmental influences. However, due to the prevalent use of time-averaged and cumulative data in macroecological analyses, the majority of the patterns that emerge from research in this field can be regarded as static. Here we review the application of dynamic macroecological analyses to changes in relationships between macroecological variables on seasonal to decadal scales. We illustrate the strength of this perspective for documenting changing patterns and testing hypotheses related to these dynamics on ecological time-scales. Location Studies were compiled and reviewed from terrestrial and aquatic ecosystems. Methods We review examples of temporal changes in macroecological patterns driven by recent anthropogenic influences and environmental change. Results The dynamic nature of macroecological patterns on ecological time-scales has been revealed in recent years across a wide range of ecosystems, largely through the development, maintenance and analysis of biotic and environmental monitoring time series. The resultant analyses complement examinations of dynamics over evolutionary time and have similarly revealed that static portrayals can conceal important temporal dynamics that underlie the patterns of interest. As a consequence, static depictions, resting as they do on comparative analyses in which the validity of space-for-time substitutions is assumed, may be of limited use for testing hypotheses related to the mechanisms underlying the patterns revealed and, by extension, the development of reliable predictions of future states. Main conclusions Recent dynamic macroecological analyses have demonstrated the utility of combined spatial and temporal replication, and have contributed to hypothesis testing related to the mechanistic processes underlying changes in macroecological patterns on ecological time-scales. We suggest four specific avenues of future research to further the development and application of temporal approaches on similar time-scales within the field of macroecology.}, - langid = {english}, - keywords = {Abundance,body size,climate change,conservation,geographical range,human impacts,space-for-time substitution,species richness,temporal trends,trophic control}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1466-8238.2009.00482.x}, - file = {/Users/renatadiaz/Zotero/storage/B6IWGZBA/Fisher et al. - 2010 - Dynamic macroecology on ecological time-scales.pdf;/Users/renatadiaz/Zotero/storage/Y5QKYM26/Fisher et al. - 2010 - Dynamic macroecology on ecological time-scales.pdf;/Users/renatadiaz/Zotero/storage/JWGLELVL/j.1466-8238.2009.00482.html;/Users/renatadiaz/Zotero/storage/LG8YR25Q/j.1466-8238.2009.00482.html} -} - -@article{fontrodona-eslava, - title = {Numerical Abundance and Biomass Reveal Different Temporal Trends of Functional Diversity Change in Tropical Fish Assemblages}, - author = {{Fontrodona-Eslava}, Ada and Deacon, Amy E. and Ramnarine, Indar W. and Magurran, Anne E.}, - journal = {Journal of Fish Biology}, - volume = {n/a}, - number = {n/a}, - issn = {1095-8649}, - doi = {10.1111/jfb.14812}, - abstract = {Understanding how the biodiversity of freshwater fish assemblages changes over time is an important challenge. Until recently most emphasis has been on taxonomic diversity, but it is now clear that measures of functional diversity (FD) can shed new light on the mechanisms that underpin this temporal change. Fish biologists use different currencies, such as numerical abundance and biomass, to measure the abundance of fish species. Nonetheless, because they are not necessarily equivalent, these alternative currencies have the potential to reveal different insights into trends of FD in natural assemblages. In this study, the authors asked how conclusions about temporal trends in FD are influenced by the way in which the abundance of species has been quantified. To do this, the authors computed two informative metrics, for each currency, for 16 freshwater fish assemblages in Trinidad's Northern Range that had been surveyed repeatedly over 5 years. The authors found that numerical abundance and biomass uncover different directional trends in these assemblages for each facet of FD, and as such inform hypotheses about the ways in which these systems are being restructured. On the basis of these results, the authors concluded that a combined approach, in which both currencies are used, contributes to our understanding of the ecological processes that are involved in biodiversity change in freshwater fish assemblages.}, - copyright = {\textcopyright{} 2021 The Authors. Journal of Fish Biology published by John Wiley \& Sons Ltd on behalf of Fisheries Society of the British Isles.}, - langid = {english}, - keywords = {biomass,freshwater fish,functional diversity,numerical abundance}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jfb.14812}, - file = {/Users/renatadiaz/Zotero/storage/DD4L73G6/Fontrodona-Eslava et al. - Numerical abundance and biomass reveal different t.pdf;/Users/renatadiaz/Zotero/storage/HTP6ZQ7X/jfb.html} -} - -@misc{frameshiftconsulting, - title = {Frame {{Shift Consulting}}}, - author = {{Frame Shift Consulting}}, - journal = {https://frameshiftconsulting.com/}, - abstract = {The leader in ally skills training}, - howpublished = {https://frameshiftconsulting.com/}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/4YISZ56V/frameshiftconsulting.com.html} -} - -@misc{frameshiftconsulting2016, - title = {Ally {{Skills Workshop}}}, - author = {Frame Shift Consulting}, - year = {2016}, - month = jan, - journal = {Frame Shift Consulting}, - abstract = {Looking for practical, actionable diversity and inclusion training that people love? The Ally Skills Workshop teaches simple everyday techniques people can use to make their workplaces more inclusi\ldots}, - howpublished = {https://frameshiftconsulting.com/ally-skills-workshop/}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VIT2HVP8/ally-skills-workshop.html} -} - -@article{frank2009, - title = {The Common Patterns of Nature}, - author = {Frank, S. A.}, - year = {2009}, - month = aug, - journal = {Journal of Evolutionary Biology}, - volume = {22}, - number = {8}, - pages = {1563--1585}, - issn = {1010061X, 14209101}, - doi = {10.1111/j.1420-9101.2009.01775.x}, - abstract = {We typically observe large-scale outcomes that arise from the interactions of many hidden, small-scale processes. Examples include age of disease onset, rates of amino acid substitutions and composition of ecological communities. The macroscopic patterns in each problem often vary around a characteristic shape that can be generated by neutral processes. A neutral generative model assumes that each microscopic process follows unbiased or random stochastic fluctuations: random connections of network nodes; amino acid substitutions with no effect on fitness; species that arise or disappear from communities randomly. These neutral generative models often match common patterns of nature. In this paper, I present the theoretical background by which we can understand why these neutral generative models are so successful. I show where the classic patterns come from, such as the Poisson pattern, the normal or Gaussian pattern and many others. Each classic pattern was often discovered by a simple neutral generative model. The neutral patterns share a special characteristic: they describe the patterns of nature that follow from simple constraints on information. For example, any aggregation of processes that preserves information only about the mean and variance attracts to the Gaussian pattern; any aggregation that preserves information only about the mean attracts to the exponential pattern; any aggregation that preserves information only about the geometric mean attracts to the power law pattern. I present a simple and consistent informational framework of the common patterns of nature based on the method of maximum entropy. This framework shows that each neutral generative model is a special case that helps to discover a particular set of informational constraints; those informational constraints define a much wider domain of non-neutral generative processes that attract to the same neutral pattern.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/MPJGSQR2/Frank - 2009 - The common patterns of nature.pdf;/Users/renatadiaz/Zotero/storage/PQXMTCH4/Frank - 2009 - The common patterns of nature.pdf} -} - -@article{frank2011, - title = {Measurement Scale in Maximum Entropy Models of Species Abundance: {{Measurement}} Scale and Pattern}, - shorttitle = {Measurement Scale in Maximum Entropy Models of Species Abundance}, - author = {Frank, S. A.}, - year = {2011}, - month = mar, - journal = {Journal of Evolutionary Biology}, - volume = {24}, - number = {3}, - pages = {485--496}, - issn = {1010061X}, - doi = {10.1111/j.1420-9101.2010.02209.x}, - abstract = {The consistency of the species abundance distribution across diverse communities has attracted widespread attention. In this paper, I argue that the consistency of pattern arises because diverse ecological mechanisms share a common symmetry with regard to measurement scale. By symmetry, I mean that different ecological processes preserve the same measure of information and lose all other information in the aggregation of various perturbations. I frame these explanations of symmetry, measurement, and aggregation in terms of a recently developed extension to the theory of maximum entropy. I show that the natural measurement scale for the species abundance distribution is log-linear: the information in observations at small population sizes scales logarithmically and, as population size increases, the scaling of information grades from logarithmic to linear. Such log-linear scaling leads naturally to a gamma distribution for species abundance, which matches well with the observed patterns. Much of the variation between samples can be explained by the magnitude at which the measurement scale grades from logarithmic to linear. This measurement approach can be applied to the similar problem of allelic diversity in population genetics and to a wide variety of other patterns in biology.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/G5Q3HI88/Frank - 2011 - Measurement scale in maximum entropy models of spe.pdf} -} - -@article{frank2011a, - title = {A Simple Derivation and Classification of Common Probability Distributions Based on Information Symmetry and Measurement Scale}, - author = {Frank, S. A. and Smith, E.}, - year = {2011}, - journal = {Journal of Evolutionary Biology}, - volume = {24}, - number = {3}, - pages = {469--484}, - issn = {1420-9101}, - doi = {10.1111/j.1420-9101.2010.02204.x}, - abstract = {Commonly observed patterns typically follow a few distinct families of probability distributions. Over one hundred years ago, Karl Pearson provided a systematic derivation and classification of the common continuous distributions. His approach was phenomenological: a differential equation that generated common distributions without any underlying conceptual basis for why common distributions have particular forms and what explains the familial relations. Pearson's system and its descendants remain the most popular systematic classification of probability distributions. Here, we unify the disparate forms of common distributions into a single system based on two meaningful and justifiable propositions. First, distributions follow maximum entropy subject to constraints, where maximum entropy is equivalent to minimum information. Second, different problems associate magnitude to information in different ways, an association we describe in terms of the relation between information invariance and measurement scale. Our framework relates the different continuous probability distributions through the variations in measurement scale that change each family of maximum entropy distributions into a distinct family. From our framework, future work in biology can consider the genesis of common patterns in a new and more general way. Particular biological processes set the relation between the information in observations and magnitude, the basis for information invariance, symmetry and measurement scale. The measurement scale, in turn, determines the most likely probability distributions and observed patterns associated with particular processes. This view presents a fundamentally derived alternative to the largely unproductive debates about neutrality in ecology and evolution.}, - copyright = {\textcopyright{} 2011 The Authors. Journal of Evolutionary Biology \textcopyright{} 2011 European Society For Evolutionary Biology}, - langid = {english}, - keywords = {population genetics,theory}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1420-9101.2010.02204.x}, - file = {/Users/renatadiaz/Zotero/storage/ANFULDJJ/Frank and Smith - 2011 - A simple derivation and classification of common p.pdf;/Users/renatadiaz/Zotero/storage/YWACP7K8/j.1420-9101.2010.02204.html} -} - -@article{frank2014, - title = {Generative Models versus Underlying Symmetries to Explain Biological Pattern}, - author = {Frank, S. A.}, - year = {2014}, - journal = {Journal of Evolutionary Biology}, - volume = {27}, - number = {6}, - pages = {1172--1178}, - issn = {1420-9101}, - doi = {10.1111/Jeb.12388}, - abstract = {Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative models confirm the plausibility of an explanation and make testable hypotheses for further experiments. However, studies rarely consider the broad family of alternative models that match the same observed pattern. The symmetries that define the broad class of matching models are in fact the only aspects of information truly revealed by observed pattern. Commonly observed patterns derive from simple underlying symmetries. This article illustrates the problem by showing the symmetry associated with the observed rate of increase in fitness in a constant environment. That underlying symmetry reveals how each particular generative model defines a single example within the broad class of matching models. Further progress on the relation between pattern and process requires deeper consideration of the underlying symmetries.}, - langid = {english}, - keywords = {evolutionary genetics,extreme value theory,limiting distributions,mathematical models,systems biology,theoretical biology}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/Jeb.12388}, - file = {/Users/renatadiaz/Zotero/storage/5Y7J86KA/Frank - 2014 - Generative models versus underlying symmetries to .pdf;/Users/renatadiaz/Zotero/storage/HYHENV7J/Jeb.html} -} - -@article{frank2016, - title = {Common {{Probability Patterns Arise}} from {{Simple Invariances}}}, - author = {Frank, Steven}, - year = {2016}, - month = may, - journal = {Entropy}, - volume = {18}, - number = {5}, - pages = {192}, - issn = {1099-4300}, - doi = {10.3390/e18050192}, - abstract = {Shift and stretch invariance lead to the exponential-Boltzmann probability distribution. Rotational invariance generates the Gaussian distribution. Particular scaling relations transform the canonical exponential and Gaussian patterns into the variety of commonly observed patterns. The scaling relations themselves arise from the fundamental invariances of shift, stretch and rotation, plus a few additional invariances. Prior work described the three fundamental invariances as a consequence of the equilibrium canonical ensemble of statistical mechanics or the Jaynesian maximization of information entropy. By contrast, I emphasize the primacy and sufficiency of invariance alone to explain the commonly observed patterns. Primary invariance naturally creates the array of commonly observed scaling relations and associated probability patterns, whereas the classical approaches derived from statistical mechanics or information theory require special assumptions to derive commonly observed scales.}, - langid = {english}, - keywords = {extreme value distributions,information theory,maximum entropy,measurement,statistical mechanics}, - file = {/Users/renatadiaz/Zotero/storage/9QWE29UB/Frank - 2016 - Common Probability Patterns Arise from Simple Inva.pdf;/Users/renatadiaz/Zotero/storage/WQHR89PV/Frank - 2016 - Common Probability Patterns Arise from Simple Inva.pdf;/Users/renatadiaz/Zotero/storage/ZN7SHSQZ/htm.html} -} - -@article{frank2016a, - title = {The Invariances of Power Law Size Distributions}, - author = {Frank, Steven A.}, - year = {2016}, - month = nov, - journal = {F1000Research}, - volume = {5}, - pages = {2074}, - issn = {2046-1402}, - doi = {10.12688/f1000research.9452.3}, - abstract = {Size varies. Small things are typically more frequent than large things. The logarithm of frequency often declines linearly with the logarithm of size. That power law relation forms one of the common patterns of nature. Why does the complexity of nature reduce to such a simple pattern? Why do things as different as tree size and enzyme rate follow similarly simple patterns? Here I analyze such patterns by their invariant properties. For example, a common pattern should not change when adding a constant value to all observations. That shift is essentially the renumbering of the points on a ruler without changing the metric information provided by the ruler. A ruler is shift invariant only when its scale is properly calibrated to the pattern being measured. Stretch invariance corresponds to the conservation of the total amount of something, such as the total biomass and consequently the average size. Rotational invariance corresponds to pattern that does not depend on the order in which underlying processes occur, for example, a scale that additively combines the component processes leading to observed values. I use tree size as an example to illustrate how the key invariances shape pattern. A simple interpretation of common pattern follows. That simple interpretation connects the normal distribution to a wide variety of other common patterns through the transformations of scale set by the fundamental invariances.}, - pmcid = {PMC5115223}, - pmid = {27928497}, - file = {/Users/renatadiaz/Zotero/storage/F3RL96MV/Frank - 2016 - The invariances of power law size distributions.pdf} -} - -@article{frank2019, - title = {The Common Patterns of Abundance: The Log Series and {{Zipf}}'s Law}, - shorttitle = {The Common Patterns of Abundance}, - author = {Frank, Steven A.}, - year = {2019}, - month = mar, - journal = {F1000Research}, - volume = {8}, - pages = {334}, - issn = {2046-1402}, - doi = {10.12688/f1000research.18681.1}, - abstract = {In a language corpus, the probability that a word occurs n times is often proportional to 1/ n 2 . Assigning rank, s , to words according to their abundance, log s vs log n typically has a slope of minus one. That simple Zipf's law pattern also arises in the population sizes of cities, the sizes of corporations, and other patterns of abundance. By contrast, for the abundances of different biological species, the probability of a population of size n is typically proportional to 1/ n , declining exponentially for larger n , the log series pattern. This article shows that the differing patterns of Zipf's law and the log series arise as the opposing endpoints of a more general theory. The general theory follows from the generic form of all probability patterns as a consequence of conserved average values and the associated invariances of scale. To understand the common patterns of abundance, the generic form of probability distributions plus the conserved average abundance is sufficient. The general theory includes cases that are between the Zipf and log series endpoints, providing a broad framework for analyzing widely observed abundance patterns.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/FS3BKHQD/Frank - 2019 - The common patterns of abundance the log series a.pdf;/Users/renatadiaz/Zotero/storage/3T6G8SVR/v1.html} -} - -@article{frank2019a, - title = {Invariance in Ecological Pattern}, - author = {Frank, Steven A. and Bascompte, Jordi}, - year = {2019}, - month = dec, - journal = {F1000Research}, - volume = {8}, - pages = {2093}, - issn = {2046-1402}, - doi = {10.12688/f1000research.21586.1}, - abstract = {Background: The abundance of different species in a community often follows the log series distribution. Other ecological patterns also have simple forms. Why does the complexity and variability of ecological systems reduce to such simplicity? Common answers include maximum entropy, neutrality, and convergent outcome from different underlying biological processes. Methods: This article proposes a more general answer based on the concept of invariance, the property by which a pattern remains the same after transformation. Invariance has a long tradition in physics. For example, general relativity emphasizes the need for the equations describing the laws of physics to have the same form in all frames of reference. Results: By bringing this unifying invariance approach into ecology, we show that the log series pattern dominates when the consequences of processes acting on abundance are invariant to the addition or multiplication of abundance by a constant. The lognormal pattern dominates when the processes acting on net species growth rate obey rotational invariance (symmetry) with respect to the summing up of the individual component processes. Conclusions: Recognizing how these invariances connect pattern to process leads to a synthesis of previous approaches. First, invariance provides a simpler and more fundamental maximum entropy derivation of the log series distribution. Second, invariance provides a simple derivation of the key result from neutral theory: the log series at the metacommunity scale and a clearer form of the skewed lognormal at the local community scale. The invariance expressions are easy to understand because they uniquely describe the basic underlying components that shape pattern.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VXNNXJBZ/Frank and Bascompte - 2019 - Invariance in ecological pattern.pdf} -} - -@article{franzman2021, - title = {Shifting Macroecological Patterns and Static Theory Failure in a Stressed Alpine Plant Community}, - author = {Franzman, Juliette and Brush, Micah and Umemura, Kaito and Ray, Courtenay and Blonder, Benjamin and Harte, John}, - year = {2021}, - journal = {Ecosphere}, - volume = {12}, - number = {6}, - pages = {e03548}, - issn = {2150-8925}, - doi = {10.1002/ecs2.3548}, - abstract = {Accumulating evidence suggests that ecological communities undergoing change in response to either anthropogenic or natural disturbances exhibit macroecological patterns that differ from those observed in similar types of communities in relatively undisturbed sites. In contrast to such cross-site comparisons, however, there are few empirical studies of shifts over time in the shapes of macroecological patterns. Here, we provide a dramatic example of a plant community in which the species\textendash area relationship and the species-abundance distribution change markedly over a period of six years. These patterns increasingly deviate from the predictions of the maximum entropy theory of ecology (METE), which successfully predicts macroecological patterns in relatively static systems. The error in the species\textendash area relationship prediction additionally correlates over time with increased stress measured as mortality minus recruitment, providing a link between demography and the failure of macroecological theory. Information on the dynamic state of an ecosystem inferred from snapshot measurements of macroecological community structure can potentially assist in identifying causes and consequences of disturbance and extending the domain of current theories and models to disturbed ecosystems.}, - langid = {english}, - keywords = {alpine vegetation,demographic decline,disturbance ecology,drought,ecological theory,maximum entropy,species-abundance distribution,species–area relationship}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3548}, - file = {/Users/renatadiaz/Zotero/storage/D8BIQVPM/Franzman et al. - 2021 - Shifting macroecological patterns and static theor.pdf;/Users/renatadiaz/Zotero/storage/85CY73ST/ecs2.html} -} - -@article{fraser2021, - title = {Investigating {{Biotic Interactions}} in {{Deep Time}}}, - author = {Fraser, Danielle and Soul, Laura C. and T{\'o}th, Anik{\'o} B. and Balk, Meghan A. and Eronen, Jussi T. and {Pineda-Munoz}, Silvia and Shupinski, Alexandria B. and Villase{\~n}or, Amelia and Barr, W. Andrew and Behrensmeyer, Anna K. and Du, Andrew and Faith, J. Tyler and Gotelli, Nicholas J. and Graves, Gary R. and Jukar, Advait M. and Looy, Cindy V. and Miller, Joshua H. and Potts, Richard and Lyons, S. Kathleen}, - year = {2021}, - month = jan, - journal = {Trends in Ecology \& Evolution}, - volume = {36}, - number = {1}, - pages = {61--75}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2020.09.001}, - abstract = {Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.}, - langid = {english}, - keywords = {biotic interactions,extinction,fossil record,macroecology,macroevolution,paleobiology,paleontology}, - file = {/Users/renatadiaz/Zotero/storage/XAN2JTPE/Fraser et al. - 2021 - Investigating Biotic Interactions in Deep Time.pdf;/Users/renatadiaz/Zotero/storage/QH89PRRB/S0169534720302500.html} -} - -@article{frenzel2016, - title = {Bird Communities in Agricultural Landscapes: {{What}} Are the Current Drivers of Temporal Trends?}, - shorttitle = {Bird Communities in Agricultural Landscapes}, - author = {Frenzel, Mark and Everaars, Jeroen and Schweiger, Oliver}, - year = {2016}, - month = jun, - journal = {Ecological Indicators}, - volume = {65}, - pages = {113--121}, - issn = {1470160X}, - doi = {10.1016/j.ecolind.2015.11.020}, - abstract = {Bird populations are declining in agricultural landscapes, which is ongoing for decades now. With standardized breeding bird observation data of five years within 2001\textendash 2014 from six sites in Central Germany we investigated whether trends in bird abundance are reflected by trends in species richness and whether these trends depend on the landscape context. We further analyzed whether trends and their dependencies on the landscape context differ among species groups according to their particular traits. For most of the groups (farmland birds, large birds, resident birds, short distance migrators, insectivores, granivores and birds of prey) we found declining trends in abundance. However, these trends were not reflected by species richness. In contrast to our expectations, high amounts of semi-natural habitats in the landscape did not buffer the overall negative trends. Surprisingly, bird abundance declined most in landscapes characterized by larger ranges in altitude and initially highest bird abundance in 2001. We conclude that flat landscapes in Central Germany have been utilized with high intensity already for a long time and they simply maintained their already low bird abundance. On the other hand, a recent increase in agricultural intensity in landscapes with marked altitudinal reliefs, and presumably less usability and productivity, causes the drastic declines in bird abundances. Since these strong declines are not related to habitat loss, we assume that changes in the management of agricultural fields are responsible.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/4JK22GCE/Frenzel et al. - 2016 - Bird communities in agricultural landscapes What .pdf} -} - -@article{fristoe2015, - title = {Energy Use by Migrants and Residents in {{North American}} Breeding Bird Communities}, - author = {Fristoe, Trevor S.}, - year = {2015}, - journal = {Global Ecology and Biogeography}, - volume = {24}, - number = {4}, - pages = {406--415}, - issn = {1466-8238}, - doi = {10.1111/geb.12262}, - abstract = {Aim Of the order of 5 billion birds comprising more than 700,000 tonnes of biomass migrate across North America every year to exploit seasonal resource pulses at high latitudes during breeding. Despite this impressive scale, little is known about the metabolic role of these migrants in their breeding grounds across temperate ecosystems. I estimate the energy use of short- and long-distance migrant passerines as well as residents in over 2000 breeding bird communities covering the geographic scope of North America. My aim was to characterize the geographic patterns of energy use by each migratory group and test the hypothesis that seasonal patterns of resource availability structure temperate breeding bird communities. Location North America from 25 to 69\textdegree{} N. Methods I estimated the energy use of migrant and resident passerines using abundance data from the North American Breeding Bird Survey and scaling relationships for field metabolic rate as a function of body size. Linear regression was used to test the relationship between energy use by each migratory group and latitude as well as indirect measures of environmental productivity during different seasons. Results Energy use by all groups showed a strong relationship with latitude except for long-distance migrants, which were surprisingly invariant across geography. Energy use by migrants was highest in environments with low winter productivity and high seasonality, while resident energy use was highest where annual productivity was the highest. Main conclusions Migrant passerines contribute significantly to temperate breeding bird communities, especially in high latitudes. They account for 78\% of consumption in habitats north of 50\textdegree{} N compared with 1.7\% in the subtropics south of 35\textdegree{} N. Short-distance migrants are especially important to community energy use in the habitats where migrants consume the most. Future shifts in breeding bird community composition are likely to occur as climate change alters seasonal cycles of resource availability.}, - langid = {english}, - keywords = {Breeding Bird Survey,climate change,community assembly,energetics,latitudinal gradient,macroecology,metabolic ecology,metabolism,Migration,seasonality}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12262}, - file = {/Users/renatadiaz/Zotero/storage/MBL8XHNK/Fristoe - 2015 - Energy use by migrants and residents in North Amer.pdf;/Users/renatadiaz/Zotero/storage/WGQLNV7J/Fristoe - 2015 - Energy use by migrants and residents in North Amer.pdf;/Users/renatadiaz/Zotero/storage/DQGXWRB6/geb.html;/Users/renatadiaz/Zotero/storage/IGGBJMUA/geb.html} -} - -@article{gardner2011, - title = {Declining Body Size: A Third Universal Response to Warming?}, - shorttitle = {Declining Body Size}, - author = {Gardner, Janet L. and Peters, Anne and Kearney, Michael R. and Joseph, Leo and Heinsohn, Robert}, - year = {2011}, - month = jun, - journal = {Trends in Ecology \& Evolution}, - volume = {26}, - number = {6}, - pages = {285--291}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2011.03.005}, - abstract = {A recently documented correlate of anthropogenic climate change involves reductions in body size, the nature and scale of the pattern leading to suggestions of a third universal response to climate warming. Because body size affects thermoregulation and energetics, changing body size has implications for resilience in the face of climate change. A review of recent studies shows heterogeneity in the magnitude and direction of size responses, exposing a need for large-scale phylogenetically controlled comparative analyses of temporal size change. Integrative analyses of museum data combined with new theoretical models of size-dependent thermoregulatory and metabolic responses will increase both understanding of the underlying mechanisms and physiological consequences of size shifts and, therefore, the ability to predict the sensitivities of species to climate change.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/53JQ9QB3/S0169534711000759.html} -} - -@article{gardner2011a, - title = {Declining Body Size: A Third Universal Response to Warming?}, - shorttitle = {Declining Body Size}, - author = {Gardner, Janet L. and Peters, Anne and Kearney, Michael R. and Joseph, Leo and Heinsohn, Robert}, - year = {2011}, - month = jun, - journal = {Trends in Ecology \& Evolution}, - volume = {26}, - number = {6}, - pages = {285--291}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2011.03.005}, - abstract = {A recently documented correlate of anthropogenic climate change involves reductions in body size, the nature and scale of the pattern leading to suggestions of a third universal response to climate warming. Because body size affects thermoregulation and energetics, changing body size has implications for resilience in the face of climate change. A review of recent studies shows heterogeneity in the magnitude and direction of size responses, exposing a need for large-scale phylogenetically controlled comparative analyses of temporal size change. Integrative analyses of museum data combined with new theoretical models of size-dependent thermoregulatory and metabolic responses will increase both understanding of the underlying mechanisms and physiological consequences of size shifts and, therefore, the ability to predict the sensitivities of species to climate change.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/66NF7DZV/S0169534711000759.html} -} - -@article{gardner2014, - title = {Temporal Patterns of Avian Body Size Reflect Linear Size Responses to Broadscale Environmental Change over the Last 50 Years}, - author = {Gardner, Janet L. and Amano, Tatsuya and Backwell, Patrica R. Y. and Ikin, Karen and Sutherland, William J. and Peters, Anne}, - year = {2014}, - journal = {Journal of Avian Biology}, - volume = {45}, - number = {6}, - pages = {529--535}, - issn = {1600-048X}, - doi = {10.1111/jav.00431}, - abstract = {Alongside well researched shifts in species' distributions and phenology, reduction in the body size of organisms has been suggested as a third universal response to contemporary climate change. Despite mounting evidence for declining body size, several recent reviews highlight studies reporting increases in body size or no change over time. This variability in response may derive from the geographic scale of contributing studies, masking species-level responses to broad-scale environmental change and instead reflecting local influences on single populations. Using museum specimens, we examine temporal patterns of body size of 24 Australian passerine species, sampling multiple populations across the geographic ranges of each species between 1960 and 2007. Generalised additive models indictated that the majority (67\%) of species showed important inter-annual body size variation, and there was striking cross-species similarity in temporal size patterns. Most displayed near-linear or linear, unidirectional size trends, suggesting a pervasive and directional change in environmental conditions, consistent with climate change. For species showing linear size responses, the absolute rate of size change ranged between 0.016 and 0.114\% of body size (wing length) per year, consistent with studies on other continents. Overall, 38\% (9/24) of species showed temporal declines in body size and 21\% (5/24) showed increases, consistent with the variability and direction of size responses thus far documented among populations; declining body size is a pervasive response to climate change but it is not universal.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jav.00431}, - file = {/Users/renatadiaz/Zotero/storage/C4JXXKUC/Gardner et al. - 2014 - Temporal patterns of avian body size reflect linea.pdf;/Users/renatadiaz/Zotero/storage/C8AD3D8T/jav.html} -} - -@article{gastonkevinj1993, - title = {Comparing {{Animals}} and {{Automobiles}}: {{A Vehicle}} for {{Understanding Body Size}} and {{Abundance Relationships}} in {{Species Assemblages}}?}, - shorttitle = {Comparing {{Animals}} and {{Automobiles}}}, - author = {{Gaston, Kevin J} and {Blackburn, Tim M} and {Lawton, John H}}, - year = {1993}, - month = jan, - journal = {Oikos}, - volume = {66}, - number = {1}, - pages = {172--179}, - publisher = {{Munksgaard International Publishers, Ltd.}}, - issn = {00301299}, - doi = {10.2307/3545211}, - keywords = {Animals,Automobiles,Beetles,Biology,Body length,Body size,Engines,Insect ecology,Population ecology,Species} -} - -@book{gastonkevinj2000, - title = {Pattern and {{Process}} in {{Macroecology}}}, - author = {Gaston, Kevin J and Blackburn, Tim M}, - year = {2000}, - publisher = {{Blackwell Science Ltd}}, - isbn = {978-0-632-05653-8} -} - -@article{gaynor2022, - title = {Ten Simple Rules to Cultivate Belonging in Collaborative Data Science Research Teams}, - author = {Gaynor, Kaitlyn M. and Azevedo, Therese and Boyajian, Clarissa and Brun, Julien and Budden, Amber E. and Cole, Allie and Csik, Samantha and DeCesaro, Joe and {Do-Linh}, Halina and Dudney, Joan and Garc{\'i}a, Carmen Galaz and Leonard, Scout and Lyon, Nicholas J. and Marks, Althea and Parish, Julia and Phillips, Alexandra A. and Scarborough, Courtney and Smith, Joshua and Thompson, Marcus and Poulsen, Camila Vargas and Fong, Caitlin R.}, - year = {2022}, - month = nov, - journal = {PLOS Computational Biology}, - volume = {18}, - number = {11}, - pages = {e1010567}, - publisher = {{Public Library of Science}}, - issn = {1553-7358}, - doi = {10.1371/journal.pcbi.1010567}, - langid = {english}, - keywords = {Careers,Careers in research,Culture,Human learning,Open science,Scientists,Software tools,Verbal communication}, - file = {/Users/renatadiaz/Zotero/storage/8DPP2SYQ/Gaynor et al. - 2022 - Ten simple rules to cultivate belonging in collabo.pdf;/Users/renatadiaz/Zotero/storage/ZY857JA8/article.html} -} - -@book{geluso2009, - title = {Distributional Records for Seven Species of Mammals in Southern {{New Mexico}} /}, - author = {Geluso, Keith}, - year = {2009}, - publisher = {{Museum of Texas Tech University,}}, - address = {{Lubbock, TX :}}, - doi = {10.5962/bhl.title.157003}, - abstract = {Geographic distributions of mammals are not static, and natural changes in distribution often are related to changes in habitat and climate. Mammalian distributions also can change with human introductions, lack of prior surveys, and misidentification of museum specimens. Here, I report on distributional records for seven species of mammals in southern New Mexico, including Nasua narica, Ammospermophilus harrisii, Chaetodipus baileyi, Dipodomys merriami, Peromyscus truei, Sigmodon fulviventer, and Sigmodon hispidus. For one species (A. harrisii), new records likely reflect a distributional shift related to recent changes in habitat, whereas others (C. baileyi, D. merriami, P. truei, S. fulviventer, and S. hispidus) likely represent overlooked populations because of a paucity of published surveys in the region. For N. narica, data include details on localities of record and reproductive data for a species previously known from the region but lacking specific details. Continued surveys and documentation of distributional limits of mammals will allow us to better evaluate how environmental changes affect biological communities and will help us to interpret new extra-limital records.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/FA4YB5W2/Geluso - 2009 - Distributional records for seven species of mammal.pdf;/Users/renatadiaz/Zotero/storage/HCV43UFK/Geluso - 2009 - Distributional records for seven species of mammal.pdf} -} - -@article{goheen2005, - title = {Intra-Guild Compensation Regulates Species Richness in Desert Rodents}, - author = {Goheen, J. R. and White, E. P. and Ernest, S. K. M. and Brown, J. H.}, - year = {2005}, - month = mar, - journal = {Ecology}, - volume = {86}, - number = {3}, - pages = {567--573}, - publisher = {{Wiley}}, - address = {{Hoboken}}, - issn = {0012-9658}, - doi = {10.1890/04-1475}, - abstract = {Evidence from numerous studies suggests that species richness is an emergent property of local communities. The maintenance of species richness, despite changes in species composition and environmental conditions, requires compensatory colonization and extinction events with species coming from a regional pool. Using long-term data from a rodent community in the Chihuahuan Desert, we use randomization methods to. test the null hypothesis that changes in species richness occur randomly. We find that the dynamics of species richness differ significantly from a random process, and that these nonrandom dynamics occur largely within the most speciose guild. Finally, we propose a general framework for assessing the importance of species compensation in maintaining biodiversity within local communities. Our results highlight the importance of niche complementarity and compensation in maintaining relatively constant species richness over time.}, - langid = {english}, - keywords = {Arizona (USA),Chihuahuan Desert,colonization-extinction dynamics,competition,desert rodents,diversity,dynamics,ecological communities,ecosystem,island biogeography,local richness,long-term,maintenance,mammals,perspective,Portal,randomization test,regional processes,regional species pool,species compensation}, - annotation = {WOS:000227659700004}, - file = {/Users/renatadiaz/Zotero/storage/ETTG8S73/Goheen et al. - 2005 - Intra-guild compensation regulates species richnes.pdf} -} - -@article{goheen2013, - title = {Piecewise {{Disassembly}} of a {{Large-Herbivore Community}} across a {{Rainfall Gradient}}: {{The UHURU Experiment}}}, - shorttitle = {Piecewise {{Disassembly}} of a {{Large-Herbivore Community}} across a {{Rainfall Gradient}}}, - author = {Goheen, Jacob R. and Palmer, Todd M. and Charles, Grace K. and Helgen, Kristofer M. and Kinyua, Stephen N. and Maclean, Janet E. and Turner, Benjamin L. and Young, Hillary S. and Pringle, Robert M.}, - year = {2013}, - month = feb, - journal = {PLOS ONE}, - volume = {8}, - number = {2}, - pages = {e55192}, - publisher = {{Public Library of Science}}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0055192}, - abstract = {Large mammalian herbivores (LMH) strongly influence plant communities, and these effects can propagate indirectly throughout food webs. Most existing large-scale manipulations of LMH presence/absence consist of a single exclusion treatment, and few are replicated across environmental gradients. Thus, important questions remain about the functional roles of different LMH, and how these roles depend on abiotic context. In September 2008, we constructed a series of 1-ha herbivore-exclusion plots across a 20-km rainfall gradient in central Kenya. Dubbed "UHURU" (Ungulate Herbivory Under Rainfall Uncertainty), this experiment aims to illuminate the ecological effects of three size classes of LMH, and how rainfall regimes shape the direction and magnitude of these effects. UHURU consists of four treatments: total-exclusion (all ungulate herbivores), mesoherbivore-exclusion (LMH {$>$}120-cm tall), megaherbivore-exclusion (elephants and giraffes), and unfenced open plots. Each treatment is replicated three times at three locations (``sites'') along the rainfall gradient: low (440 mm/year), intermediate (580 mm/year), and high (640 mm/year). There was limited variation across sites in soil attributes and LMH activity levels. Understory-plant cover was greater in plots without mesoherbivores, but did not respond strongly to the exclusion of megaherbivores, or to the additional exclusion of dik-dik and warthog. Eleven of the thirteen understory plant species that responded significantly to exclusion treatment were more common in exclusion plots than open ones. Significant interactions between site and treatment on plant communities, although uncommon, suggested that differences between treatments may be greater at sites with lower rainfall. Browsers reduced densities of several common overstory species, along with growth rates of the three dominant Acacia species. Small-mammal densities were 2\textendash 3 times greater in total-exclusion than in open plots at all sites. Although we expect patterns to become clearer with time, results from 2008\textendash 2012 show that the effects of excluding successively smaller-bodied subsets of the LMH community are generally non-additive for a given response variable, and inconsistent across response variables, indicating that the different LMH size classes are not functionally redundant. Several response variables showed significant treatment-by-site interactions, suggesting that the nature of plant-herbivore interactions can vary across restricted spatial scales.}, - langid = {english}, - keywords = {Acacia,Elephants,Herbivory,Plant communities,Plant-herbivore interactions,Plants,Species diversity,Zebras}, - file = {/Users/renatadiaz/Zotero/storage/9LSZHX9Y/Goheen et al. - 2013 - Piecewise Disassembly of a Large-Herbivore Communi.pdf;/Users/renatadiaz/Zotero/storage/E39FTQWQ/article.html} -} - -@article{gomez-rodriguez2015, - title = {Validating the Power of Mitochondrial Metagenomics for Community Ecology and Phylogenetics of Complex Assemblages}, - author = {{G{\'o}mez-Rodr{\'i}guez}, Carola and {Crampton-Platt}, Alex and Timmermans, Martijn J. T. N. and Baselga, Andr{\'e}s and Vogler, Alfried P.}, - year = {2015}, - journal = {Methods in Ecology and Evolution}, - volume = {6}, - number = {8}, - pages = {883--894}, - issn = {2041-210X}, - doi = {10.1111/2041-210X.12376}, - abstract = {The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of {$>$}2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes generated for 156 species (89\% of species in the study); (ii) mitogenomes obtained by the de novo assembly of sequence reads from the real-world communities; and (iii) a custom set of DNA barcode (cox1-5{${'}$}) sequences. Species detection against the custom-built reference genomes was very high ({$>$}90\%). False presences were rare against mitogenomes but slightly higher against the barcode references. False absences were mainly due to the incompleteness of the reference databases and, thus, more prevalent in the de novo data set. Biomass (abundance \texttimes{} body length) and read numbers were strongly correlated, demonstrating the potential of mitochondrial metagenomics for studies of species abundance. A phylogenetic tree from the mitogenomes showed high congruence with known relationships in Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity between sites were highly consistent with data from morphological identifications. The power of mitochondrial metagenomics results from the possibility of rapid assembly of mitogenomes from mixtures of specimens and the use of read counts for accurate estimates of key parameters of biodiversity directly from community samples.}, - langid = {english}, - keywords = {beta diversity,biodiversity monitoring,Chrysomelidae,Coleoptera,genome skimming,mitometagenomics,next-generation sequencing,phylobeta}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12376}, - file = {/Users/renatadiaz/Zotero/storage/HKNC8G9Y/Gómez-Rodríguez et al. - 2015 - Validating the power of mitochondrial metagenomics.pdf;/Users/renatadiaz/Zotero/storage/ELI6VM7B/2041-210X.html} -} - -@article{gonzalez2009, - title = {The {{Causes}} and {{Consequences}} of {{Compensatory Dynamics}} in {{Ecological Communities}}}, - author = {Gonzalez, Andrew and Loreau, Michel}, - year = {2009}, - month = dec, - journal = {Annual Review of Ecology, Evolution, and Systematics}, - volume = {40}, - number = {1}, - pages = {393--414}, - issn = {1543-592X, 1545-2069}, - doi = {10.1146/annurev.ecolsys.39.110707.173349}, - abstract = {Ecological communities are constantly responding to environmental change. Theory and evidence suggest that the loss or decline of stress-intolerant species can be compensated for by the growth of other species. Compensatory dynamics are a long-term feature of community dynamics across a broad range of models, and they can have strong stabilizing effects at the community level. Coexistence theory indicates that distinct environmental responses are required for compensatory dynamics and deemphasizes competition. Compensatory dynamics have been detected under experimental conditions, but are not dominant in a metanalysis of field surveys. Recent progress has been made in quantitative methods that detect compensatory dynamics at different temporal scales. Appropriate null models are required to sharpen our understanding of compensatory dynamics in nature. An integrated theory of compensation and compensatory dynamics will improve our ability to understand when communities maintain sufficient response diversity to buffer the effects of environmental change and anthropogenic stress.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/CFDPB35W/Gonzalez and Loreau - 2009 - The Causes and Consequences of Compensatory Dynami.pdf;/Users/renatadiaz/Zotero/storage/UK36CAZP/Gonzalez and Loreau - 2009 - The Causes and Consequences of Compensatory Dynami.pdf} -} - -@article{goodman2012, - title = {Avian Body Size Changes and Climate Change: Warming or Increasing Variability?}, - shorttitle = {Avian Body Size Changes and Climate Change}, - author = {Goodman, Rae E. and Lebuhn, Gretchen and Seavy, Nathaniel E. and Gardali, Thomas and {Bluso-Demers}, Jill D.}, - year = {2012}, - journal = {Global Change Biology}, - volume = {18}, - number = {1}, - pages = {63--73}, - issn = {1365-2486}, - doi = {10.1111/j.1365-2486.2011.02538.x}, - abstract = {There has been a growing interest in whether established ecogeographical patterns, such as Bergmann's rule, explain changes in animal morphology related to climate change. Bergmann's rule has often been used to predict that body size will decrease as the climate warms, but the predictions about how body size will change are critically dependent on the mechanistic explanation behind the rule. To investigate change in avian body size in western North America, we used two long-term banding data sets from central California, USA; the data spanned 40 years (1971\textendash 2010) at one site and 27 years (1983\textendash 2009) at the other. We found that wing length of birds captured at both sites has been steadily increasing at a rate of 0.024\textendash 0.084\% per year. Although changes in body mass were not always significant, when they were, the trend was positive and the magnitudes of significant trends were similar to those for wing length (0.040\textendash 0.112\% per year). There was no clear difference between the rates of change of long-distance vs. short-distance migrants or between birds that bred locally compared to those that bred to the north of the sites. Previous studies from other regions of the world have documented decreases in avian body size and have used Bergmann's rule and increases in mean temperature to explain these shifts. Because our results do not support this pattern, we propose that rather than responding to increasing mean temperatures, avian body size in central California may be influenced by changing climatic variability or changes in primary productivity. More information on regional variation in the rates of avian body size change will be needed to test these hypotheses.}, - langid = {english}, - keywords = {Bergmann's Rule,body mass,California,climatic variability,ecogeographic rules,ecotypic variation,energy reserves,morphology,wing length}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2486.2011.02538.x}, - file = {/Users/renatadiaz/Zotero/storage/B7ZKXTTV/j.1365-2486.2011.02538.html} -} - -@book{gotelli1996, - title = {Null Models in Ecology}, - author = {Gotelli, Nicholas J. and Graves, Gary R.}, - year = {1996}, - file = {/Users/renatadiaz/Zotero/storage/AB5D2XII/Gotelli and Graves - 1996 - Null models in ecology.pdf} -} - -@incollection{gotelli2011, - title = {Estimating Species Richness}, - booktitle = {Biological {{Diversity}}: {{Frontiers}} in {{Measurement}} and {{Assessment}}}, - author = {Gotelli, Nicholas J and Colwell, Robert K}, - editor = {Magurran, Anne E. and McGill, Brian J.}, - year = {2011}, - pages = {39--54}, - publisher = {{Oxford University Press}}, - address = {{Oxford, UNITED KINGDOM}}, - isbn = {978-0-19-157684-3}, - keywords = {Biodiversity -- Monitoring.,Biodiversity conservation.,Biodiversity.} -} - -@article{gotelli2017, - title = {Community-Level Regulation of Temporal Trends in Biodiversity}, - author = {Gotelli, Nicholas J. and Shimadzu, Hideyasu and Dornelas, Maria and McGill, Brian and Moyes, Faye and Magurran, Anne E.}, - year = {2017}, - month = jul, - journal = {Science Advances}, - volume = {3}, - number = {7}, - pages = {e1700315}, - issn = {2375-2548}, - doi = {10.1126/sciadv.1700315}, - abstract = {Many theoretical models of community dynamics predict that species richness (S) and total abundance (N) are regulated in their temporal fluctuations. We present novel evidence for widespread regulation of biodiversity. For 59 plant and animal assemblages from around the globe monitored annually for a decade or more, the majority exhibited regulated fluctuations compared to the null hypothesis of an unconstrained random walk. However, there was little evidence for statistical artifacts, regulation driven by correlations with average annual temperature, or local-scale compensatory fluctuations in S or N. In the absence of major environmental perturbations, such as urbanization or cropland transformation, species richness and abundance may be buffered and exhibit some resilience in their temporal trajectories. These results suggest that regulatory processes are occurring despite unprecedented environmental change, highlighting the need for community-level assessment of biodiversity trends, as well as extensions of existing theory to address open source pools and shifting environmental conditions. Temporal fluctuations in species richness are frequently regulated, exhibiting a tendency to return toward a central level. Temporal fluctuations in species richness are frequently regulated, exhibiting a tendency to return toward a central level.}, - copyright = {Copyright \textcopyright{} 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/GXX6N4ZU/Gotelli et al. - 2017 - Community-level regulation of temporal trends in b.pdf;/Users/renatadiaz/Zotero/storage/JMEAP9E6/Gotelli et al. - 2017 - Community-level regulation of temporal trends in b.pdf;/Users/renatadiaz/Zotero/storage/C3H2YEND/tab-pdf.html;/Users/renatadiaz/Zotero/storage/WFY87QSC/e1700315.html} -} - -@article{gravel2016, - title = {Stability and Complexity in Model Meta-Ecosystems}, - author = {Gravel, Dominique and Massol, Fran{\c c}ois and Leibold, Mathew A.}, - year = {2016}, - month = aug, - journal = {Nature Communications}, - volume = {7}, - pages = {12457}, - issn = {2041-1723}, - doi = {10.1038/ncomms12457}, - abstract = {The diversity of life and its organization in networks of interacting species has been a long-standing theoretical puzzle for ecologists. Ever since May's provocative paper challenging whether `large complex systems [are] stable' various hypotheses have been proposed to explain when stability should be the rule, not the exception. Spatial dynamics may be stabilizing and thus explain high community diversity, yet existing theory on spatial stabilization is limited, preventing comparisons of the role of dispersal relative to species interactions. Here we incorporate dispersal of organisms and material into stability\textendash complexity theory. We find that stability criteria from classic theory are relaxed in direct proportion to the number of ecologically distinct patches in the meta-ecosystem. Further, we find the stabilizing effect of dispersal is maximal at intermediate intensity. Our results highlight how biodiversity can be vulnerable to factors, such as landscape fragmentation and habitat loss, that isolate local communities.}, - copyright = {2016 Nature Publishing Group}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/3BYUXXMN/Gravel et al. - 2016 - Stability and complexity in model meta-ecosystems.pdf;/Users/renatadiaz/Zotero/storage/I2GL9986/ncomms12457.html} -} - -@article{greener2022, - title = {A Guide to Machine Learning for Biologists}, - author = {Greener, Joe G. and Kandathil, Shaun M. and Moffat, Lewis and Jones, David T.}, - year = {2022}, - month = jan, - journal = {Nature Reviews Molecular Cell Biology}, - volume = {23}, - number = {1}, - pages = {40--55}, - publisher = {{Nature Publishing Group}}, - issn = {1471-0080}, - doi = {10.1038/s41580-021-00407-0}, - abstract = {The expanding scale and inherent complexity of biological data have encouraged a growing use of machine learning in biology to build informative and predictive models of the underlying biological processes. All machine learning techniques fit models to data; however, the specific methods are quite varied and can at first glance seem bewildering. In this Review, we aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to specific types of biological data, and also discuss some best practices and points to consider when one is embarking on experiments involving machine learning. Some emerging directions in machine learning methodology are also~discussed.}, - copyright = {2021 Springer Nature Limited}, - langid = {english}, - keywords = {Bioinformatics,Computational biology and bioinformatics}, - file = {/Users/renatadiaz/Zotero/storage/RKJIQ38A/Greener et al. - 2022 - A guide to machine learning for biologists.pdf;/Users/renatadiaz/Zotero/storage/7HLAM4Y3/s41580-021-00407-0.html} -} - -@article{greener2022a, - title = {A Guide to Machine Learning for Biologists}, - author = {Greener, Joe G. and Kandathil, Shaun M. and Moffat, Lewis and Jones, David T.}, - year = {2022}, - month = jan, - journal = {Nature Reviews Molecular Cell Biology}, - volume = {23}, - number = {1}, - pages = {40--55}, - issn = {1471-0072, 1471-0080}, - doi = {10.1038/s41580-021-00407-0}, - abstract = {The expanding scale and inherent complexity of biological data have encouraged a growing use of machine learning in biology to build informative and predictive models of the underlying biological processes. All machine learning techniques fit models to data; however, the specific methods are quite varied and can at first glance seem bewildering. In this Review, we aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to specific types of biological data, and also discuss some best practices and points to consider when one is embarking on experiments involving machine learning. Some emerging directions in machine learning methodology are also discussed.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/FPUV98SD/Greener et al. - 2022 - A guide to machine learning for biologists.pdf} -} - -@article{griffiths1986, - title = {Size-{{Abundance Relations}} in {{Communities}}}, - author = {Griffiths, David}, - year = {1986}, - month = feb, - journal = {The American Naturalist}, - volume = {127}, - number = {2}, - pages = {140--166}, - issn = {0003-0147, 1537-5323}, - doi = {10.1086/284475}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/CU3ATDBE/Griffiths - 1986 - Size-Abundance Relations in Communities.pdf} -} - -@article{haegeman2008, - title = {Limitations of Entropy Maximization in Ecology}, - author = {Haegeman, Bart and Loreau, Michel}, - year = {2008}, - journal = {Oikos}, - volume = {117}, - number = {11}, - pages = {1700--1710}, - issn = {1600-0706}, - doi = {10.1111/j.1600-0706.2008.16539.x}, - abstract = {Applying ideas of statistical mechanics in ecology have recently received quite some attention. The entropy maximization (EM) formalism looks particularly attractive, as it provides a simple algorithm to infer detailed system variables from a limited number of constraints. However, we point out that a blind application of this formalism can easily lead to wrong conclusions. To illustrate this, we reanalyze an ecological data set that has been used to claim the good performance of EM in predicting species abundances from trait measurements. We show that these results are entirely due to the restrictive constraints, and do not provide any support for the applicability of EM in ecology. By comparing with a simple example from physics, we indicate which characteristic mechanism of EM, and of statistical mechanics in general, is missing for the ecological example. This analysis introduces a series of methods to evaluate future attempts to apply EM in ecology.}, - copyright = {\textcopyright{} 2008 The Authors}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/E4PYX7I7/Haegeman and Loreau - 2008 - Limitations of entropy maximization in ecology.pdf;/Users/renatadiaz/Zotero/storage/XZGEFHUH/Haegeman and Loreau - 2008 - Limitations of entropy maximization in ecology.pdf;/Users/renatadiaz/Zotero/storage/67CYUHJQ/j.1600-0706.2008.16539.html;/Users/renatadiaz/Zotero/storage/E3WCQ4X5/j.1600-0706.2008.16539.html} -} - -@article{hajibabaei2022, - title = {Demystifying {{eDNA}} Validation}, - author = {Hajibabaei, Mehrdad}, - year = {2022}, - month = oct, - journal = {Trends in Ecology \& Evolution}, - volume = {37}, - number = {10}, - pages = {826--828}, - publisher = {{Elsevier}}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2022.06.015}, - langid = {english}, - pmid = {35902292}, - file = {/Users/renatadiaz/Zotero/storage/SXTWBU3U/Hajibabaei - 2022 - Demystifying eDNA validation.pdf;/Users/renatadiaz/Zotero/storage/NLPJ3B8F/S0169-5347(22)00166-5.html} -} - -@article{hampton2015, - title = {The {{Tao}} of Open Science for Ecology}, - author = {Hampton, Stephanie E. and Anderson, Sean S. and Bagby, Sarah C. and Gries, Corinna and Han, Xueying and Hart, Edmund M. and Jones, Matthew B. and Lenhardt, W. Christopher and MacDonald, Andrew and Michener, William K. and Mudge, Joe and Pourmokhtarian, Afshin and Schildhauer, Mark P. and Woo, Kara H. and Zimmerman, Naupaka}, - year = {2015}, - journal = {Ecosphere}, - volume = {6}, - number = {7}, - pages = {art120}, - issn = {2150-8925}, - doi = {10.1890/ES14-00402.1}, - abstract = {The field of ecology is poised to take advantage of emerging technologies that facilitate the gathering, analyzing, and sharing of data, methods, and results. The concept of transparency at all stages of the research process, coupled with free and open access to data, code, and papers, constitutes ``open science.'' Despite the many benefits of an open approach to science, a number of barriers to entry exist that may prevent researchers from embracing openness in their own work. Here we describe several key shifts in mindset that underpin the transition to more open science. These shifts in mindset include thinking about data stewardship rather than data ownership, embracing transparency throughout the data life-cycle and project duration, and accepting critique in public. Though foreign and perhaps frightening at first, these changes in thinking stand to benefit the field of ecology by fostering collegiality and broadening access to data and findings. We present an overview of tools and best practices that can enable these shifts in mindset at each stage of the research process, including tools to support data management planning and reproducible analyses, strategies for soliciting constructive feedback throughout the research process, and methods of broadening access to final research products.}, - langid = {english}, - keywords = {data management,ecology,open access,open science,reproducible research}, - file = {/Users/renatadiaz/Zotero/storage/D7Y5URJQ/Hampton et al. - 2015 - The Tao of open science for ecology.pdf;/Users/renatadiaz/Zotero/storage/Z5Q4QWGD/ES14-00402.html} -} - -@article{hankin2007, - title = {Introducing Untb, an {{R}} Package for Simulating Ecological Drift under the Unified Nuetral Theory of Biodiversity}, - author = {Hankin, Robin K. S.}, - year = {2007}, - month = sep, - journal = {Journal of Statistical Software}, - volume = {22}, - number = {12} -} - -@article{harris2015, - title = {Generating Realistic Assemblages with a Joint Species Distribution Model}, - author = {Harris, David J.}, - year = {2015}, - journal = {Methods in Ecology and Evolution}, - volume = {6}, - number = {4}, - pages = {465--473}, - issn = {2041-210X}, - doi = {10.1111/2041-210X.12332}, - abstract = {Species distribution models (SDMs) represent important analytical and predictive tools for ecologists. Until now, these models have either assumed (i) that species' occurrence probabilities are uncorrelated or (ii) that species respond linearly to preselected environmental variables. These two assumptions currently prevent ecologists from modelling assemblages with realistic co-occurrence and species richness properties. This paper introduces a stochastic feedforward neural network, called `mistnet', which makes neither assumption. Thus, unlike most SDMs, mistnet can account for non-independent co-occurrence patterns driven by unobserved environmental heterogeneity. And unlike several recently proposed joint SDMs, the model can also learn nonlinear functions relating species' occurrence probabilities to environmental predictors. Mistnet makes more accurate predictions about the North American bird communities found along Breeding Bird Survey transects than several alternative methods tested. In particular, typical assemblages held out of sample for validation were each tens of thousands of times more likely under the mistnet model than under independent combinations of single-species predictions. Apart from improved accuracy, mistnet shows two other important benefits for ecological research and management. First: by analysing co-occurrence data, mistnet can identify unmeasured \textendash{} and perhaps unanticipated \textendash{} environmental variables that drive species turnover. For example, the model identified a strong grassland/forest gradient, even though only temperature and precipitation were given as model inputs. Second: mistnet is able to take advantage of outside information to guide its predictions towards more realistic assemblages. For example, mistnet automatically adjusts its expectations to include more forest-associated species in response to a stray observation of a forest-dwelling warbler.}, - langid = {english}, - keywords = {birds,breeding bird survey,neural network,probabilistic graphical model,species assemblages,species distribution model}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12332}, - file = {/Users/renatadiaz/Zotero/storage/IBL32V3I/Harris - 2015 - Generating realistic assemblages with a joint spec.pdf;/Users/renatadiaz/Zotero/storage/XEERFQYK/2041-210X.html} -} - -@article{harris2018, - title = {Forecasting Biodiversity in Breeding Birds Using Best Practices}, - author = {Harris, David J. and Taylor, Shawn D. and White, Ethan P.}, - year = {2018}, - month = feb, - journal = {PeerJ}, - volume = {6}, - pages = {e4278}, - issn = {2167-8359}, - doi = {10.7717/peerj.4278}, - abstract = {Biodiversity forecasts are important for conservation, management, and evaluating how well current models characterize natural systems. While the number of forecasts for biodiversity is increasing, there is little information available on how well these forecasts work. Most biodiversity forecasts are not evaluated to determine how well they predict future diversity, fail to account for uncertainty, and do not use time-series data that captures the actual dynamics being studied. We addressed these limitations by using best practices to explore our ability to forecast the species richness of breeding birds in North America. We used hindcasting to evaluate six different modeling approaches for predicting richness. Hindcasts for each method were evaluated annually for a decade at 1,237 sites distributed throughout the continental United States. All models explained more than 50\% of the variance in richness, but none of them consistently outperformed a baseline model that predicted constant richness at each site. The best practices implemented in this study directly influenced the forecasts and evaluations. Stacked species distribution models and ``naive'' forecasts produced poor estimates of uncertainty and accounting for this resulted in these models dropping in the relative performance compared to other models. Accounting for observer effects improved model performance overall, but also changed the rank ordering of models because it did not improve the accuracy of the ``naive'' model. Considering the forecast horizon revealed that the prediction accuracy decreased across all models as the time horizon of the forecast increased. To facilitate the rapid improvement of biodiversity forecasts, we emphasize the value of specific best practices in making forecasts and evaluating forecasting methods.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/PXSF292Y/4278.pdf} -} - -@article{harte2008, - title = {Maximum {{Entropy}} and the {{State-Variable Approach}} to {{Macroecology}}}, - author = {Harte, J. and Zillio, T. and Conlisk, E. and Smith, A. B.}, - year = {2008}, - journal = {Ecology}, - volume = {89}, - number = {10}, - pages = {2700--2711}, - issn = {1939-9170}, - doi = {10.1890/07-1369.1}, - abstract = {The biodiversity scaling metrics widely studied in macroecology include the species\textendash area relationship (SAR), the scale-dependent species\textendash abundance distribution (SAD), the distribution of masses or metabolic energies of individuals within and across species, the abundance\textendash energy or abundance\textendash mass relationship across species, and the species-level occupancy distributions across space. We propose a theoretical framework for predicting the scaling forms of these and other metrics based on the state-variable concept and an analytical method derived from information theory. In statistical physics, a method of inference based on information entropy results in a complete macro-scale description of classical thermodynamic systems in terms of the state variables volume, temperature, and number of molecules. In analogy, we take the state variables of an ecosystem to be its total area, the total number of species within any specified taxonomic group in that area, the total number of individuals across those species, and the summed metabolic energy rate for all those individuals. In terms solely of ratios of those state variables, and without invoking any specific ecological mechanisms, we show that realistic functional forms for the macroecological metrics listed above are inferred based on information entropy. The Fisher log series SAD emerges naturally from the theory. The SAR is predicted to have negative curvature on a log\textendash log plot, but as the ratio of the number of species to the number of individuals decreases, the SAR becomes better and better approximated by a power law, with the predicted slope z in the range of 0.14\textendash 0.20. Using the 3/4 power mass\textendash metabolism scaling relation to relate energy requirements and measured body sizes, the Damuth scaling rule relating mass and abundance is also predicted by the theory. We argue that the predicted forms of the macroecological metrics are in reasonable agreement with the patterns observed from plant census data across habitats and spatial scales. While this is encouraging, given the absence of adjustable fitting parameters in the theory, we further argue that even small discrepancies between data and predictions can help identify ecological mechanisms that influence macroecological patterns.}, - langid = {english}, - keywords = {biodiversity,endemics–area relationship,energy distribution,macroecology,maximum entropy,metabolic theory,spatial pattern,spatial scaling,species–abundance distribution,species–area relationship,state variables}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/07-1369.1}, - file = {/Users/renatadiaz/Zotero/storage/Y6SVMQTI/Harte et al. - 2008 - Maximum Entropy and the State-Variable Approach to.pdf;/Users/renatadiaz/Zotero/storage/CN2HLGF9/07-1369.html} -} - -@book{harte2011, - title = {Maximum {{Entropy}} and {{Ecology}}: {{A Theory}} of {{Abundance}}, {{Distribution}}, and {{Energetics}}}, - shorttitle = {Maximum {{Entropy}} and {{Ecology}}}, - author = {Harte, John}, - year = {2011}, - month = jun, - publisher = {{Oxford University Press}}, - doi = {10.1093/acprof:oso/9780199593415.001.0001}, - isbn = {978-0-19-959341-5}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/6Y6TMGYP/Harte - 2011 - Maximum Entropy and Ecology A Theory of Abundance.pdf} -} - -@article{harte2014, - title = {Maximum Information Entropy: A Foundation for Ecological Theory}, - shorttitle = {Maximum Information Entropy}, - author = {Harte, John and Newman, Erica A.}, - year = {2014}, - month = jul, - journal = {Trends in Ecology \& Evolution}, - volume = {29}, - number = {7}, - pages = {384--389}, - issn = {1872-8383}, - doi = {10.1016/j.tree.2014.04.009}, - abstract = {The maximum information entropy (MaxEnt) principle is a successful method of statistical inference that has recently been applied to ecology. Here, we show how MaxEnt can accurately predict patterns such as species-area relationships (SARs) and abundance distributions in macroecology and be a foundation for ecological theory. We discuss the conceptual foundation of the principle, why it often produces accurate predictions of probability distributions in science despite not incorporating explicit mechanisms, and how mismatches between predictions and data can shed light on driving mechanisms in ecology. We also review possible future extensions of the maximum entropy theory of ecology (METE), a potentially important foundation for future developments in ecological theory.}, - langid = {english}, - pmid = {24863182}, - keywords = {Animal Distribution,ecological theory,Ecology,information entropy,macroecology,MaxEnt,maximum entropy theory of ecology,Models; Biological,Models; Statistical,Plant Dispersal,Population Density}, - file = {/Users/renatadiaz/Zotero/storage/LEG2DH4L/S0169534714001037.html} -} - -@article{harte2015, - title = {Integrating Macroecological Metrics and Community Taxonomic Structure}, - author = {Harte, John and Rominger, Andrew and Zhang, Wenyu}, - year = {2015}, - journal = {Ecology Letters}, - volume = {18}, - number = {10}, - pages = {1068--1077}, - issn = {1461-0248}, - doi = {10.1111/ele.12489}, - abstract = {We extend macroecological theory based on the maximum entropy principle from species level to higher taxonomic categories, thereby predicting distributions of species richness across genera or families and the dependence of abundance and metabolic rate distributions on taxonomic tree structure. Predictions agree with qualitative trends reported in studies on hyper-dominance in tropical tree species, mammalian body size distributions and patterns of rarity in worldwide plant communities. Predicted distributions of species richness over genera or families for birds, arthropods, plants and microorganisms are in excellent agreement with data. Data from an intertidal invertebrate community, but not from a dispersal-limited forest, are in excellent agreement with a predicted new relationship between body size and abundance. Successful predictions of the original species level theory are unmodified in the extended theory. By integrating macroecology and taxonomic tree structure, maximum entropy may point the way towards a unified framework for understanding phylogenetic community structure.}, - langid = {english}, - keywords = {Abundance distribution,energy equivalence,macroecology,maximum entropy,metabolic rate distribution,taxonomic tree}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12489}, - file = {/Users/renatadiaz/Zotero/storage/CDUGZQRB/Harte et al. - 2015 - Integrating macroecological metrics and community .pdf;/Users/renatadiaz/Zotero/storage/HGW2WYKQ/Harte et al. - 2015 - Integrating macroecological metrics and community .pdf;/Users/renatadiaz/Zotero/storage/4BIX6RVZ/ele.html;/Users/renatadiaz/Zotero/storage/KGLGERWY/ele.html} -} - -@article{harte2017, - title = {Metabolic Partitioning across Individuals in Ecological Communities}, - author = {Harte, John and Newman, Erica A. and Rominger, Andrew J.}, - year = {2017}, - journal = {Global Ecology and Biogeography}, - volume = {26}, - number = {9}, - pages = {993--997}, - issn = {1466-8238}, - doi = {10.1111/geb.12621}, - abstract = {The mechanistic origin and shape of body-size distributions within communities are of considerable interest in ecology. A recently proposed light-limitation model provides a good fit to the distribution of tree sizes in a tropical forest plot. The maximum entropy theory of ecology (METE) also predicts size distributions, but without explicit mechanistic assumptions, and thus its predictions should hold in ecosystems generally, regardless of whether they are light limited. A comparison of the form and success of the predictions of the model and the theory can provide insight into the role that mechanisms play in shaping patterns in macroecology. The prediction by the METE of the size distribution of organisms is remarkably similar in form to that of the model: power-law behaviour in the size range where the light-limitation model predicts a power law, and exponential behaviour in the size range where the model predicts an exponential tail. The METE prediction matches data widely, including data in ecosystems where light is not limiting. We show examples for three disparate communities: trees in a tropical forest plot; herbaceous plants in a treeless subalpine meadow; and island arthropods. We conclude that the success of METE's predicted form across systems, including those that are clearly not light limited, enriches our capacity to predict patterns in macroecology without making explicit mechanistic assumptions and provides a unified framework that can capture ubiquitous features of those patterns across diverse ecosystems governed by a variety of mechanisms.}, - langid = {english}, - keywords = {body-size distribution,community structure,macroecology,metabolic rate distribution,metabolism}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12621}, - file = {/Users/renatadiaz/Zotero/storage/LN882UCX/Harte et al. - 2017 - Metabolic partitioning across individuals in ecolo.pdf;/Users/renatadiaz/Zotero/storage/TFQ6J68X/geb.html} -} - -@article{harte2021, - title = {{{DynaMETE}}: A Hybrid {{MaxEnt-plus-mechanism}} Theory of Dynamic Macroecology}, - shorttitle = {{{DynaMETE}}}, - author = {Harte, John and Umemura, Kaito and Brush, Micah}, - year = {2021}, - journal = {Ecology Letters}, - volume = {24}, - number = {5}, - pages = {935--949}, - issn = {1461-0248}, - doi = {10.1111/ele.13714}, - abstract = {The Maximum Entropy Theory of Ecology (METE) predicts the shapes of macroecological metrics in relatively static ecosystems, across spatial scales, taxonomic categories and habitats, using constraints imposed by static state variables. In disturbed ecosystems, however, with time-varying state variables, its predictions often fail. We extend macroecological theory from static to dynamic by combining the MaxEnt inference procedure with explicit mechanisms governing disturbance. In the static limit, the resulting theory, DynaMETE, reduces to METE but also predicts a new scaling relationship among static state variables. Under disturbances, expressed as shifts in demographic, ontogenic growth or migration rates, DynaMETE predicts the time trajectories of the state variables as well as the time-varying shapes of macroecological metrics such as the species abundance distribution and the distribution of metabolic rates over individuals. An iterative procedure for solving the dynamic theory is presented. Characteristic signatures of the deviation from static predictions of macroecological patterns are shown to result from different kinds of disturbance. By combining MaxEnt inference with explicit dynamical mechanisms of disturbance, DynaMETE is a candidate theory of macroecology for ecosystems responding to anthropogenic or natural disturbances.}, - langid = {english}, - keywords = {Abundance distribution,disturbance,DynaMETE,dynamics,macroecology,maximum entropy,mechanism,metabolic rate distribution,METE}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13714}, - file = {/Users/renatadiaz/Zotero/storage/EC8S2PWD/Harte et al. - 2021 - DynaMETE a hybrid MaxEnt-plus-mechanism theory of.pdf;/Users/renatadiaz/Zotero/storage/4R3S3TMN/ele.html} -} - -@article{harte2022, - title = {An Equation of State Unifies Diversity, Productivity, Abundance and Biomass}, - author = {Harte, John and Brush, Micah and Newman, Erica A. and Umemura, Kaito}, - year = {2022}, - month = aug, - journal = {Communications Biology}, - volume = {5}, - number = {1}, - pages = {1--6}, - publisher = {{Nature Publishing Group}}, - issn = {2399-3642}, - doi = {10.1038/s42003-022-03817-8}, - abstract = {To advance understanding of biodiversity and ecosystem function, ecologists seek widely applicable relationships among species diversity and other ecosystem characteristics such as species productivity, biomass, and abundance. These metrics vary widely across ecosystems and no relationship among any combination of them that is valid across habitats, taxa, and spatial scales, has heretofore been found. Here we derive such a relationship, an equation of state, among species richness, energy flow, biomass, and abundance by combining results from the Maximum Entropy Theory of Ecology and the Metabolic Theory of Ecology. It accurately captures the relationship among these state variables in 42 data sets, including vegetation and arthropod communities, that span a wide variety of spatial scales and habitats. The success of our ecological equation of state opens opportunities for estimating difficult-to-measure state variables from measurements of others, adds support for two current theories in ecology, and is a step toward unification in ecology.}, - copyright = {2022 The Author(s)}, - langid = {english}, - keywords = {Macroecology,Theoretical ecology}, - file = {/Users/renatadiaz/Zotero/storage/Y7RI27MQ/Harte et al. - 2022 - An equation of state unifies diversity, productivi.pdf;/Users/renatadiaz/Zotero/storage/TIGV9W8Y/s42003-022-03817-8.html} -} - -@book{hastie2009, - title = {The {{Elements}} of {{Statistical Learning}}}, - author = {Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome}, - year = {2009}, - edition = {Second}, - publisher = {{Springer}}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/R5TAVTNM/Tibshirani and Friedman - Valerie and Patrick Hastie.pdf} -} - -@article{hastings2004, - title = {Transients: The Key to Long-Term Ecological Understanding?}, - shorttitle = {Transients}, - author = {Hastings, Alan}, - year = {2004}, - month = jan, - journal = {Trends in Ecology \& Evolution}, - volume = {19}, - number = {1}, - pages = {39--45}, - issn = {01695347}, - doi = {10.1016/j.tree.2003.09.007}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/FU59XUEM/Hastings - 2004 - Transients the key to long-term ecological unders.pdf} -} - -@article{hastings2018, - title = {Transient Phenomena in Ecology}, - author = {Hastings, Alan and Abbott, Karen C. and Cuddington, Kim and Francis, Tessa and Gellner, Gabriel and Lai, Ying-Cheng and Morozov, Andrew and Petrovskii, Sergei and Scranton, Katherine and Zeeman, Mary Lou}, - year = {2018}, - month = sep, - journal = {Science}, - volume = {361}, - number = {6406}, - publisher = {{American Association for the Advancement of Science}}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.aat6412}, - abstract = {Making sense of transient dynamics Ecological systems can switch between alternative dynamic states. For example, the species composition of the community can change or nutrient dynamics can shift, even if there is little or no change in underlying environmental conditions. Such switches can be abrupt or more gradual, and a growing number of studies examine the transient dynamics between one state and another\textemdash particularly in the context of anthropogenic global change. Hastings et al. review current knowledge of transient dynamics, showing that hitherto idiosyncratic and individual patterns can be classified into a coherent framework, with important general lessons and directions for future study. Science, this issue p. eaat6412 Structured Abstract BACKGROUNDMuch of ecological theory and the understanding of ecological systems has been based on the idea that the observed states and dynamics of ecological systems can be represented by stable asymptotic behavior of models describing these systems. Beginning with early work by Lotka and Volterra through the seminal work of May in the 1970s, this view has dominated much of ecological thinking, although concepts such as the idea of tipping points in ecological systems have played an increasingly important role. In contrast to the implied long time scales of asymptotic behavior in mathematical models, both observations of ecological systems and questions related to the management of ecological systems are typically focused on relatively short time scales.A number of models and observations demonstrate possible transient behavior that may persist over very long time periods, followed by rapid changes in dynamics. In these examples, focusing solely on the long-term behavior of systems would be misleading. A long transient is a persistent dynamical regime\textemdash including near-constant dynamics, cyclic dynamics, or even apparently chaotic dynamics\textemdash that persists for more than a few and as many as tens of generations, but which is not the stable long-term dynamic that would eventually occur. These examples have demonstrated the potential importance of transients but have often appeared to be a set of idiosyncratic cases. What is needed is an organized approach that describes when a transient behavior is likely to appear, predicts what factors enhance long transients, and describes the characteristics of this transient behavior. A theory of long ecological transients is a counterpart to the related question of tipping points, where previous work based on an analysis of simple bifurcations has provided broad insights. ADVANCESJust as ideas based on the saddle-node bifurcation provide a basis for understanding tipping points, a suite of ideas from dynamical systems provides a way to organize a systematic study of transient dynamics in ecological systems. As illustrated in the figure, a relatively small number of ideas from dynamical systems are used to categorize the different ways that transients can arise. Translating these abstract results from dynamical systems into observations about both ecological models and ecological system dynamics, it is possible to understand when transients are likely to occur and the various properties of these transients, with implications for ecosystem management and basic ecological theory. Transients can provide an explanation for observed regime shifts that does not depend on underlying environmental changes. Systems that continually change rapidly between different long-lasting dynamics, such as insect outbreaks, may most usefully be viewed using the framework of long transients.An initial focus on conceptual systems, such as two-species systems, establishes the ubiquity of transients and an understanding of what ecological aspects can lead to transients, including the presence of multiple time scales and particular nonlinear interactions. The influences of stochasticity and more realistic higher-dimensional dynamics are shown to increase the likelihood, and possibly the temporal extent, of transient dynamics. OUTLOOKThe development of such a framework for organizing the study of transients in ecological systems opens up a number of avenues for future research and application. The approach we describe also raises important questions for further development in dynamical systems. We have not, for example, emphasized nonautonomous systems, which may be required to understand the implications of a changing environment for transients. Systems with explicit time dependence as well as stochastic nonlinear systems still present great mathematical challenges.Implications for management and basic ecological understanding depend on both the results we describe and future developments. A recognition of the difficulty of prediction caused by long transients, and of the corresponding need to match dynamics to transient behaviors of models, shows that basing either management or interpretation of ecological observations only on long-term dynamics can be seriously flawed. {$<$}img class="fragment-image" aria-describedby="F1-caption" src="https://science.sciencemag.org/content/sci/361/6406/eaat6412/F1.medium.gif"/{$>$} Download high-res image Open in new tab Download Powerpoint Two ways that long transients arise in ecology, illustrated as a ball rolling downhill.(A) Slow transition away from a ghost attractor: a state that is not an equilibrium, but would be under slightly different conditions. (B) Lingering near a saddle: a state that is attracting from some directions but repelling from others. Additional factors such as stochasticity, multiple time scales, and high system dimension can extend transients. The importance of transient dynamics in ecological systems and in the models that describe them has become increasingly recognized. However, previous work has typically treated each instance of these dynamics separately. We review both empirical examples and model systems, and outline a classification of transient dynamics based on ideas and concepts from dynamical systems theory. This classification provides ways to understand the likelihood of transients for particular systems, and to guide investigations to determine the timing of sudden switches in dynamics and other characteristics of transients. Implications for both management and underlying ecological theories emerge.}, - chapter = {Review}, - copyright = {Copyright \textcopyright{} 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. http://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.}, - langid = {english}, - pmid = {30190378}, - file = {/Users/renatadiaz/Zotero/storage/YC7GWSH8/Hastings et al. - 2018 - Transient phenomena in ecology.pdf;/Users/renatadiaz/Zotero/storage/2S43X4F5/tab-pdf.html} -} - -@misc{havstad2019, - title = {Perennial Grass Recovery Following Livestock Overgazing and Shrub Removal: An Experiment at the {{Jornada Experimental Range}} ({{Jornada Basin LTER}}), 1996-2016}, - shorttitle = {Perennial Grass Recovery Following Livestock Overgazing and Shrub Removal}, - author = {Havstad, Kris and Bestelmeyer, Brandon}, - year = {2019}, - publisher = {{Environmental Data Initiative}}, - doi = {10.6073/PASTA/CC0B40F7A34E52B612F384FF0F246E06}, - abstract = {The objective of this ongoing study is to determine the effect of cattle grazing and shrub removal on the decline and recovery of perennial grasses in a mesquite-invaded black grama grassland on sandy soils in the northern Chihuahuan Desert. The experiment was implemented as a randomized complete block with 3 levels of grazing (summer, winter, and control) and 2 levels of shrub treatment (shrub removal and control) in each of 3 replicate blocks. The 18 experimental units are 0.5 ha (70 x 70 m) exclosures constructed in a mesquite-invaded black grama grassland in the southwest portion of the Jornada Experimental Range in Dona Ana County, New Mexico, USA. Vegetation sampling was conducted with the line-point intercept method. Initial pre-treatment sampling occurred in 1996. Grazing treatments removed 65-80\% of aboveground perennial grass biomass over 24-36 hour periods in each of four years from summer 1996 to winter 2000; shrub removal occurred during this time as well. No livestock grazing or shrub removal have occurred since 2000. Post-treatment sampling occurred in 2002, 2009, and 2016.}, - langid = {english} -} - -@article{he2011, - title = {Species\textendash Area Relationships Always Overestimate Extinction Rates from Habitat Loss}, - author = {He, Fangliang and Hubbell, Stephen P.}, - year = {2011}, - month = may, - journal = {Nature}, - volume = {473}, - number = {7347}, - pages = {368--371}, - publisher = {{Nature Publishing Group}}, - issn = {1476-4687}, - doi = {10.1038/nature09985}, - abstract = {There is broad agreement that Earth is facing a biodiversity crisis, but estimating extinction rates remains a daunting task, not least because it is almost impossible to determine when the very last individual of a species has died. Fangliang He and Stephen Hubbell demonstrate that a widely used indirect method of estimating extinction rates \textemdash{} based on backward extrapolation of species\textendash area relationship data \textemdash{} tends to overestimate the problem. As an example, they cite data on passerine bird species in the United States. He and Hubbell stress that habitat loss remains a real and growing threat to biodiversity, although we need to develop more reliable means of monitoring the situation.}, - copyright = {2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, - langid = {english}, - keywords = {Conservation biology,Evolutionary ecology}, - file = {/Users/renatadiaz/Zotero/storage/CMS62VQT/He and Hubbell - 2011 - Species–area relationships always overestimate ext.pdf;/Users/renatadiaz/Zotero/storage/9SPZP2V9/nature09985.html} -} - -@article{he2021, - title = {Relative Importance of Deterministic and Stochastic Processes for Beta Diversity of Bird Assemblages in {{Yunnan}}, {{China}}}, - author = {He, Xuelian and Brown, Calum and Lin, Luxiang}, - year = {2021}, - journal = {Ecosphere}, - volume = {12}, - number = {6}, - pages = {e03545}, - issn = {2150-8925}, - doi = {10.1002/ecs2.3545}, - abstract = {Evaluating the relative importance of deterministic and stochastic processes underlying taxonomic and functional beta diversity is crucial in community ecology, because it can reveal the dominant processes of community assembly. However, studies of bird communities remain rare and of limited spatial extents. In this study, we described the taxonomic and functional beta diversity patterns of 32 passerine bird assemblages of Yunnan Province, China. We constructed null models based on observed species beta diversity and used multiple regressions on distance matrices to evaluate the relative contributions of deterministic and stochastic processes to passerine bird assemblage dissimilarity. Our results showed significant geographic distance decay in taxonomic and functional similarity, with passerine bird assemblages located in the northwest and southwest of the province having higher functional beta diversity values than expected. Environmental distance and geographic distance explained a similar amount taxonomic beta diversity, but environmental distance explained much more functional beta diversity. Our results suggest that both deterministic and stochastic processes drive taxonomic beta diversity, but that deterministic processes, particularly environmental filtering, play a dominant role in driving functional beta diversity of passerine bird assemblages at sub-national scale.}, - langid = {english}, - keywords = {beta diversity,community assembly,county resolution,environmental filtering,functional traits,passerine bird assemblage}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3545}, - file = {/Users/renatadiaz/Zotero/storage/NPAZ8Y6A/He et al. - 2021 - Relative importance of deterministic and stochasti.pdf;/Users/renatadiaz/Zotero/storage/FBPS2A3L/ecs2.html} -} - -@article{hembry2020, - title = {Ecological {{Interactions}} and {{Macroevolution}}: {{A New Field}} with {{Old Roots}}}, - shorttitle = {Ecological {{Interactions}} and {{Macroevolution}}}, - author = {Hembry, David H. and Weber, Marjorie G.}, - year = {2020}, - month = nov, - journal = {Annual Review of Ecology, Evolution, and Systematics}, - volume = {51}, - number = {1}, - pages = {215--243}, - publisher = {{Annual Reviews}}, - issn = {1543-592X}, - doi = {10.1146/annurev-ecolsys-011720-121505}, - abstract = {Linking interspecific interactions (e.g., mutualism, competition, predation, parasitism) to macroevolution (evolutionary change on deep timescales) is a key goal in biology. The role of species interactions in shaping macroevolutionary trajectories has been studied for centuries and remains a cutting-edge topic of current research. However, despite its deep historical roots, classic and current approaches to this topic are highly diverse. Here, we combine historical and contemporary perspectives on the study of ecological interactions in macroevolution, synthesizing ideas across eras to build a zoomed-out picture of the big questions at the nexus of ecology and macroevolution. We discuss the trajectory of this important and challenging field, dividing research into work done before the 1970s, research between 1970 and 2005, and work done since 2005. We argue that in response to long-standing questions in paleobiology, evidence accumulated to date has demonstrated that biotic interactions (including mutualism) can influence lineage diversification and trait evolution over macroevolutionary timescales, and we outline major open questions for future research in the field.}, - file = {/Users/renatadiaz/Zotero/storage/GSGA9IWM/annurev-ecolsys-011720-121505.html} -} - -@article{henderson2010, - title = {Linking Species Abundance Distributions in Numerical Abundance and Biomass through Simple Assumptions about Community Structure}, - author = {Henderson, Peter A. and Magurran, Anne E.}, - year = {2010}, - month = may, - journal = {Proceedings of the Royal Society B: Biological Sciences}, - volume = {277}, - number = {1687}, - pages = {1561--1570}, - publisher = {{Royal Society}}, - doi = {10.1098/rspb.2009.2189}, - abstract = {Species abundance distributions (SADs) are widely used as a tool for summarizing ecological communities but may have different shapes, depending on the currency used to measure species importance. We develop a simple plotting method that links SADs in the alternative currencies of numerical abundance and biomass and is underpinned by testable predictions about how organisms occupy physical space. When log numerical abundance is plotted against log biomass, the species lie within an approximately triangular region. Simple energetic and sampling constraints explain the triangular form. The dispersion of species within this triangle is the key to understanding why SADs of numerical abundance and biomass can differ. Given regular or random species dispersion, we can predict the shape of the SAD for both currencies under a variety of sampling regimes. We argue that this dispersion pattern will lie between regular and random for the following reasons. First, regular dispersion patterns will result if communities are comprised groups of organisms that use different components of the physical space (e.g. open water, the sea bed surface or rock crevices in a marine fish assemblage), and if the abundance of species in each of these spatial guilds is linked to the way individuals of varying size use the habitat. Second, temporal variation in abundance and sampling error will tend to randomize this regular pattern. Data from two intensively studied marine ecosystems offer empirical support for these predictions. Our approach also has application in environmental monitoring and the recognition of anthropogenic disturbance, which may change the shape of the triangular region by, for example, the loss of large body size top predators that occur at low abundance.}, - keywords = {biomass,community structure,guilds,relative abundance,species abundance,species abundance distribution}, - file = {/Users/renatadiaz/Zotero/storage/FHWLK8XL/Henderson and Magurran - 2010 - Linking species abundance distributions in numeric.pdf} -} - -@article{hernandez2011, - title = {Tale of Two Metrics: Density and Biomass in a Desert Rodent Community}, - shorttitle = {Tale of Two Metrics}, - author = {Hern{\'a}ndez, Lucina and Laundr{\'e}, John W. and {Gonz{\'a}lez-Romero}, Alberto and {L{\'o}pez-Portillo}, Jorge and Grajales, Karina M.}, - year = {2011}, - month = aug, - journal = {Journal of Mammalogy}, - volume = {92}, - number = {4}, - pages = {840--851}, - issn = {0022-2372}, - doi = {10.1644/10-MAMM-A-175.1}, - abstract = {Numerous studies have been made of rodent population and community dynamics, especially in arid ecosystems. Most have centered on understanding how total and species-specific densities of rodents change over time. The standing biomass each species contributes also is important to the energy available to the mesocarnivore community. Although density and standing biomass are related, how they might differ and if those differences are of importance to community structure and function have not received much attention. We analyzed 12 years of rodent density and body mass data from the Chihuahuan Desert in northern Mexico. Data were collected yearly in spring and fall from radial livetrapping webs. Total density and biomass changed significantly in a parallel manner from year to year, and both were related to precipitation and percent cover of grass and forbs. Based on density and biomass, the rodent community was dominated by 2 or 3 principal species. However, on a species-specific level, the numerically dominant species was a small-bodied granivore (Chaetodipus nelsoni), and a large-bodied folivore (Neotoma albigula) dominated in biomass. As total density increased, the proportion contributed by dominant species decreased. As total biomass increased, the proportion in the 2 dominant species increased and accounted for approximately 80\% of total biomass. Over the 12 years of the study, species distributions based on density showed no directional change. In contrast, biomass of the rodent community gradually concentrated in a single, large-bodied folivore, N. albigula. Although total density and biomass responded similarly to precipitation and plant productivity, considerable differences between these 2 characteristics existed in their species-specific contributions to and changes within the community. The significance of these differences relative to foraging strategies and variable feeding opportunities within the community is discussed.}, - file = {/Users/renatadiaz/Zotero/storage/85Q3HMUX/Hernández et al. - 2011 - Tale of two metrics density and biomass in a dese.pdf;/Users/renatadiaz/Zotero/storage/8J9EA7LZ/Hernández et al. - 2011 - Tale of two metrics density and biomass in a dese.pdf;/Users/renatadiaz/Zotero/storage/B3GBYKTM/Hernández et al. - 2011 - Tale of two metrics density and biomass in a dese.pdf} -} - -@article{heske1993, - title = {Effects of Kangaroo Rat Exclusion on Vegetation Structure and Plant Species Diversity in the {{Chihuahuan Desert}}}, - author = {Heske, Edward J. and Brown, James H. and Guo, Qinfeng}, - year = {1993}, - month = oct, - journal = {Oecologia}, - volume = {95}, - number = {4}, - pages = {520--524}, - issn = {1432-1939}, - doi = {10.1007/BF00317436}, - abstract = {Long-term (1977\textendash 90) experimental exclusion of three species of kangaroo rats from study plots in the Chihuahuan Desert resulted in significant increases in abundance of a tall annual grass (Aristida adscensionis) and a perennial bunch grass (Eragrostis lehmanniana). This change in the vegetative cover affected use of these plots by several other rodent species and by foraging birds. The mechanism producing this change probably involves a combination of decreased soil disturbance and reduced predation on large-sized seeds when kangaroo rats are absent. Species diversity of summer annual dicots was greater on plots where kangaroo rats were present, as predicted by keystone predator models. However, it is not clear whether this was caused directly by activities of the kangaroo rats or indirectly as a consequence of the increase in grass cover. No experimental effect on species diversity of winter annual dicots was detected. Our study site was located in a natural transition between desert scrub and grassland, where abiotic conditions and the effects of organisms may be particularly influential in determining the structure and composition of vegetation. Under these conditions kangaroo rats have a dramatic effect on plant cover and species composition.}, - langid = {english} -} - -@article{heske1994, - title = {Long-{{Term Experimental Study}} of a {{Chihuahuan Desert Rodent Community}}: 13 {{Years}} of {{Competition}}}, - shorttitle = {Long-{{Term Experimental Study}} of a {{Chihuahuan Desert Rodent Community}}}, - author = {Heske, Edward J. and Brown, James H. and Mistry, Shahroukh}, - year = {1994}, - journal = {Ecology}, - volume = {75}, - number = {2}, - pages = {438--445}, - issn = {1939-9170}, - doi = {10.2307/1939547}, - abstract = {An experimental study of competition between kangaroo rats (Dipodomys spp.) and other sympatric desert rodents using exclosures with 'semipermeable' fences has been continuously maintained at a site in the northern Chihuahuan Desert since 1977. A new set of experimental manipulations begun in 1988 at the same site repeated this study. As reported previously for this community, exclusion of three species of Dipodomys from both original and new experimental plots resulted in greater abundances of five species of small granivorous rodents (Chaetodipus penicillatus, Perognathus flavus, Peromyscus eremicus, P. maniculatus, Reithrodontomys megalotis) on these plots relative to controls. In contrast, there were no significant treatment effects on the abundances of insectivorous grasshopper mice (Onychomys spp.). The long time lag before the response by small granivores to Dipodomys removal observed in the original experiment was not repeated in the experiment begun in 1988. Long\textemdash term (10 yr) exclusion of kangaroo rats from experimental plots has resulted in changes in vegetative cover, particularly increased grassiness, on these plots relative to controls. We used the repetition of the Dipodomys exclusion experiment in 1988 to evaluate the importance of this potential indirect effect of kangaroo rats on other rodents in this community. By examining differences in rodent capture numbers on the original and new sets of Dipodomys exclusion plots, we could identify four species (C. penicillatus, Perognathus flavus, Peromyscus eremicus, P. maniculatus) whose responses to Kangaroo rat removal reflected direct competition from kangaroo rats, one species (R. megalotis) whose response reflected both direct and indirect (via vegetation changes and habitat selection) effects, and two species (Sigmodon hispidus, S. fulviventer) whose responses reflected only vegetation\textemdash mediated effects. The continuous presence of competition between small granivores and kangaroo rats over the 13\textemdash yr study despite large, specie\textemdash specific fluctuations in abundances suggests that competition is pervasive within this community.}, - copyright = {\textcopyright{} 1994 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1939547}, - file = {/Users/renatadiaz/Zotero/storage/J9H455VY/Heske et al. - 1994 - Long-Term Experimental Study of a Chihuahuan Deser.pdf;/Users/renatadiaz/Zotero/storage/CXDZKUMX/1939547.html;/Users/renatadiaz/Zotero/storage/J47B9AVV/1939547.html} -} - -@article{hocking2013, - title = {Salmon Subsidize an Escape from a Size Spectrum}, - author = {Hocking, Morgan D. and Dulvy, Nicholas K. and Reynolds, John D. and Ring, Richard A. and Reimchen, Thomas E.}, - year = {2013}, - month = feb, - journal = {Proceedings of the Royal Society B: Biological Sciences}, - volume = {280}, - number = {1753}, - pages = {20122433}, - publisher = {{Royal Society}}, - doi = {10.1098/rspb.2012.2433}, - abstract = {A general rule in ecology is that the abundance of species or individuals in communities sharing a common energy source decreases with increasing body size. However, external energy inputs in the form of resource subsidies can modify this size spectrum relationship. Here, we provide the first test of how a marine resource subsidy can affect size spectra of terrestrial communities, based on energy derived from Pacific salmon carcasses affecting a forest soil community beside streams in western Canada. Using both species-based and individual approaches, we found size structuring in this forest soil community, and transient community-wide doubling of standing biomass in response to energy pulses from Pacific salmon carcasses. One group of species were clear outliers in the middle of the size spectrum relationship: larval calliphorid and dryomyzid flies, which specialize on salmon carcasses, and which showed a tenfold increase in biomass in their size class when salmon were available. Thus, salmon subsidize their escape from the size spectrum. These results suggest that using a size-based perspective of resource subsidies can provide new insights into the structure and functioning of food webs.}, - file = {/Users/renatadiaz/Zotero/storage/ABUE93X6/Hocking et al. - 2013 - Salmon subsidize an escape from a size spectrum.pdf;/Users/renatadiaz/Zotero/storage/82DUX63Y/rspb.2012.html} -} - -@article{hoffmann1995, - title = {Effects of {{Selective Seed Predation}} by {{Rodents}} on {{Shortgrass Establishment}}}, - author = {Hoffmann, Lyn A. and Redente, Edward F. and McEwen, Lowell C.}, - year = {1995}, - journal = {Ecological Applications}, - volume = {5}, - number = {1}, - pages = {200--208}, - issn = {1939-5582}, - doi = {10.2307/1942063}, - abstract = {Our experiment tested whether selective seed predation by rodents affects the establishment of blue grama (Bouteloua gracilis) and buffalo grass (Buchloe dactyloides) at a disturbed site in the Colorado shortgrass steppe. We hypothesized that foraging rodent granivores respond positively to large seed sizes and to high seed densities, and we predicted that intensive foraging would constrain grass establishment. Capture-recapture studies confirmed that heteromyid granivores, kangaroo rats (Dipodomys ordii) and hispid pocket mice (Perognathus hispidus), comprised 48\% of the local rodent community. Seeds of blue grama and buffalo grass were shallowly planted at three densities in replicated plots within and outside rodent exclosures. The frequency of digging in seeded rows (seed predation) and the frequency of herbivory on seedling were calculated. We assessed grass establishment using seedling frequency and harvested aboveground biomass. Seed foraging was related positively to seed size, but foraging responses to seed densities were not confirmed. Herbivory on seedlings was not intensive and was similar between the two grasses. Seedling frequency and harvested biomass numbers for the species with the larger seeds, buffalo grass, were reduced more in rodent-accessible plots than were values for blue grama. Rodent seed predation can constrain the establishment of large-seeded species, but results should be interpreted to reflect site-specific conditions and the characteristics of seeded species.}, - copyright = {\textcopyright{} 1995 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1942063} -} - -@article{holling1992, - title = {Cross-{{Scale Morphology}}, {{Geometry}}, and {{Dynamics}} of {{Ecosystems}}}, - author = {Holling, C. S.}, - year = {1992}, - journal = {Ecological Monographs}, - volume = {62}, - number = {4}, - pages = {447--502}, - issn = {1557-7015}, - doi = {10.2307/2937313}, - abstract = {This paper tests the proposition that a small set of plant, animal, and abiotic processes structure ecosystems across scales in time and space. Earlier studies have suggested that these key structuring processes establish a small number of dominant temporal frequencies that entrain other processes. These frequencies often differ from each other by at least an order of magnitude. If true, ecosystems therefore will have a few dominant frequencies that are endogenously driven and that are discontinuously distributed. This paper additionally tests the proposition that these structuring processes should also generate a discontinuous distribution of spatial structures coupled with the discontinuous frequencies. If that is the case, animals living in specific landscapes should demonstrate the existence of this lumpy architecture by showing gaps in the distribution of their sizes. This proved to be the case for birds and mammals of the boreal region forest and the short\textemdash grass prairie. Alternative hypotheses to explain the body mass clumps include architectural, developmental, historical, and trophic causes. These were all tested by comparing body\textemdash mass clump distributions (1) in ecosystems having different spatial structures (forest, grassland, and marine pelagic) and (2) in different animal groups having different body plans (birds and mammals) or feeding habits (carnivore, omnivore, and herbivore). The only hypothesis that could not be rejected is that the body\textemdash mass clumps are entrained by discontinuous hierarchical structures and textures of the landscape. There is evidence for at least eight distinct habitat 'quanta,' each defined by a distinct texture at a specific range of scales. These eight quanta together cover tens of centimetres to hundreds of kilometres in space and at least months to millennia in time. There is a striking similarity, but not identity, between the clump structure of prairie and boreal animals. This indicates that many processes that form qualitative habitat structure are common to both landscapes or ecosystems, but a few are landscape specific, particularly over larger scales. That conclusion is extended to all terrestrial ecosystems by an analysis of the body\textemdash mass clump structure of all North American birds. In contrast, there are striking differences in clump structure between landscapes and 'waterscapes,' indicating that fundamentally different processes shape structure in terrestrial and open ocean systems. The discontinuous body\textemdash mass structure provides a bioassay of discontinuous ecosystem structure. Mammalian carnivores, omnivores, and herbivores all show the same number of body\textemdash mass clumps, and the gaps in these distributions occur at the same body masses. Mammals and birds show the same number of body\textemdash mass clumps, but the mass gaps for mammals occur at larger sizes than those for birds in such a way that the log\textemdash transformed body\textemdash mass gaps for mammals are correlated linearly with those for birds. Hence there is a simple cross\textemdash calibration between the mammal and bird bioassays. I compiled and analyzed published data on home ranges in order to convert body masses into an absolute linear measure of geometric structures in the landscape. A new and general equation was developed relating home\textemdash range size to body mass, and was tested by reanalyzing published data for mammalian carnivores, omnivores, and herbivores and for birds. I conclude: (1) Birds and mammals of all trophic levels utilize resources in their foraging areas in the same way by measuring the spatial grain of habitat patches with a resolution defined as a function of their size (i.e., the animal's step length or minimum unit of measurement). The step length is a morphological function of the size of animals and is not significantly affected by trophic status or taxonomy of the groups considered. That explains why all trophic levels and both birds and mammals show the same qualitative body\textemdash mass clump structure. (2) Home\textemdash range data can convert the body\textemdash mass data to a quantitative estimate of texture, i.e., of fractal dimension of the landscape. The landscape forms a hierarchy that contains breaks in object sizes, object proximities, and textures at particular scales. Animals also demonstrate a hierarchy of decisions whose target suddenly shifts at specific scales in space and time. The interaction between these two hierarchies produces the discontinuous body\textemdash mass clump structure. The breaks in geometry in the landscape occur because structuring processes exert their influence over defined ranges of scale. The temporal and architectural structure of habitat quanta are in general determined by three classes of processes, each dominating over three different ranges of scale. Vegetative processes that determine plant growth, plant form, and soil structure dominate the formation of texture at fine microscales of centimetres to tens of metres in space and days to decades in time. At the other, macroscale extreme, slow geomorphological processes dominate the formation of a topographic and edaphic structure at large scales of hundreds to thousands of kilometres and centuries to millennia. At the mesoscales in between, contagious disturbance processes such as fire, insect outbreak, plant disease, and water flow dominate the formation of patterns over spatial scales of hundreds of metres to hundreds of kilometres. In addition, the direct impacts of grazing by large herbivores and of human activities, and the indirect effects of large predators and animal disease, further transform spatial patterns over these meso\textemdash scales. These processes operate on time scales of years to decades, making them critically important in determining whether present local, regional, and global human influences will trigger a transition in vegetation types, and, if so, how rapidly. The paper provides a direction for the development of programs to evaluate, monitor, and predict ecosystem and community changes across scales. The necessary research elements include (1) models that incorporate a few scale\textemdash dependent structuring processes to allow cross\textemdash scale analysis; (2) comparative studies of different disturbed and undisturbed landscapes using the animal body\textemdash mass bioassay technique to identify critical scales of ecosystem geometry; (3) analysis of remote imagery to identify spatial discontinuities and regions of scale invariance; and (4) behavioral studies of the hierarchy of animal decisions to identify species groups vulnerable to predicted (using models) or observed (using remote imagery) changes in vegetation geometry.}, - copyright = {\textcopyright{} 1992 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/2937313}, - file = {/Users/renatadiaz/Zotero/storage/MPZLABG7/Holling - Cross-Scale Morphology, Geometry, and Dynamics of .pdf;/Users/renatadiaz/Zotero/storage/U5NQ2WI7/2937313.html} -} - -@article{holt1994, - title = {Simple {{Rules}} for {{Interspecific Dominance}} in {{Systems}} with {{Exploitative}} and {{Apparent Competition}}}, - author = {Holt, Robert D. and Grover, James and Tilman, David}, - year = {1994}, - month = nov, - journal = {The American Naturalist}, - volume = {144}, - number = {5}, - pages = {741--771}, - issn = {0003-0147}, - doi = {10.1086/285705}, - abstract = {Because mechanistic models of interspecific interactions are often complex, one should deliberately seek simple unifying principles that transcend system-specific details. Earlier work on resource competition has led to the "R* rule," which states that a dominant competitor suppresses resources to a lower level than any other competing species. This rule describes the outcome of even ornate models of competition. Here we show that analogous simple rules can characterize systems with predation. We first demonstrate, for a simple two-prey, one-predator model without resource competition but with a predator numerical response leading to apparent competition, that the winning prey supports (and withstands) the higher predator density; that is, the outcome is described by a "P* rule." We then develop a general model in which predation is inflicted evenhandedly on two prey species competing for a single resource and show that the R* and P* rules hold: the winning prey both depresses resources to the lowest level and sustains the higher predator density. We next examine a more complex model with differential predation. Assuming a closed system (i.e., a fixed nutrient pool), we portray the four-dimensional system dynamics in a two-dimensional graphical model, and we assess the domain of applicability of simple dominance rules in more complex systems. We address the generality of our conclusions and end by examining the implications of different, reasonable biological constraints for community structure.}, - file = {/Users/renatadiaz/Zotero/storage/Y2FRA8MS/285705.html} -} - -@book{holyoak2005, - title = {Metacommunities: {{Spatial Dynamics}} and {{Ecological Communities}}}, - shorttitle = {Metacommunities}, - author = {Holyoak, Marcel and Leibold, Mathew A. and Holt, Robert D.}, - year = {2005}, - month = oct, - publisher = {{University of Chicago Press}}, - abstract = {Until recently community ecology\textemdash a science devoted to understanding the patterns and processes of species distribution and abundance\textemdash focused mainly on specific and often limited scales of a single community. Since the 1970s, for example, metapopulation dynamics\textemdash studies of interacting groups of populations connected through movement\textemdash concentrated on the processes of population turnover, extinction, and establishment of new populations. Metacommunities takes the hallmarks of metapopulation theory to the next level by considering a group of communities, each of which may contain numerous populations, connected by species interactions within communities and the movement of individuals between communities. In examining communities open to dispersal, the book unites a broad range of ecological theories, presenting some of the first empirical investigations and revealing the value of the metacommunity approach. The collection of empirical, theoretical, and synthetic chapters in Metacommunities seeks to understand how communities work in fragmented landscapes. Encouraging community ecologists to rethink some of the leading theories of population and community dynamics, Metacommunities urges ecologists to expand the spatiotemporal scales of their research.}, - googlebooks = {J4iy6Jl0a0MC}, - isbn = {978-0-226-35064-6}, - langid = {english}, - keywords = {Nature / Ecology,Nature / General} -} - -@article{houlahan2007, - title = {Compensatory Dynamics Are Rare in Natural Ecological Communities.}, - author = {Houlahan, J. E. and Currie, D. J. and Cottenie, K. and Cumming, G. S. and Ernest, S. K. M. and Findlay, C. S. and Fuhlendorf, S. D. and Stevens, R. D. and Willis, T. J. and Woiwod, I. P. and Wondzell, S. M.}, - year = {2007}, - journal = {Proceedings of the National Academy of Sciences. 104(9): 3273-3277}, - abstract = {Publication from the USDA Forest Service Southern Research Station}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VSQIJB5L/Houlahan et al. - 2007 - Compensatory dynamics are rare in natural ecologic.pdf;/Users/renatadiaz/Zotero/storage/INJBJRUJ/29712.html} -} - -@book{hubbell2001, - title = {The {{Unified Neutral Theory}} of {{Biodiversity}} and {{Biogeography}} ({{MPB-32}})}, - author = {Hubbell, Stephen P.}, - year = {2001}, - publisher = {{Princeton University Press}}, - abstract = {Despite its supreme importance and the threat of its global crash, biodiversity remains poorly understood both empirically and theoretically. This ambitious book presents a new, general neutral theory to explain the origin, maintenance, and loss of biodiversity in a biogeographic context. Until now biogeography (the study of the geographic distribution of species) and biodiversity (the study of species richness and relative species abundance) have had largely disjunct intellectual histories. In this book, Stephen Hubbell develops a formal mathematical theory that unifies these two fields. When a speciation process is incorporated into Robert H. MacArthur and Edward O. Wilson's now classical theory of island biogeography, the generalized theory predicts the existence of a universal, dimensionless biodiversity number. In the theory, this fundamental biodiversity number, together with the migration or dispersal rate, completely determines the steady-state distribution of species richness and relative species abundance on local to large geographic spatial scales and short-term to evolutionary time scales. Although neutral, Hubbell's theory is nevertheless able to generate many nonobvious, testable, and remarkably accurate quantitative predictions about biodiversity and biogeography. In many ways Hubbell's theory is the ecological analog to the neutral theory of genetic drift in genetics. The unified neutral theory of biogeography and biodiversity should stimulate research in new theoretical and empirical directions by ecologists, evolutionary biologists, and biogeographers.}, - isbn = {978-0-691-02128-7} -} - -@article{hughes2008, - title = {Ecological Consequences of Genetic Diversity}, - author = {Hughes, A. Randall and Inouye, Brian D. and Johnson, Marc T. J. and Underwood, Nora and Vellend, Mark}, - year = {2008}, - journal = {Ecology Letters}, - volume = {11}, - number = {6}, - pages = {609--623}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2008.01179.x}, - abstract = {Understanding the ecological consequences of biodiversity is a fundamental challenge. Research on a key component of biodiversity, genetic diversity, has traditionally focused on its importance in evolutionary processes, but classical studies in evolutionary biology, agronomy and conservation biology indicate that genetic diversity might also have important ecological effects. Our review of the literature reveals significant effects of genetic diversity on ecological processes such as primary productivity, population recovery from disturbance, interspecific competition, community structure, and fluxes of energy and nutrients. Thus, genetic diversity can have important ecological consequences at the population, community and ecosystem levels, and in some cases the effects are comparable in magnitude to the effects of species diversity. However, it is not clear how widely these results apply in nature, as studies to date have been biased towards manipulations of plant clonal diversity, and little is known about the relative importance of genetic diversity vs. other factors that influence ecological processes of interest. Future studies should focus not only on documenting the presence of genetic diversity effects but also on identifying underlying mechanisms and predicting when such effects are likely to occur in nature.}, - langid = {english}, - keywords = {Biodiversity,community genetics,ecosystem function,evolutionary ecology,genetic variance,rapid evolution}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2008.01179.x}, - file = {/Users/renatadiaz/Zotero/storage/DQP7W4S9/Hughes et al. - 2008 - Ecological consequences of genetic diversity.pdf;/Users/renatadiaz/Zotero/storage/UC779QNY/j.1461-0248.2008.01179.html} -} - -@article{hughes2015, - title = {Theories and {{Models}} of {{Species Abundance}}}, - author = {Hughes, R. G.}, - year = {2015}, - month = oct, - journal = {The American Naturalist}, - publisher = {{University of Chicago Press}}, - issn = {0003-0147}, - doi = {10.1086/284611}, - abstract = {Three theories of explanation for the observed patterns of species abundance in samples from animal and plant communities are reviewed. These are the nichepreemption hypothesis associated with the ...}, - copyright = {Copyright 1986 The University of Chicago}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/3MC3P483/284611.html} -} - -@article{hughes2017, - title = {Long-{{Term Studies Contribute Disproportionately}} to {{Ecology}} and {{Policy}}}, - author = {Hughes, Brent B. and {Beas-Luna}, Rodrigo and Barner, Allison K. and Brewitt, Kimberly and Brumbaugh, Daniel R. and {Cerny-Chipman}, Elizabeth B. and Close, Sarah L. and Coblentz, Kyle E. and {de Nesnera}, Kristin L. and Drobnitch, Sarah T. and Figurski, Jared D. and Focht, Becky and Friedman, Maya and Freiwald, Jan and Heady, Kristen K. and Heady, Walter N. and Hettinger, Annaliese and Johnson, Angela and Karr, Kendra A. and Mahoney, Brenna and Moritsch, Monica M. and Osterback, Ann-Marie K. and Reimer, Jessica and Robinson, Jonathan and Rohrer, Tully and Rose, Jeremy M. and Sabal, Megan and Segui, Leah M. and Shen, Chenchen and Sullivan, Jenna and Zuercher, Rachel and Raimondi, Peter T. and Menge, Bruce A. and {Grorud-Colvert}, Kirsten and Novak, Mark and Carr, Mark H.}, - year = {2017}, - month = mar, - journal = {BioScience}, - volume = {67}, - number = {3}, - pages = {271--281}, - issn = {0006-3568}, - doi = {10.1093/biosci/biw185}, - abstract = {As the contribution for long-term ecological and environmental studies (LTEES) to our understanding of how species and ecosystems respond to a changing global climate becomes more urgent, the relative number and investment in LTEES are declining. To assess the value of LTEES to advancing the field of ecology, we evaluated relationships between citation rates and study duration, as well as the representation of LTEES with the impact factors of 15 ecological journals. We found that the proportionate representation of LTEES increases with journal impact factor and that the positive relationship between citation rate and study duration is stronger as journal impact factor increases. We also found that the representation of LTEES in reports written to inform policy was greater than their representation in the ecological literature and that their authors particularly valued LTEES. We conclude that the relative investment in LTEES by ecologists and funders should be seriously reconsidered for advancing ecology and its contribution to informing environmental policy.}, - file = {/Users/renatadiaz/Zotero/storage/TZAUXLSI/Hughes et al. - 2017 - Long-Term Studies Contribute Disproportionately to.pdf;/Users/renatadiaz/Zotero/storage/VAXUFIJS/3057250.html} -} - -@article{hurlbert, - title = {The {{Effect}} of {{Energy}} and {{Seasonality}} on {{Avian Species Richness}} and {{Community Composition}}}, - author = {Hurlbert, Allen H and Haskell, John P}, - pages = {15}, - abstract = {We analyzed geographic patterns of richness in both the breeding and winter season in relation to a remotely sensed index of seasonal production (normalized difference vegetation index [NDVI]) and to measures of habitat heterogeneity at four different spatial resolutions. The relationship between avian richness and NDVI was consistent between seasons, suggesting that the way in which available energy is converted to bird species is similar at these ecologically distinct times of year. The number and proportion of migrant species in breeding communities also increased predictably with the degree of seasonality. The NDVI was a much better predictor of seasonal richness at finer spatial scales, whereas habitat heterogeneity best predicted richness at coarser spatial resolutions. While we find strong support for a positive relationship between available energy and species richness, seasonal NDVI explained at most 61\% of the variation in richness. Seasonal NDVI and habitat heterogeneity together explain up to 69\% of the variation in richness.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/3ERYTDHI/Hurlbert and Haskell - The Effect of Energy and Seasonality on Avian Spec.pdf;/Users/renatadiaz/Zotero/storage/P8V4PDSC/Hurlbert and Haskell - The Effect of Energy and Seasonality on Avian Spec.pdf} -} - -@article{hurlbert2004, - title = {Species-Energy Relationships and Habitat Complexity in Bird Communities}, - author = {Hurlbert, Allen H.}, - year = {2004}, - month = aug, - journal = {Ecology Letters}, - volume = {7}, - number = {8}, - pages = {714--720}, - issn = {1461-023X, 1461-0248}, - doi = {10.1111/j.1461-0248.2004.00630.x}, - abstract = {Species\textendash energy theory is a commonly invoked theory predicting a positive relationship between species richness and available energy. The More Individuals Hypothesis (MIH) attempts to explain this pattern, and assumes that areas with greater food resources support more individuals, and that communities with more individuals include more species. Using a large dataset for North American birds, I tested these predictions of the MIH, and also examined the effect of habitat complexity on community structure. I found qualitative support for the relationships predicted by the MIH, however, the MIH alone was inadequate for fully explaining richness patterns. Communities in more productive sites had more individuals, but they also had more even relative abundance distributions such that a given number of individuals yielded a greater number of species. Richness and evenness were also higher in structurally complex forests compared to structurally more simple grasslands when controlling for available energy.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/AQV4NQ74/Hurlbert - 2004 - Species-energy relationships and habitat complexit.pdf} -} - -@article{hutchinson2019, - title = {Seeing the Forest for the Trees: {{Putting}} Multilayer Networks to Work for Community Ecology}, - shorttitle = {Seeing the Forest for the Trees}, - author = {Hutchinson, Matthew C. and Mora, Bernat Bramon and Pilosof, Shai and Barner, Allison K. and K{\'e}fi, Sonia and Th{\'e}bault, Elisa and Jordano, Pedro and Stouffer, Daniel B.}, - year = {2019}, - journal = {Functional Ecology}, - volume = {33}, - number = {2}, - pages = {206--217}, - issn = {1365-2435}, - doi = {10.1111/1365-2435.13237}, - abstract = {A framework for the description and analysis of multilayer networks is established in statistical physics, and calls are increasing for their adoption by community ecologists. Multilayer networks in community ecology will allow space, time and multiple interaction types to be incorporated into species interaction networks. While the multilayer network framework is applicable to ecological questions, it is one thing to be able to describe ecological communities as multilayer networks and another for multilayer networks to actually prove useful for answering ecological questions. Importantly, documenting multilayer network structure requires substantially greater empirical investment than standard ecological networks. In response, we argue that this additional effort is worthwhile and describe a series of research lines where we expect multilayer networks will generate the greatest impact. Inter-layer edges are the key component that differentiate multilayer networks from standard ecological networks. Inter-layer edges join different networks\textemdash termed layers\textemdash together and represent ecological processes central to the species interactions studied (e.g., inter-layer edges representing movement for networks separated in space). Inter-layer edges may take a variety of forms, be species- or network-specific, and be measured with a large suite of empirical techniques. Additionally, the sheer size of ecological multilayer networks also requires some changes to empirical data collection around interaction quantification, collaborative efforts and collation in public databases. Network ecology has already touched on a wide swath of ecology and evolutionary biology. Because network stability and patterns of species linkage are the most developed areas of network ecology, they are a natural starting place for multilayer investigations. However, multilayer networks will also provide novel insights to niche partitioning, the connection between traits and species' interactions, and even the geographic mosaic of co-evolution. Synthesis. Multilayer networks provide a formal way to bring together the study of species interaction networks and the processes that influence them. However, describing inter-layer edges and the increasing amounts of data required represent challenges. The pay-off for added investment will be ecological networks that describe the composition and capture the dynamics of ecological communities more completely and, consequently, have greater power for understanding the patterns and processes that underpin diversity in ecological communities. A plain language summary is available for this article.}, - copyright = {\textcopyright{} 2018 The Authors. Functional Ecology \textcopyright{} 2018 British Ecological Society}, - langid = {english}, - keywords = {ecological community,ecological network,food webs,interaction turnover,multilayer,multiplex,species interactions}, - annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2435.13237}, - file = {/Users/renatadiaz/Zotero/storage/KNW6RCJH/Hutchinson et al. - 2019 - Seeing the forest for the trees Putting multilaye.pdf;/Users/renatadiaz/Zotero/storage/9VZQDHDE/1365-2435.html} -} - -@article{inger2015, - title = {Common {{European}} Birds Are Declining Rapidly While Less Abundant Species' Numbers Are Rising}, - author = {Inger, Richard and Gregory, Richard and Duffy, James P. and Stott, Iain and Vo{\v r}{\'i}{\v s}ek, Petr and Gaston, Kevin J.}, - year = {2015}, - journal = {Ecology Letters}, - volume = {18}, - number = {1}, - pages = {28--36}, - issn = {1461-0248}, - doi = {10.1111/ele.12387}, - abstract = {Biodiversity is undergoing unprecedented global decline. Efforts to slow this rate have focused foremost on rarer species, which are at most risk of extinction. Less interest has been paid to more common species, despite their greater importance in terms of ecosystem function and service provision. How rates of decline are partitioned between common and less abundant species remains unclear. Using a 30-year data set of 144 bird species, we examined Europe-wide trends in avian abundance and biomass. Overall, avian abundance and biomass are both declining with most of this decline being attributed to more common species, while less abundant species showed an overall increase in both abundance and biomass. If overall avian declines are mainly due to reductions in a small number of common species, conservation efforts targeted at rarer species must be better matched with efforts to increase overall bird numbers, if ecological impacts of birds are to be maintained.}, - langid = {english}, - keywords = {Abundance,avian,biomass,birds,common,conservation,declines,ecosystem services,rare,rarity}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12387}, - file = {/Users/renatadiaz/Zotero/storage/4BM8BTW7/Inger et al. - 2015 - Common European birds are declining rapidly while .pdf;/Users/renatadiaz/Zotero/storage/R3J9SJ7E/ele.html} -} - -@article{isaac2013, - title = {The Paradox of Energy Equivalence}, - author = {Isaac, Nick J. B. and Storch, David and Carbone, Chris}, - year = {2013}, - journal = {Global Ecology and Biogeography}, - volume = {22}, - number = {1}, - pages = {1--5}, - issn = {1466-8238}, - doi = {10.1111/j.1466-8238.2012.00782.x}, - abstract = {Energy equivalence, the notion that population energy flux is independent of body mass, has become a key concept in ecology. We argue that energy equivalence is not an ecological `rule', as claimed, but a flawed concept beset by circular reasoning. In fact, the independence of mass and energy flux is a null hypothesis. We show that our mechanistic understanding of size\textendash density relationships (SDRs) follows directly from this null model and the assumption that energy limits abundance. Paradoxically, without this assumption energy equivalence has no meaning and we lack a mechanistic understanding for SDRs. We derive an expression for the strength (r 2) of SDRs under the null model, which provides a framework within which to compare published SDRs. This confirms that tight correlations between mass and abundance are a trivial consequence of the span of body masses considered. Our model implies that energy flux varies by five to six orders of magnitude among similarly sized mammals and to a far greater extent in birds. We conclude that the energetic paradigm can be strengthened by considering alternative, non-energetic, hypotheses.}, - langid = {english}, - keywords = {Abundance,Damuth's rule,ecology,energetics,invariance,macroecology,metabolic scaling,null models,size–density relationship}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1466-8238.2012.00782.x}, - file = {/Users/renatadiaz/Zotero/storage/9UPZT9Z2/Isaac et al. - 2013 - The paradox of energy equivalence.pdf;/Users/renatadiaz/Zotero/storage/M8G6QPZS/j.1466-8238.2012.00782.html} -} - -@article{isbell2011, - title = {High Plant Diversity Is Needed to Maintain Ecosystem Services}, - author = {Isbell, Forest and Calcagno, Vincent and Hector, Andy and Connolly, John and Harpole, W. Stanley and Reich, Peter B. and {Scherer-Lorenzen}, Michael and Schmid, Bernhard and Tilman, David and {van Ruijven}, Jasper and Weigelt, Alexandra and Wilsey, Brian J. and Zavaleta, Erika S. and Loreau, Michel}, - year = {2011}, - month = sep, - journal = {Nature}, - volume = {477}, - number = {7363}, - pages = {199--202}, - publisher = {{Nature Publishing Group}}, - issn = {1476-4687}, - doi = {10.1038/nature10282}, - abstract = {Biodiversity\textendash ecosystem function experiments have shown the importance of a diverse range of species for the health of ecosystems, but the number of species needed to maintain ecosystem functioning and services remains unclear. A meta-analysis of biodiversity research now shows, surprisingly, that 84\% of grassland plant species have promoted ecosystem functioning at least once. Different species were important in different years, in different places and for different functions. These results strongly suggest that most grassland plant species provide ecosystem services. Consequently, even a few extinctions could have a deleterious effect.}, - copyright = {2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, - langid = {english}, - keywords = {Biodiversity,Ecosystem services}, - annotation = {Bandiera\_abtest: a Cg\_type: Nature Research Journals Primary\_atype: Research Subject\_term: Biodiversity;Ecosystem services Subject\_term\_id: biodiversity;ecosystem-services}, - file = {/Users/renatadiaz/Zotero/storage/M6E2MRUV/Isbell et al. - 2011 - High plant diversity is needed to maintain ecosyst.pdf;/Users/renatadiaz/Zotero/storage/3IXUPHCW/nature10282.html} -} - -@article{jarzyna2017, - title = {A near Half-Century of Temporal Change in Different Facets of Avian Diversity}, - author = {Jarzyna, Marta A. and Jetz, Walter}, - year = {2017}, - journal = {Global Change Biology}, - volume = {23}, - number = {8}, - pages = {2999--3011}, - issn = {1365-2486}, - doi = {10.1111/gcb.13571}, - abstract = {Assessments of spatial patterns of biodiversity change are essential to detect a signature of anthropogenic impacts, inform monitoring and conservation programs, and evaluate implications of biodiversity loss to humans. While taxonomic diversity (TD) is the most commonly assessed attribute of biodiversity, it misses the potential functional or phylogenetic implications of species losses or gains for ecosystems. Functional diversity (FD) and phylogenetic diversity (PD) are able to capture these important trait-based and phylogenetic attributes of species, but their changes have to date only been evaluated over limited spatial and temporal extents. Employing a novel framework for addressing detectability, we here comprehensively assess a near half-century of changes in local TD, FD, and PD of breeding birds across much of North America to examine levels of congruency in changes among these biodiversity facets and their variation across spatial and environmental gradients. Time-series analysis showed significant and continuous increases in all three biodiversity attributes until ca. 2000, followed by a slow decline since. Comparison of avian diversity at the beginning and end of the temporal series revealed net increase in TD, FD, and PD, but changes in TD were larger than those in FD and PD, suggesting increasing biotic homogenization of avian assemblages throughout the United States. Changes were greatest at high elevations and latitudes \textendash{} consistent with purported effects of ongoing climate change on biodiversity. Our findings highlight the potential of combining new types of data with novel statistical models to enable a more integrative monitoring and assessment of the multiple facets of biodiversity.}, - langid = {english}, - keywords = {biodiversity,birds,detectability,functional diversity,imperfect detection,occupancy modeling,phylogenetic diversity}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.13571}, - file = {/Users/renatadiaz/Zotero/storage/3EWC56FE/Jarzyna and Jetz - 2017 - A near half-century of temporal change in differen.pdf;/Users/renatadiaz/Zotero/storage/ZZGI859F/Jarzyna and Jetz - 2017 - A near half-century of temporal change in differen.pdf;/Users/renatadiaz/Zotero/storage/BL9TZK79/gcb.html;/Users/renatadiaz/Zotero/storage/P5BDNDHM/gcb.html} -} - -@article{jaynes1957, - title = {Information {{Theory}} and {{Statistical Mechanics}}}, - author = {Jaynes, E. T.}, - year = {1957}, - month = may, - journal = {Physical Review}, - volume = {106}, - number = {4}, - pages = {620--630}, - issn = {0031-899X}, - doi = {10.1103/PhysRev.106.620}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/S7ZIRS4F/Jaynes - 1957 - Information Theory and Statistical Mechanics.pdf;/Users/renatadiaz/Zotero/storage/TTGQH84K/Jaynes - 1957 - Information Theory and Statistical Mechanics.pdf;/Users/renatadiaz/Zotero/storage/BIYX67UX/PhysRev.106.html} -} - -@article{jaynes1982, - title = {On the Rationale of Maximum-Entropy Methods}, - author = {Jaynes, E.T.}, - year = {1982}, - month = sep, - journal = {Proceedings of the IEEE}, - volume = {70}, - number = {9}, - pages = {939--952}, - issn = {1558-2256}, - doi = {10.1109/PROC.1982.12425}, - abstract = {We discuss the relations between maximum-entropy (MAXENT) and other methods of spectral analysis such as the Schuster, Blackman-Tukey, maximum-likelihood, Bayesian, and Autoregressive (AR, ARMA, or ARIMA) models, emphasizing that they are not in conflict, but rather are appropriate in different problems. We conclude that: 1) "Orthodox" sampling theory methods are useful in problems where we have a known model (sampling distribution) for the properties of the noise, but no appreciable prior information about the quantities being estimated. 2) MAXENT is optimal in problems where we have prior information about multiplicities, but no noise. 3) The full Bayesian solution includes both of these as special cases and is needed in problems where we have both prior information and noise. 4) AR models are in one sense a special case of MAXENT, but in another sense they are ubiquitous in all spectral analysis problems with discrete time series. 5) Empirical methods such as Blackman-Tukey, which do not invoke even a likelihood function, are useful in the preliminary, exploratory phase of a problem where our knowledge is sufficient to permit intuitive judgments about how to organize a calculation (smoothing, decimation, windows, prewhitening, padding with zeroes, etc.) but insufficient to set up a quantitative model which would do the proper things for us automatically and optimally.}, - keywords = {Bayesian methods,Feeds,Maximum likelihood estimation,Phase estimation,Phase noise,Physics,Sampling methods,Smoothing methods,Spectral analysis,Statistical distributions}, - file = {/Users/renatadiaz/Zotero/storage/3Z69KFTX/Jaynes - 1982 - On the rationale of maximum-entropy methods.pdf;/Users/renatadiaz/Zotero/storage/BXN5N79U/1456693.html} -} - -@article{ji2020, - title = {Macroecological Dynamics of Gut Microbiota}, - author = {Ji, Brian W. and Sheth, Ravi U. and Dixit, Purushottam D. and Tchourine, Konstantine and Vitkup, Dennis}, - year = {2020}, - month = may, - journal = {Nature Microbiology}, - volume = {5}, - number = {5}, - pages = {768--775}, - publisher = {{Nature Publishing Group}}, - issn = {2058-5276}, - doi = {10.1038/s41564-020-0685-1}, - abstract = {The gut microbiota is now widely recognized as a dynamic ecosystem that plays an important role in health and disease. Although current sequencing technologies make it possible to explore how relative abundances of host-associated bacteria change over time, the biological processes governing microbial dynamics remain poorly understood. Therefore, as in other ecological systems, it is important to identify quantitative relationships describing various aspects of gut microbiota dynamics. In the present study, we use multiple high-resolution time series data obtained from humans and mice to demonstrate that, despite their inherent complexity, gut microbiota dynamics can be characterized by several robust scaling relationships. Interestingly, the observed patterns are highly similar to those previously identified across diverse ecological communities and economic systems, including the temporal fluctuations of animal and plant populations and the performance of publicly traded companies. Specifically, we find power-law relationships describing short- and long-term changes in gut microbiota abundances, species residence and return times, and the correlation between the mean and the temporal variance of species abundances. The observed scaling laws are altered in mice receiving different diets and are affected by context-specific perturbations in humans. We use the macroecological relationships to reveal specific bacterial taxa, the dynamics of which are substantially perturbed by dietary and environmental changes. Overall, our results suggest that a quantitative macroecological framework will be important for characterizing and understanding the complex dynamics of diverse microbial communities.}, - copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VNSIGEQJ/Ji et al. - 2020 - Macroecological dynamics of gut microbiota.pdf;/Users/renatadiaz/Zotero/storage/BJTIPRPQ/s41564-020-0685-1.html} -} - -@article{joanes1998, - title = {Comparing Measures of Sample Skewness and Kurtosis}, - author = {Joanes, D. N. and Gill, C. A.}, - year = {1998}, - journal = {Journal of the Royal Statistical Society: Series D (The Statistician)}, - volume = {47}, - number = {1}, - pages = {183--189}, - issn = {1467-9884}, - doi = {10.1111/1467-9884.00122}, - abstract = {Over the years, various measures of sample skewness and kurtosis have been proposed. Comparisons are made between those measures adopted by well-known statistical computing packages, focusing on bias and mean-squared error for normal samples, and presenting some comparisons from simulation results for non-normal samples}, - langid = {english}, - keywords = {Bias,Kurtosis,Mean-squared error,Skewness}, - annotation = {\_eprint: https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/1467-9884.00122}, - file = {/Users/renatadiaz/Zotero/storage/3XB8U48S/Joanes and Gill - 1998 - Comparing measures of sample skewness and kurtosis.pdf;/Users/renatadiaz/Zotero/storage/UQ3PQMAV/1467-9884.html} -} - -@article{jost2006, - title = {Entropy and Diversity}, - author = {Jost, Lou}, - year = {2006}, - journal = {Oikos}, - volume = {113}, - number = {2}, - pages = {363--375}, - issn = {1600-0706}, - doi = {10.1111/j.2006.0030-1299.14714.x}, - abstract = {Entropies such as the Shannon\textendash Wiener and Gini\textendash Simpson indices are not themselves diversities. Conversion of these to effective number of species is the key to a unified and intuitive interpretation of diversity. Effective numbers of species derived from standard diversity indices share a common set of intuitive mathematical properties and behave as one would expect of a diversity, while raw indices do not. Contrary to Keylock, the lack of concavity of effective numbers of species is irrelevant as long as they are used as transformations of concave alpha, beta, and gamma entropies. The practical importance of this transformation is demonstrated by applying it to a popular community similarity measure based on raw diversity indices or entropies. The standard similarity measure based on untransformed indices is shown to give misleading results, but transforming the indices or entropies to effective numbers of species produces a stable, easily interpreted, sensitive general similarity measure. General overlap measures derived from this transformed similarity measure yield the Jaccard index, S\o rensen index, Horn index of overlap, and the Morisita\textendash Horn index as special cases.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.2006.0030-1299.14714.x}, - file = {/Users/renatadiaz/Zotero/storage/RTHVKGKU/j.2006.0030-1299.14714.html} -} - -@article{kartzinel2014, - title = {Plant and Small-Mammal Responses to Large-Herbivore Exclusion in an {{African}} Savanna: Five Years of the {{UHURU}} Experiment}, - shorttitle = {Plant and Small-Mammal Responses to Large-Herbivore Exclusion in an {{African}} Savanna}, - author = {Kartzinel, Tyler R. and Goheen, Jacob R. and Charles, Grace K. and DeFranco, Elyse and Maclean, Janet E. and Otieno, Tobias O. and Palmer, Todd M. and Pringle, Robert M.}, - year = {2014}, - journal = {Ecology}, - volume = {95}, - number = {3}, - pages = {787--787}, - issn = {1939-9170}, - doi = {10.1890/13-1023R.1}, - abstract = {Assessing the direct and indirect consequences of nonrandom species removal within guilds of strongly interacting species, such as large mammalian herbivores, is an important goal in basic and applied ecology. The ecological impacts of such perturbations are often contingent on abiotic conditions, which have hindered efforts to generalize the results of field experiments. Thus, there is a need for experiments that selectively remove different species from ecologically important guilds and that are replicated across environmental gradients. In 2008, we constructed a series of size-selective large-herbivore exclosures across a natural rainfall gradient in semi-arid Kenyan savanna. This experiment (``UHURU'', for ungulate herbivory under rainfall uncertainty) aims to (a) characterize the effects of successively removing the largest size classes of herbivores from the system and (b) evaluate how the direction and magnitude of these effects are shaped by variation in precipitation regimes. UHURU consists of three electrically fenced herbivore-exclusion treatments and an unfenced control, applied to blocks of contiguous 1-ha plots. The three fenced treatments are: ``Mega'' (exclusion of elephants and giraffes only); ``Meso'' (exclusion of both megaherbivores and mesoherbivores, {$\sim$}40 kg and larger); and ``Total'' (exclusion of all herbivores {$\geq$}5 kg). Each block of treatments is replicated three times at each of three sites along the 20-km rainfall gradient (increasing from 439 mm/yr in the north to 639 mm/yr in the south, with little background variation in soil attributes and species composition). We present data, spanning 2008\textendash 2013, from (a) biannual surveys of understory plants at 49 staked grid points within each of the 36 1-ha plots (1764 total stakes); (b) annual woody-plant censuses within the central 0.36 ha of each plot; (c) annual and semi-annual monitoring of individually marked woody plants; (d) small-mammal capture\textendash mark\textendash recapture sessions conducted every other month in total-exclusion and open plots; (e) daily rainfall monitoring throughout the course of the experiment; and (f) quarterly large-mammal dung surveys.}, - langid = {english}, - keywords = {body size,climate,competition and facilitation,ecological field experiments,elephants,extinction,indirect species interactions,Kenya (East Africa),rodents,top-down control,ungulate herbivory}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/13-1023R.1}, - file = {/Users/renatadiaz/Zotero/storage/U8C98DQ2/Kartzinel et al. - 2014 - Plant and small-mammal responses to large-herbivor.pdf;/Users/renatadiaz/Zotero/storage/LI8CX789/13-1023R.html} -} - -@article{kawecki2008, - title = {Adaptation to {{Marginal Habitats}}}, - author = {Kawecki, Tadeusz J.}, - year = {2008}, - journal = {Annual Review of Ecology, Evolution, and Systematics}, - volume = {39}, - pages = {321--342}, - publisher = {{Annual Reviews}}, - issn = {1543-592X}, - abstract = {The ability to adapt to marginal habitats, in which survival and reproduction are initially poor, plays a crucial role in the evolution of ecological niches and species ranges. Adaptation to marginal habitats may be limited by genetic, developmental, and functional constraints, but also by consequences of demographic characteristics of marginal populations. Marginal populations are often sparse, fragmented, prone to local extinctions, or are demographic sinks subject to high immigration from high-quality core habitats. This makes them demographically and genetically dependent on core habitats and prone to gene flow counteracting local selection. Theoretical and empirical research in the past decade has advanced our understanding of conditions that favor adaptation to marginal habitats despite those limitations. This review is an attempt at synthesis of those developments and of the emerging conceptual framework.} -} - -@article{keil2018, - title = {Macroecological and Macroevolutionary Patterns Emerge in the Universe of {{GNU}}/{{Linux}} Operating Systems}, - author = {Keil, Petr and MacDonald, A. a. M. and Ramirez, Kelly S. and Bennett, Joanne M. and {Garc{\'i}a-Pe{\~n}a}, Gabriel E. and Yguel, Benjamin and Bourgeois, B{\'e}renger and Meyer, Carsten}, - year = {2018}, - journal = {Ecography}, - volume = {41}, - number = {11}, - pages = {1788--1800}, - issn = {1600-0587}, - doi = {10.1111/ecog.03424}, - abstract = {What leads to classically recognized patterns of biodiversity remains an open and contested question. It remains unknown if observed patterns are generated by biological or non-biological mechanisms, or if we should expect the patterns to emerge in non-biological systems. Here, we employ analogies between GNU/Linux operating systems (distros), a non-biological system, and biodiversity, and we look for a number of well-established ecological and evolutionary patterns in the Linux universe. We demonstrate that patterns of the Linux universe generally match macroecological patterns. Particularly, Linux distro commonness and rarity follow a skewed distribution with a clear excess of rare distros, we observed a power law mean-variance scaling of temporal fluctuation, but there is only a weak relationship between niche breadth (number of software packages) and commonness. The diversity in the Linux universe also follows general macroevolutionary patterns: the number of phylogenetic lineages increases linearly through time, with clear per-species diversification and extinction slowdowns, something that has been indirectly estimated, but not directly observed in biology. Moreover, the composition of functional traits (software packages) exhibits significant phylogenetic signal. The emergence of macroecological patterns across Linux suggests that the patterns are produced independently of system identity, which points to the possibility of non-biological drivers of fundamental biodiversity patterns. At the same time, our study provides a step towards using Linux as a model system for exploring macroecological and macroevolutionary patterns.}, - copyright = {\textcopyright{} 2018 The Authors}, - langid = {english}, - keywords = {complex systems,cultural evolution,Debian,speciation,species-abundance distribution,Taylor's power law}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.03424}, - file = {/Users/renatadiaz/Zotero/storage/TGG5QL96/Keil et al. - 2018 - Macroecological and macroevolutionary patterns eme.pdf;/Users/renatadiaz/Zotero/storage/AMN2XXTD/ecog.html} -} - -@article{keith2009, - title = {Taxonomic Homogenization of Woodland Plant Communities over 70 Years}, - author = {Keith, Sally A. and Newton, Adrian C. and Morecroft, Michael D. and Bealey, Clive E. and Bullock, James M.}, - year = {2009}, - month = oct, - journal = {Proceedings of the Royal Society B: Biological Sciences}, - volume = {276}, - number = {1672}, - pages = {3539--3544}, - publisher = {{Royal Society}}, - doi = {10.1098/rspb.2009.0938}, - abstract = {Taxonomic homogenization (TH) is the increasing similarity of the species composition of ecological communities over time. Such homogenization represents a form of biodiversity loss and can result from local species turnover. Evidence for TH is limited, reflecting a lack of suitable historical datasets, and previous analyses have generated contrasting conclusions. We present an analysis of woodland patches across a southern English county (Dorset) in which we quantified 70 years of change in the composition of vascular plant communities. We tested the hypotheses that over this time patches decreased in species richness, homogenized, or shifted towards novel communities. Although mean species richness at the patch scale did not change, we found increased similarity in species composition among woodlands over time. We concluded that the woodlands have undergone TH without experiencing declines in local diversity or shifts towards novel communities. Analysis of species characteristics suggested that these changes were not driven by non-native species invasions or climate change, but instead reflected reorganization of the native plant communities in response to eutrophication and increasingly shaded conditions. These analyses provide, to our knowledge, the first direct evidence of TH in the UK and highlight the potential importance of this phenomenon as a contributor to biodiversity loss.}, - keywords = {biodiversity,biotic homogenization,conservation,environmental change}, - file = {/Users/renatadiaz/Zotero/storage/258P7HW3/Keith et al. - 2009 - Taxonomic homogenization of woodland plant communi.pdf} -} - -@article{kelt2011, - title = {Comparative Ecology of Desert Small Mammals: A Selective Review of the Past 30 Years}, - shorttitle = {Comparative Ecology of Desert Small Mammals}, - author = {Kelt, Douglas A.}, - year = {2011}, - month = dec, - journal = {Journal of Mammalogy}, - volume = {92}, - number = {6}, - pages = {1158--1178}, - publisher = {{Oxford Academic}}, - issn = {0022-2372}, - doi = {10.1644/10-MAMM-S-238.1}, - abstract = {Abstract. Rooted in the conceptual revolutions of the 1960s and 1970s, contemporary research on the ecology of desert small mammals has progressed markedly in}, - langid = {english}, - keywords = {Africa,bottom-up control,competition,dependent habitat selection,ecological engineers,find buried seeds,food-hoarding behavior,foraging,hairy-footed gerbils,keystone species,North America,north-central chile,Palearctic,plant-species diversity,predation,rats dipodomys-merriami,South America,tucos ctenomys-mendocinus,vizcacha lagostomus-maximus}, - file = {/Users/renatadiaz/Zotero/storage/JAXG8FZX/Kelt - 2011 - Comparative ecology of desert small mammals a sel.pdf;/Users/renatadiaz/Zotero/storage/SNS3QVQI/Kelt - 2011 - Comparative ecology of desert small mammals a sel.pdf;/Users/renatadiaz/Zotero/storage/TWHLS3LK/957842.html} -} - -@article{kelt2015, - title = {Energetic Compensation Is Historically Contingent and Not Supported for Small Mammals in {{South American}} or {{Asian}} Deserts}, - author = {Kelt, Douglas A. and Aliperti, Jaclyn R. and Meserve, Peter L. and Milstead, W. Bryan and Previtali, M. Andrea and Gutierrez, Julio R.}, - year = {2015}, - month = jun, - journal = {Ecology}, - volume = {96}, - number = {6}, - pages = {1702--1712}, - publisher = {{Wiley}}, - address = {{Hoboken}}, - issn = {0012-9658}, - doi = {10.1890/14-1569.1}, - abstract = {Understanding the nature of faunal assembly and community structure remains central to ecology. Research in North American deserts and some tropical forests provides evidence of energetic compensation and zero-sum dynamics, suggesting that species in some natural assemblages may be replaced with limited impact on ecosystem function. Experimental removal of a dominant small mammal (degu, Octodon degus) from replicate plots in semiarid coastal thorn-scrub habitat in north-central Chile revealed no evidence for energetic or functional compensation; energy consumption remained significantly lower on degu exclusions relative to control plots after 17 years of exclusion. This occurred in spite of the fact that the geographic species pools for South American sites generally are similar in size to those of most North American sites (mean and median number of species, 16.3 and 21.5 vs. 21.0 and 20, respectively). A macroecological assessment of energetically equivalent species at 394 arid sites in North America, the Gobi Desert, and South America indicated that the number of potentially equivalent species was lower than (Gobi) or similar to (South America) that found in North America, but when segregated by trophic groups, these faunas differed markedly. North American sites included large numbers of granivorous species whereas South American sites were dominated by omnivores. The more general trophic strategy in the latter sites would be expected to facilitate compensatory responses within local faunas, suggesting either that our site is anomalous or that other factors are governing local dynamics. Further research is needed to understand the generality of compensatory dynamics within natural systems, as this mechanism has direct relevance to discussions on ecological resilience in the face of ongoing environmental change.}, - langid = {english}, - keywords = {biotic interactions,community ecology,community structure,degu,deserts,ecology,energetic compensation,feeding-habits,functional redundancy,functional redundancy,historical contingency,new-world,north-central chile,north-central Chile,Octodon degus,rodent,scrub community,species coexistence,species redundancy,trophic strategy,zero-sum,zero-sum dynamics,zero-sum dynamics}, - annotation = {WOS:000356021700025}, - file = {/Users/renatadiaz/Zotero/storage/BFEGBJ2Y/Kelt et al. - 2015 - Energetic compensation is historically contingent .pdf;/Users/renatadiaz/Zotero/storage/FXKHBUUA/Kelt et al. - 2015 - Energetic compensation is historically contingent .pdf;/Users/renatadiaz/Zotero/storage/YUCIE2IR/Kelt et al. - 2015 - Energetic compensation is historically contingent .pdf;/Users/renatadiaz/Zotero/storage/3U4Y3I7P/14-1569.html} -} - -@article{kendall1998, - title = {{The macroecology of population dynamics: Taxonomic and biogeographic patterns in population cycles}}, - shorttitle = {{The macroecology of population dynamics}}, - author = {Kendall, Bruce E. and Prendergast, John and Bj{\o}rnstad, Ottar N.}, - year = {1998}, - month = jan, - journal = {Ecology Letters}, - volume = {1}, - number = {3}, - pages = {160--164}, - publisher = {{Wiley-Blackwell}}, - issn = {1461-023X}, - doi = {10.1046/j.1461-0248.1998.00037.x}, - langid = {English (US)}, - file = {/Users/renatadiaz/Zotero/storage/XJ8SJQH5/Kendall et al. - 1998 - The macroecology of population dynamics Taxonomic.pdf;/Users/renatadiaz/Zotero/storage/FWWSK7L5/the-macroecology-of-population-dynamics-taxonomic-and-biogeograph.html} -} - -@article{kennedy2020, - title = {On the Authenticity of {{COVID-19}} Case Figures}, - author = {Kennedy, Adrian Patrick and Yam, Sheung Chi Phillip}, - year = {2020}, - month = dec, - journal = {PLOS ONE}, - volume = {15}, - number = {12}, - pages = {e0243123}, - publisher = {{Public Library of Science}}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0243123}, - abstract = {In this article, we study the applicability of Benford's law and Zipf's law to national COVID-19 case figures with the aim of establishing guidelines upon which methods of fraud detection in epidemiology, based on formal statistical analysis, can be developed. Moreover, these approaches may also be used in evaluating the performance of public health surveillance systems. We provide theoretical arguments for why the empirical laws should hold in the early stages of an epidemic, along with preliminary empirical evidence in support of these claims. Based on data published by the World Health Organization and various national governments, we find empirical evidence that suggests that both Benford's law and Zipf's law largely hold across countries, and deviations can be readily explained. To the best of our knowledge, this paper is among the first to present a practical application of Zipf's law to fraud detection.}, - langid = {english}, - keywords = {China,Computational linguistics,COVID 19,Epidemiology,Infectious disease surveillance,Public and occupational health,Russia,Virus testing}, - file = {/Users/renatadiaz/Zotero/storage/CFEJNDA7/Kennedy and Yam - 2020 - On the authenticity of COVID-19 case figures.pdf;/Users/renatadiaz/Zotero/storage/MKLN4PRD/Kennedy and Yam - 2020 - On the authenticity of COVID-19 case figures.pdf;/Users/renatadiaz/Zotero/storage/X7JP37NA/article.html} -} - -@book{kerr2001, - title = {The {{Biomass Spectrum}}: {{A Predator-Prey Theory}} of {{Aquatic Production}}}, - shorttitle = {The {{Biomass Spectrum}}}, - author = {Kerr, S. R. and Dickie, L. M.}, - year = {2001}, - month = nov, - pages = {352 Pages}, - publisher = {{Columbia University Press}}, - abstract = {Kerr and Dickie propose the development of a new ecological theory, one that can lead to a more effective remedy for the drastic effects of heavy fishing on natural communities of organisms in both marine and freshwater environments.By plotting the densities of the biomass of all organisms in a given community by body-size classes, the authors provide empirical evidence of what they term "the biomass body-size spectrum" in the world's oceans. After examining this evidence, they propose an underlying theory of predator-prey energy transfer: larger species eat smaller species, providing energy exchange across all species within an ecosystem. Providing the first comprehensive synthesis of the energy flow within the biomass spectrum, this book demonstrates not only a new understanding of the self-organizing properties of ecological production systems but also the potential of the biomass spectrum methodology for offering practical remedies when these natural systems are exploited by humans.}, - isbn = {978-0-231-50734-9} -} - -@article{khamis1997, - title = {The Delta-Corrected {{Kolmogorov-Smirnov}} Test for the Two-Parameter {{Weibull}} Distribution}, - author = {Khamis, H. J.}, - year = {1997}, - month = jun, - journal = {Journal of Applied Statistics}, - volume = {24}, - number = {3}, - pages = {301--318}, - issn = {02664763}, - doi = {10.1080/02664769723701}, - abstract = {SUMMARY Monte Carlo simulation techniques are used to create tables of critical values for the delta-corrected Kolmogorov-Smirnov statistic-a modification of the classical Kolmogorov-Smirnov statistic-for the Weibull distribution with known location parameter and unknown shape and scale parameters. The power of the proposed test is investigated relative to values of delta in the unit interval and relative to a wide variety of alternative distributions. The results indicate that using the delta-correction can lead to as many as 8.4 percentage points more power than can be achieved with the classical Kolmogorov-Smirnov test, with no change in the size of the test. Furthermore, carrying out the delta-corrected test involves no more steps or calculations than for the classical Kolmogorov-Smirnov test. In general, it is shown that a slight modification-or correction-in the definition of the empirical distribution function of the Kolmogorov-Smirnov test can lead to power enhancement without changing the type I error rate of the test. Two examples clearly show the effectiveness of the delta-corrected test. The delta-corrected Kolmogorov-Smirnov test is recommended for testing the goodness of fit to the twoparameter Weibull distribution.}, - keywords = {SIMULATION methods \& models,STATISTICAL hypothesis testing,WEIBULL distribution}, - file = {/Users/renatadiaz/Zotero/storage/8GE5637K/Khamis - 1997 - The delta-corrected Kolmogorov-Smirnov test for th.pdf} -} - -@article{kim2009, - title = {{{SELECTING THE NUMBER OF CHANGE-POINTS IN SEGMENTED LINE REGRESSION}}}, - author = {Kim, Hyune-Ju and Yu, Binbing and Feuer, Eric J.}, - year = {2009}, - month = may, - journal = {Statistica Sinica}, - volume = {19}, - number = {2}, - pages = {597--609}, - issn = {1017-0405}, - abstract = {Segmented line regression has been used in many applications, and the problem of estimating the number of change-points in segmented line regression has been discussed in . This paper studies asymptotic properties of the number of change-points selected by the permutation procedure of . This procedure is based on a sequential application of likelihood ratio type tests, and controls the over-fitting probability by its design. In this paper we show that, under some conditions, the number of change-points selected by the permutation procedure is consistent. Via simulations, the permutation procedure is compared with such information-based criterior as the Bayesian Information Criterion (BIC), the Akaike Information Criterion (AIC), and Generalized Cross Validation (GCV).}, - pmcid = {PMC2737518}, - pmid = {19738935}, - file = {/Users/renatadiaz/Zotero/storage/XX5YX3X6/Kim et al. - 2009 - SELECTING THE NUMBER OF CHANGE-POINTS IN SEGMENTED.pdf} -} - -@article{kim2016, - title = {Consistent Model Selection in Segmented Line Regression}, - author = {Kim, Jeankyung and Kim, Hyune-Ju}, - year = {2016}, - month = mar, - journal = {Journal of Statistical Planning and Inference}, - volume = {170}, - pages = {106--116}, - issn = {0378-3758}, - doi = {10.1016/j.jspi.2015.09.008}, - abstract = {The Schwarz criterion or Bayes Information Criterion (BIC) is often used to select a model dimension, and some variations of the BIC have been proposed in the context of change-point problems. In this paper, we consider a segmented line regression model with an unknown number of change-points and study asymptotic properties of Schwarz type criteria in selecting the number of change-points. Noticing the over-estimating tendency of the traditional BIC observed in some empirical studies and being motivated by asymptotic behavior of the modified BIC proposed by Zhang and Siegmund (2007), we consider a variation of the Schwarz type criterion that applies a harsher penalty equivalent to the model with one additional unknown parameter per segment. For the segmented line regression model without the continuity constraint, we prove the consistency of the number of change-points selected by the criterion with such type of a modification and summarize the simulation results that support the consistency. Further simulations are conducted for the model with the continuity constraint, and we empirically observe that the asymptotic behavior of this modified version of BIC is comparable to that of the criterion proposed by Liu et~al. (1997).}, - langid = {english}, - keywords = {Bayes Information Criterion,Model selection,Segmented line regression}, - file = {/Users/renatadiaz/Zotero/storage/JNAQVYFY/Kim and Kim - 2016 - Consistent model selection in segmented line regre.pdf;/Users/renatadiaz/Zotero/storage/FCAMEJI6/S0378375815001627.html} -} - -@article{kimura1968, - title = {Genetic Variability Maintained in a Finite Population Due to Mutational Production of Neutral and Nearly Neutral Isoalleles*}, - author = {Kimura, Motoo}, - year = {1968}, - month = jun, - journal = {Genetics Research}, - volume = {11}, - number = {3}, - pages = {247--270}, - publisher = {{Cambridge University Press}}, - issn = {1469-5073, 0016-6723}, - doi = {10.1017/S0016672300011459}, - abstract = {1. The average and the effective numbers of alleles maintained in a finite population due to mutational production of neutral isoalleles were studied by mathematical analysis and computer simulation.2. The exact formula was derived for the effective number (ne) of alleles maintained in a population of effective size Ne, assuming that there are K possible allelic states and mutation occurs with equal frequency in all directions. If the number of allelic states is so large that every mutation is to a new, not pre-existing, allele, we have ne = 4Neu+1 - 2Neu2, where u is the mutation rate. Thus, the approximation formula, ne = 4Neu+1, given by Kimura \& Crow (1964) is valid as long as 2Neu2 {$\ll$} 1.3. The formula for the average number of alleles (na) maintained in a population of actual size N and effective size Ne was derived by using the method of diffusion approximation. If every mutation is to a new, not pre-existing, allele, we obtain where M = 4Neu. The average number of alleles as a function of M and N is listed in Table 1.4. In order to check the validity of the diffusion approximations, Monte Carlo experiments were carried out using the computer IBM 7090. The experiments showed that the approximations are satisfactory for practical purposes.5. It is estimated that among the mutations produced by DNA base substitutions, synonymous mutations, that is, those which cause no alterations of amino acids, amount roughly to 0{$\cdot$}2\textendash 0{$\cdot$}3 in vertebrates. Incompletely synonymous mutations, that is, those which lead to substitution of chemically similar amino acids at a different position of the polypeptide chain from the active site and therefore produce almost no phenotypic effects, must be very common. Together with synonymous mutations, they might constitute at least some 40\% of all mutations. These considerations suggest that neutral and nearly neutral mutations must be more common than previously considered.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/QZP4KANN/Kimura - 1968 - Genetic variability maintained in a finite populat.pdf;/Users/renatadiaz/Zotero/storage/8MWJM6LI/A74BD3A5D72ED2C52444FD99DFE483EF.html} -} - -@article{kingman1982, - title = {The Coalescent}, - author = {Kingman, J. F. C.}, - year = {1982}, - month = sep, - journal = {Stochastic Processes and their Applications}, - volume = {13}, - number = {3}, - pages = {235--248}, - issn = {0304-4149}, - doi = {10.1016/0304-4149(82)90011-4}, - abstract = {The n-coalescent is a continuous-time Markov chain on a finite set of states, which describes the family relationships among a sample of n members drawn from a large haploid population. Its transition probabilities can be calculated from a factorization of the chain into two independent components, a pure death process and a discrete-time jump chain. For a deeper study, it is useful to construct a more complicated Markov process in which n-coalescents for all values of n are embedded in a natural way.}, - langid = {english}, - keywords = {coupling,exchangeability,Genetical models,haploid genealogy,jump chain,Markov process,random equivalent relations}, - file = {/Users/renatadiaz/Zotero/storage/XXEDV2MQ/Kingman - 1982 - The coalescent.pdf} -} - -@article{kirkegaard2021, - title = {Superspreading of Airborne Pathogens in a Heterogeneous World}, - author = {Kirkegaard, Julius B. and Mathiesen, Joachim and Sneppen, Kim}, - year = {2021}, - month = may, - journal = {Scientific Reports}, - volume = {11}, - number = {1}, - pages = {11191}, - publisher = {{Nature Publishing Group}}, - issn = {2045-2322}, - doi = {10.1038/s41598-021-90666-w}, - abstract = {Epidemics are regularly associated with reports of superspreading: single individuals infecting many others. How do we determine if such events are due to people inherently being biological superspreaders or simply due to random chance? We present an analytically solvable model for airborne diseases which reveal the spreading statistics of epidemics in socio-spatial heterogeneous spaces and provide a baseline to which data may be compared. In contrast to classical SIR models, we explicitly model social events where airborne pathogen transmission allows a single individual to infect many simultaneously, a key feature that generates distinctive output statistics. We find that diseases that have a short duration of high infectiousness can give extreme statistics such as 20\% infecting more than 80\%, depending on the socio-spatial heterogeneity. Quantifying this by a distribution over sizes of social gatherings, tracking data of social proximity for university students suggest that this can be a approximated by a power law. Finally, we study mitigation efforts applied to our model. We find that the effect of banning large gatherings works equally well for diseases with any duration of infectiousness, but depends strongly on socio-spatial heterogeneity.}, - copyright = {2021 The Author(s)}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/PBAQCYTZ/Kirkegaard et al. - 2021 - Superspreading of airborne pathogens in a heteroge.pdf;/Users/renatadiaz/Zotero/storage/DALBPI9P/s41598-021-90666-w.html} -} - -@article{klug2017, - title = {Analysis of High-Frequency and Long-Term Data in Undergraduate Ecology Classes Improves Quantitative Literacy}, - author = {Klug, Jennifer L. and Carey, Cayelan C. and Richardson, David C. and Darner Gougis, Rebekka}, - year = {2017}, - journal = {Ecosphere}, - volume = {8}, - number = {3}, - pages = {e01733}, - issn = {2150-8925}, - doi = {10.1002/ecs2.1733}, - abstract = {Ecologists are increasingly analyzing long-term and high-frequency sensor datasets as part of their research. As ecology becomes a more data-rich scientific discipline, the next generation of ecologists needs to develop the quantitative literacy required to effectively analyze, visualize, and interpret large datasets. We developed and assessed three modules to teach undergraduate freshwater ecology students both scientific concepts and quantitative skills needed to work with large datasets. These modules covered key ecological topics of phenology, physical mixing, and the balance between primary production and respiration, using lakes as model systems with high-frequency or long-term data. Our assessment demonstrated that participating in these modules significantly increased student comfort using spreadsheet software and their self-reported competence in performing a variety of quantitative tasks. Interestingly, students with the lowest pre-module comfort and skills achieved the biggest gains. Furthermore, students reported that participating in the modules helped them better understand the concepts presented and that they appreciated practicing quantitative skills. Our approach demonstrates that working with large datasets in ecology classrooms helps undergraduate students develop the skills and knowledge needed to help solve complex ecological problems and be more prepared for a data-intensive future.}, - langid = {english}, - keywords = {freshwater ecology,Global Lake Ecological Observatory Network,ice phenology,lake metabolism,lake stratification,Project Environmental Data-Driven Inquiry and Exploration,quantitative skills,teaching modules}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.1733}, - file = {/Users/renatadiaz/Zotero/storage/9BGC6EWJ/Klug et al. - 2017 - Analysis of high-frequency and long-term data in u.pdf;/Users/renatadiaz/Zotero/storage/LJ9W6MQM/ecs2.html} -} - -@article{koffel, - title = {A General Framework for Species-Abundance Distributions: {{Linking}} Traits and Dispersal to Explain Commonness and Rarity}, - shorttitle = {A General Framework for Species-Abundance Distributions}, - author = {Koffel, Thomas and Umemura, Kaito and Litchman, Elena and Klausmeier, Christopher A.}, - journal = {Ecology Letters}, - volume = {n/a}, - number = {n/a}, - issn = {1461-0248}, - doi = {10.1111/ele.14094}, - abstract = {Species-abundance distributions (SADs) describe the spectrum of commonness and rarity in a community. Beyond the universal observation that most species are rare and only a few common, more-precise description of SAD shape is controversial. Furthermore, the mechanisms behind SADs and how they vary along environmental gradients remain unresolved. We lack a general, non-neutral theory of SADs. Here, we develop a trait-based framework, focusing on a local community coupled to the region by dispersal. The balance of immigration and exclusion determines abundances, which vary over orders-of-magnitude. The local trait-abundance distribution (TAD) reflects a transformation of the regional TAD. The left-tail of the SAD depends on scaling exponents of the exclusion function and the regional species pool. More-complex local dynamics can lead to multimodal TADs and SADs. Connecting SADs with trait-based ecological theory provides a way to generate more-testable hypotheses on the controls over commonness and rarity in communities.}, - langid = {english}, - keywords = {competition,mass effects,metacommunity,species-abundance distributions,trait-abundance distributions,trait-based model}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.14094}, - file = {/Users/renatadiaz/Zotero/storage/LFJJSLV5/Koffel et al. - A general framework for species-abundance distribu.pdf;/Users/renatadiaz/Zotero/storage/SE8VTD6H/ele.html} -} - -@article{lamprecht2022, - title = {What {{Do We}} ({{Not}}) {{Know About Research Software Engineering}}?}, - author = {Lamprecht, Anna-Lena and {Martinez-Ortiz}, Carlos and Barker, Michelle and Bartholomew, Sadie L. and Barton, Justin and Hong, Neil Chue and Cohen, Jeremy and Druskat, Stephan and Forest, Jeremy and Grad, Jean-No{\"e}l and Katz, Daniel S. and Richardson, Robin and Rosca, Robert and Schulte, Douwe and Struck, Alexander and Weinzierl, Marion}, - year = {2022}, - month = dec, - journal = {Journal of Open Research Software}, - volume = {10}, - number = {1}, - pages = {11}, - publisher = {{Ubiquity Press}}, - issn = {2049-9647}, - doi = {10.5334/jors.384}, - abstract = {As recognition of the vital importance of software for contemporary research is increasing, Research Software Engineering (RSE) is emerging as a discipline in its own right. We present an inventory of relevant research questions about RSE as a basis for future research and initiatives to advance the field, highlighting selected literature and initiatives. This work is the outcome of a RSE community workshop held as part of the 2020 International Series of Online Research Software Events (SORSE) which identified and prioritized key questions across three overlapping themes: people, policy and infrastructure. Almost half of the questions focus on the people theme, which addresses issues related to career paths, recognition and motivation; recruitment and retention; skills; and diversity, equity and inclusion. However, the people and policy themes have the same number of prioritized questions. We recommend that different types of stakeholders, such as RSE employers and policy makers, take responsibility for supporting or encouraging answering of these questions by organizations that have an interest. Initiatives such as the International Council of RSE Associations should also be engaged in this work.}, - copyright = {Authors who publish with this journal agree to the following terms: Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access ). All third-party images reproduced on this journal are shared under Educational Fair Use. For more information on Educational Fair Use , please see this useful checklist prepared by Columbia University Libraries . All copyright of third-party content posted here for research purposes belongs to its original owners. Unless otherwise stated all references to characters and comic art presented on this journal are \textcopyright, \textregistered{} or \texttrademark{} of their respective owners. No challenge to any owner's rights is intended or should be inferred.}, - langid = {english}, - keywords = {career paths,computational science,eScience,infrastructure,research software engineering,rewards and incentives,science policy,software sustainability,training}, - file = {/Users/renatadiaz/Zotero/storage/7ZGPEGMQ/Lamprecht et al. - 2022 - What Do We (Not) Know About Research Software Engi.pdf} -} - -@article{lamy2017, - title = {The Contribution of Species\textendash Genetic Diversity Correlations to the Understanding of Community Assembly Rules}, - author = {Lamy, Thomas and Laroche, Fabien and David, Patrice and Massol, Fran{\c c}ois and Jarne, Philippe}, - year = {2017}, - journal = {Oikos}, - volume = {126}, - number = {6}, - pages = {759--771}, - issn = {1600-0706}, - doi = {10.1111/oik.03997}, - abstract = {Community genetics aims at understanding how within-species variation, species diversity and environmental factors interact to shape community assembly. An approach that emerged a few years ago has been to quantify the correlation between the neutral genetic diversity of a focal species and species diversity of the surrounding community (species\textendash genetic diversity correlations, or SGDCs). We here review this approach and discuss its interpretative framework in a community ecology context. First, we show that the case for mostly positive SGDCs is probably overstated due to publication bias \textendash{} only 11\% are significantly positive, a fraction comparable to the significantly negative ones. This suggests that variation in area and connectivity among habitat patches, theoretically leading to positive SGDCs, is not the only factor affecting SGDCs. Second, building upon previous contributions, we propose a general framework to identify the multiple factors underpinning SGDCs, and argue that it will help deepen our understanding of community assembly, especially with regard to the ecological factors playing at metacommunity scale. Our framework distinguishes between site and community factors which can affect SGDCs either positively or negatively, depending on whether the focal species and the rest of the community are similar or dissimilar, in terms of realized niches and dispersal abilities. Empirical studies should thus go beyond simply computing SGDCs, and we provide statistical methods (e.g. structural equation modelling) to decompose SGDCs into the multiple contributions of site and community factors. As an example, we use a published dataset (freshwater snail metacommunity), and show how the role of focal population size on SGDCs had hitherto not been detected. We further discuss how considering several focal species and various delimitations of the community may help one to identify clusters of ecologically similar species. We eventually highlight the benefit that SGDC studies would get from integrating {$\beta$}-diversities.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/oik.03997}, - file = {/Users/renatadiaz/Zotero/storage/3SP74ITP/Lamy et al. - 2017 - The contribution of species–genetic diversity corr.pdf;/Users/renatadiaz/Zotero/storage/WUI6B3TJ/oik.html} -} - -@article{laroche2015, - title = {A {{Neutral Theory}} for {{Interpreting Correlations}} between {{Species}} and {{Genetic Diversity}} in {{Communities}}.}, - author = {Laroche, Fabien and Jarne, Philippe and Lamy, Thomas and David, Patrice and Massol, Francois}, - year = {2015}, - month = jan, - journal = {The American Naturalist}, - volume = {185}, - number = {1}, - pages = {59--59}, - publisher = {{The University of Chicago Press}}, - issn = {0003-0147}, - doi = {10.1086/678990}, - abstract = {Spatial patterns of biological diversity have been extensively studied in ecology and population genetics, because they reflect the forces acting on biodiversity. A growing number of studies have found that genetic (within-species) and species diversity can be correlated in space (the so-called species-gene diversity correlation [SGDC]), which suggests that they are controlled by nonindependent processes. Positive SGDCs are generally assumed to arise from parallel responses of genetic and species diversity to variation in site size and connectivity. However, this argument implicitly assumes a neutral model that has yet to be developed. Here, we build such a model to predict SGDC in a metacommunity. We describe how SGDC emerges from competition within sites and variation in connectivity and carrying capacity among sites. We then introduce the formerly ignored mutation process, which affects genetic but not species diversity. When mutation rate is low, our model confirms that variation in the number of migrants among sites creates positive SGDCs. However, when considering high mutation rates, interactions between mutation, migration, and competition can produce negative SGDCs. Neutral processes thus do not always contribute positively to SGDCs. Our approach provides empirical guidelines for interpreting these novel patterns in natura with respect to evolutionary and ecological forces shaping metacommunities.}, - keywords = {coalescence,community genetics,diversity pattern,mainland-island model,neutral theory,SGDC}, - file = {/Users/renatadiaz/Zotero/storage/23DG5QJV/Laroche et al. - 2015 - A Neutral Theory for Interpreting Correlations bet.pdf;/Users/renatadiaz/Zotero/storage/CE84YD9R/Laroche et al. - 2015 - A Neutral Theory for Interpreting Correlations bet.pdf;/Users/renatadiaz/Zotero/storage/KPYVQR9I/Laroche et al. - 2015 - A Neutral Theory for Interpreting Correlations bet.pdf} -} - -@article{lawrence2019, - title = {Geo-Referenced Population-Specific Microsatellite Data across {{American}} Continents, the {{MacroPopGen Database}}}, - author = {Lawrence, Elizabeth R. and Benavente, Javiera N. and Matte, Jean-Michel and Marin, Kia and Wells, Zachery R. R. and Bernos, Tha{\"i}s A. and Krasteva, Nia and Habrich, Andrew and Nessel, Gabrielle A. and Koumrouyan, Ramela Arax and Fraser, Dylan J.}, - year = {2019}, - month = apr, - journal = {Scientific Data}, - volume = {6}, - number = {1}, - pages = {14}, - publisher = {{Nature Publishing Group}}, - issn = {2052-4463}, - doi = {10.1038/s41597-019-0024-7}, - abstract = {Population genetic data from nuclear DNA has yet to be synthesized to allow broad scale comparisons of intraspecific diversity versus species diversity. The MacroPopGen database collates and geo-references vertebrate population genetic data across the Americas from 1,308 nuclear microsatellite DNA studies, 897 species, and 9,090 genetically distinct populations where genetic differentiation (FST) was measured. Caribbean populations were particularly distinguished from North, Central, and South American populations, in having higher differentiation (FST\,=\,0.12 vs. 0.07\textendash 0.09) and lower mean numbers of alleles (MNA\,=\,4.11 vs. 4.84\textendash 5.54). While mammalian populations had lower MNA (4.86) than anadromous fish, reptiles, amphibians, freshwater fish, and birds (5.34\textendash 7.81), mean heterozygosity was largely similar across groups (0.57\textendash 0.63). Mean FST was consistently lowest in anadromous fishes (0.06) and birds (0.05) relative to all other groups (0.09\textendash 0.11). Significant differences in Family/Genera variance among continental regions or taxonomic groups were also observed. MacroPopGen can be used in many future applications including latitudinal analyses, spatial analyses (e.g. central-margin), taxonomic comparisons, regional assessments of anthropogenic impacts on biodiversity, and conservation of wild populations.}, - copyright = {2019 The Author(s)}, - langid = {english}, - keywords = {Biodiversity,Macroecology}, - annotation = {Bandiera\_abtest: a Cc\_license\_type: cc\_publicdomain Cg\_type: Nature Research Journals Primary\_atype: Research Subject\_term: Biodiversity;Macroecology Subject\_term\_id: biodiversity;macroecology}, - file = {/Users/renatadiaz/Zotero/storage/TJLSEXQ9/Lawrence et al. - 2019 - Geo-referenced population-specific microsatellite .pdf;/Users/renatadiaz/Zotero/storage/IVRHRCQB/s41597-019-0024-7.html} -} - -@article{lawton1994, - title = {What {{Do Species Do}} in {{Ecosystems}}?}, - author = {Lawton, John H.}, - year = {1994}, - journal = {Oikos}, - volume = {71}, - number = {3}, - pages = {367--374}, - publisher = {{[Nordic Society Oikos, Wiley]}}, - issn = {0030-1299}, - doi = {10.2307/3545824}, - abstract = {Three aspects of the role of species in ecosystems are reviewed. (1) Theoretically, what are the possible relationships between ecosystem processes (Likens' (1992) 'transformation and flux of energy and matter') and the species richness of communities? (2) Summaries of two experiments with artifically constructed terrestrial ecosystems in the controlled environment facility known as the Ecotron are described. The first draws attention to the role of earthworms as 'ecosystem engineers'; the second explores changes in ecosystem processes in mesocosms assembled with three different levels of biological diversity. (3) Finally, a brief summary of the concept of organisms as ecosystem engineers is provided. The review is one of a growing number of publications that attempt to break down the artificial and potentially damaging barriers that exist between ecosystem ecology and population biology. Loss of plant species may change and impair ecosystem processes under average environmental conditions, and reduce the ability of ecosystems to withstand, and recover from, extreme events. The very existence of some ecosystems depends on particular species - the major autogenic and allogenic engineers that create the system - and all ecosystems are probably modulated and modified to a significant extent by at least one species of engineer.} -} - -@article{lawton1999, - title = {Are {{There General Laws}} in {{Ecology}}?}, - author = {Lawton, John H.}, - year = {1999}, - month = feb, - journal = {Oikos}, - volume = {84}, - number = {2}, - pages = {177}, - issn = {00301299}, - doi = {10.2307/3546712}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/59DSWTY5/Lawton - 1999 - Are There General Laws in Ecology.pdf;/Users/renatadiaz/Zotero/storage/7JEKEV8N/Lawton - 1999 - Are There General Laws in Ecology.pdf;/Users/renatadiaz/Zotero/storage/KD9BC498/Lawton - 1999 - Are There General Laws in Ecology.pdf} -} - -@article{lee2022, - title = {Ten Quick Tips for Deep Learning in Biology}, - author = {Lee, Benjamin D. and Gitter, Anthony and Greene, Casey S. and Raschka, Sebastian and Maguire, Finlay and Titus, Alexander J. and Kessler, Michael D. and Lee, Alexandra J. and Chevrette, Marc G. and Stewart, Paul Allen and {Britto-Borges}, Thiago and Cofer, Evan M. and Yu, Kun-Hsing and Carmona, Juan Jose and Fertig, Elana J. and Kalinin, Alexandr A. and Signal, Brandon and Lengerich, Benjamin J. and Triche, Timothy J. and Boca, Simina M.}, - editor = {Ouellette, Francis}, - year = {2022}, - month = mar, - journal = {PLOS Computational Biology}, - volume = {18}, - number = {3}, - pages = {e1009803}, - issn = {1553-7358}, - doi = {10.1371/journal.pcbi.1009803}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/GT3QJXQD/Lee et al. - 2022 - Ten quick tips for deep learning in biology.pdf} -} - -@article{leibold1996, - title = {A {{Graphical Model}} of {{Keystone Predators}} in {{Food Webs}}: {{Trophic Regulation}} of {{Abundance}}, {{Incidence}}, and {{Diversity Patterns}} in {{Communities}}}, - shorttitle = {A {{Graphical Model}} of {{Keystone Predators}} in {{Food Webs}}}, - author = {Leibold, Mathew A.}, - year = {1996}, - month = may, - journal = {The American Naturalist}, - volume = {147}, - number = {5}, - pages = {784--812}, - issn = {0003-0147, 1537-5323}, - doi = {10.1086/285879}, - langid = {english} -} - -@article{leibold2004, - title = {Biodiversity in Metacommunities: {{Plankton}} as Complex Adaptive Systems?}, - shorttitle = {Biodiversity in Metacommunities}, - author = {Leibold, Mathew A. and Norberg, Jon}, - year = {2004}, - journal = {Limnology and Oceanography}, - volume = {49}, - number = {4part2}, - pages = {1278--1289}, - issn = {1939-5590}, - doi = {10.4319/lo.2004.49.4_part_2.1278}, - abstract = {One of the more intriguing and challenging developments in ecology and in limnology and oceanography is the expansion of the temporal and spatial scales that are being addressed by current work. Researchers are realizing that individual communities and ecosystems are not isolated from each other but rather that they are connected by exchanges of individuals (through dispersal) and materials (through spatial fluxes). From a conceptual perspective, there is a need to develop theories and hypotheses about the roles of these exchanges on different community and ecosystem attributes. Here we focus on the concept of metacommunities, to address how plankton communities are structured and how this may generate patterns of variation in planktonic ecosystems. Our premise is that planktonic systems can be understood in the framework of metacommunities and that the regulation of these metacommunities alter how they work as ``complex adaptive systems.'' We hypothesize that connectivity through dispersal of local communities that are embedded in aquatic metacommunities show a range of dynamic behaviors related to their capacity to respond adaptively to environmental change.}, - copyright = {\textcopyright{} 2004, by the Association for the Sciences of Limnology and Oceanography, Inc.}, - langid = {english}, - annotation = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2004.49.4\_part\_2.1278}, - file = {/Users/renatadiaz/Zotero/storage/JHVV5YUK/Leibold and Norberg - 2004 - Biodiversity in metacommunities Plankton as compl.pdf;/Users/renatadiaz/Zotero/storage/WNTR9HGA/lo.2004.49.4_part_2.html} -} - -@article{leibold2017, - title = {Community Assembly and the Functioning of Ecosystems: How Metacommunity Processes Alter Ecosystems Attributes}, - shorttitle = {Community Assembly and the Functioning of Ecosystems}, - author = {Leibold, Mathew A. and Chase, Jonathan M. and Ernest, S. K. Morgan}, - year = {2017}, - journal = {Ecology}, - volume = {98}, - number = {4}, - pages = {909--919}, - issn = {1939-9170}, - doi = {10.1002/ecy.1697}, - abstract = {Recent work linking community structure and ecosystem function has primarily focused on the effects of local species richness but has neglected the dispersal-dependent processes of community assembly that are ultimately involved in determining community structure and its relation to ecosystems. Here we combine simple consumer-resource competition models and metacommunity theory with discussion of case studies to outline how spatial processes within metacommunities can alter community assembly and modify expectations about how species diversity and composition influence ecosystem attributes at local scales. We argue that when community assembly is strongly limited by dispersal, this can constrain ecosystem functioning by reducing positive selection effects (reducing the probability of the most productive species becoming dominant) even though it may often also enhance complementarity (favoring combinations of species that enhance production even though they may not individually be most productive). Conversely, excess dispersal with strong source-sink relations among heterogeneous habitats can reduce ecosystem functioning by swamping local filters that would normally favor better-suited species. Ecosystem function is thus most likely maximized at intermediate levels of dispersal where both of these effects are minimized. In this scenario, we find that the selection effect is maximized, while complementarity is often reduced and local diversity may often be relatively low. Our synthesis emphasizes that it is the entire set of community assembly processes that affect the functioning of ecosystems, not just the part that determines local species richness.}, - langid = {english}, - keywords = {dispersal limitation,ecosystem function,local diversity,metacommunity,R*,regional diversity,species sorting}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.1697}, - file = {/Users/renatadiaz/Zotero/storage/GSGVAPHK/Leibold et al. - 2017 - Community assembly and the functioning of ecosyste.pdf;/Users/renatadiaz/Zotero/storage/EKJU8W5S/ecy.html} -} - -@article{leibold2017a, - title = {Community Assembly and the Functioning of Ecosystems: How Metacommunity Processes Alter Ecosystems Attributes}, - shorttitle = {Community Assembly and the Functioning of Ecosystems}, - author = {Leibold, Mathew A. and Chase, Jonathan M. and Ernest, S. K. Morgan}, - year = {2017}, - journal = {Ecology}, - volume = {98}, - number = {4}, - pages = {909--919}, - issn = {1939-9170}, - doi = {10.1002/ecy.1697}, - abstract = {Recent work linking community structure and ecosystem function has primarily focused on the effects of local species richness but has neglected the dispersal-dependent processes of community assembly that are ultimately involved in determining community structure and its relation to ecosystems. Here we combine simple consumer-resource competition models and metacommunity theory with discussion of case studies to outline how spatial processes within metacommunities can alter community assembly and modify expectations about how species diversity and composition influence ecosystem attributes at local scales. We argue that when community assembly is strongly limited by dispersal, this can constrain ecosystem functioning by reducing positive selection effects (reducing the probability of the most productive species becoming dominant) even though it may often also enhance complementarity (favoring combinations of species that enhance production even though they may not individually be most productive). Conversely, excess dispersal with strong source-sink relations among heterogeneous habitats can reduce ecosystem functioning by swamping local filters that would normally favor better-suited species. Ecosystem function is thus most likely maximized at intermediate levels of dispersal where both of these effects are minimized. In this scenario, we find that the selection effect is maximized, while complementarity is often reduced and local diversity may often be relatively low. Our synthesis emphasizes that it is the entire set of community assembly processes that affect the functioning of ecosystems, not just the part that determines local species richness.}, - langid = {english}, - keywords = {dispersal limitation,ecosystem function,local diversity,metacommunity,R*,regional diversity,species sorting}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.1697}, - file = {/Users/renatadiaz/Zotero/storage/D76EX859/Leibold et al. - 2017 - Community assembly and the functioning of ecosyste.pdf;/Users/renatadiaz/Zotero/storage/NKUG9YLS/ecy.html} -} - -@article{leigh2021, - title = {Opportunities and Challenges of Macrogenetic Studies}, - author = {Leigh, Deborah M. and {van Rees}, Charles B. and Millette, Katie L. and Breed, Martin F. and Schmidt, Chlo{\'e} and Bertola, Laura D. and Hand, Brian K. and Hunter, Margaret E. and Jensen, Evelyn L. and Kershaw, Francine and Liggins, Libby and Luikart, Gordon and Manel, St{\'e}phanie and Mergeay, Joachim and Miller, Joshua M. and Segelbacher, Gernot and Hoban, Sean and {Paz-Vinas}, Ivan}, - year = {2021}, - month = dec, - journal = {Nature Reviews Genetics}, - volume = {22}, - number = {12}, - pages = {791--807}, - publisher = {{Nature Publishing Group}}, - issn = {1471-0064}, - doi = {10.1038/s41576-021-00394-0}, - abstract = {The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.}, - copyright = {2021 Springer Nature Limited}, - langid = {english}, - keywords = {Conservation genomics,Ecology,Evolutionary biology,Genetic variation}, - file = {/Users/renatadiaz/Zotero/storage/4QZLH5QB/Leigh et al. - 2021 - Opportunities and challenges of macrogenetic studi.pdf;/Users/renatadiaz/Zotero/storage/TBVHVQVK/s41576-021-00394-0.html} -} - -@misc{lenth2021, - title = {Emmeans: {{Estimated Marginal Means}}, Aka {{Least-Squares Means}}}, - author = {Lenth, Russell V.}, - year = {2021} -} - -@article{leopold2021, - title = {Greater Local Diversity under Older Species Pools May Arise from Enhanced Competitive Equivalence}, - author = {Leopold, Devin R. and Fukami, Tadashi}, - year = {2021}, - journal = {Ecology Letters}, - volume = {24}, - number = {2}, - pages = {310--318}, - issn = {1461-0248}, - doi = {10.1111/ele.13647}, - abstract = {Ecological communities typically contain more species when located within geologically older regions. This pattern is traditionally attributed to the long-term accumulation of species in the regional species pool, with local species interactions playing a minor role. We provide evidence suggesting a more important role of local species interactions than generally assumed. We assembled 320 communities of root-associated fungi under 80 species pools, varying species pool richness and the mean age of the sites from which the fungi were collected across a 4-myr soil chronosequence. We found that local diversity increased more with increasing species pool richness when species were from older sites. We also found that older species pools had lower functional and phylogenetic diversity, indicating greater competitive equivalence among species. Our results suggest that older regions have higher local richness not simply because older pools are more speciose but also because species have evolved traits that allow them to locally co-occur.}, - copyright = {\textcopyright{} 2020 John Wiley \& Sons Ltd.}, - langid = {english}, - keywords = {biodiversity,chronosequence,coexistence,community assembly,functional diversity,regional species pool}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13647}, - file = {/Users/renatadiaz/Zotero/storage/XKXGBM6R/Leopold and Fukami - 2021 - Greater local diversity under older species pools .pdf;/Users/renatadiaz/Zotero/storage/89AKH74B/ele.html} -} - -@article{lerman1980, - title = {Fitting {{Segmented Regression Models}} by {{Grid Search}}}, - author = {Lerman, P. M.}, - year = {1980}, - journal = {Journal of the Royal Statistical Society. Series C (Applied Statistics)}, - volume = {29}, - number = {1}, - pages = {77--84}, - publisher = {{[Wiley, Royal Statistical Society]}}, - issn = {0035-9254}, - doi = {10.2307/2346413}, - abstract = {A grid-search method of fitting segmented regression curves with unknown transition points is described and compared with a standard method. It is shown to be suitable for fitting a wider class of models than the standard method and to provide as a by-product a way of making reliable inferences about the abscissae of the transitions.} -} - -@article{levin1992, - title = {The {{Problem}} of {{Pattern}} and {{Scale}} in {{Ecology}}: {{The Robert H}}. {{MacArthur Award Lecture}}}, - shorttitle = {The {{Problem}} of {{Pattern}} and {{Scale}} in {{Ecology}}}, - author = {Levin, Simon A.}, - year = {1992}, - journal = {Ecology}, - volume = {73}, - number = {6}, - pages = {1943--1967}, - issn = {1939-9170}, - doi = {10.2307/1941447}, - abstract = {It is argued that the problem of pattern and scale is the central problem in ecology, unifying population biology and ecosystems science, and marrying basic and applied ecology. Applied challenges, such as the prediction of the ecological causes and consequences of global climate change, require the interfacing of phenomena that occur on very different scales of space, time, and ecological organization. Furthermore, there is no single natural scale at which ecological phenomena should be studied; systems generally show characteristic variability on a range of spatial, temporal, and organizational scales. The observer imposes a perceptual bias, a filter through which the system is viewed. This has fundamental evolutionary significance, since every organism is an 'observer' of the environment, and life history adaptations such as dispersal and dormancy alter the perceptual scales of the species, and the observed variability. It likewise has fundamental significance for our own study of ecological systems, since the patterns that are unique to any range of scales will have unique causes and biological consequences. The key to prediction and understanding lies in the elucidation of mechanisms underlying observed patterns. Typically, these mechanisms operate at different scales than those on which the patterns are observed; in some cases, the patterns must be understood as emerging form the collective behaviors of large ensembles of smaller scale units. In other cases, the pattern is imposed by larger scale constraints. Examination of such phenomena requires the study of how pattern and variability change with the scale of description, and the development of laws for simplification, aggregation, and scaling. Examples are given from the marine and terrestrial literatures.}, - copyright = {\textcopyright{} 1992 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2307/1941447}, - file = {/Users/renatadiaz/Zotero/storage/BURC8H7R/Levin - 1992 - The Problem of Pattern and Scale in Ecology The R.pdf;/Users/renatadiaz/Zotero/storage/WFYVVB52/1941447.html} -} - -@article{levy1997, - title = {New Evidence for the Power-Law Distribution of Wealth}, - author = {Levy, Moshe and Solomon, Sorin}, - year = {1997}, - month = aug, - journal = {Physica A: Statistical Mechanics and its Applications}, - volume = {242}, - number = {1-2}, - pages = {90--94}, - issn = {03784371}, - doi = {10.1016/S0378-4371(97)00217-3}, - abstract = {We present a non-conventional approach for studying the distribution of wealth in society. We analyze data from the 1996 Forbes 400 list of the richest people in the US. Our results confirm that wealth is distributed according to a power law. The measured exponent of the power-law is 1.36. As theoretically predicted, this value is in close agreement with the exponent of the Lrvy distribution of stock market fluctuations.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/38QRUWUE/Levy and Solomon - 1997 - New evidence for the power-law distribution of wea.pdf;/Users/renatadiaz/Zotero/storage/8S9J845K/Levy and Solomon - 1997 - New evidence for the power-law distribution of wea.pdf;/Users/renatadiaz/Zotero/storage/VN8FJEP6/Levy and Solomon - 1997 - New evidence for the power-law distribution of wea.pdf} -} - -@article{lewis, - title = {The Power of Forecasts to Advance Ecological Theory}, - author = {Lewis, Abigail S. L. and Rollinson, Christine R. and Allyn, Andrew J. and Ashander, Jaime and Brodie, Stephanie and Brookson, Cole B. and Collins, Elyssa and Dietze, Michael C. and Gallinat, Amanda S. and {Juvigny-Khenafou}, Noel and Koren, Gerbrand and McGlinn, Daniel J. and Moustahfid, Hassan and Peters, Jody A. and Record, Nicholas R. and Robbins, Caleb J. and Tonkin, Jonathan and Wardle, Glenda M.}, - journal = {Methods in Ecology and Evolution}, - volume = {n/a}, - number = {n/a}, - issn = {2041-210X}, - doi = {10.1111/2041-210X.13955}, - abstract = {Ecological forecasting provides a powerful set of methods for predicting short- and long-term change in living systems. Forecasts are now widely produced, enabling proactive management for many applied ecological problems. However, despite numerous calls for an increased emphasis on prediction in ecology, the potential for forecasting to accelerate ecological theory development remains underrealized. Here, we provide a conceptual framework describing how ecological forecasts can energize and advance ecological theory. We emphasize the many opportunities for future progress in this area through increased forecast development, comparison and synthesis. Our framework describes how a forecasting approach can shed new light on existing ecological theories while also allowing researchers to address novel questions. Through rigorous and repeated testing of hypotheses, forecasting can help to refine theories and understand their generality across systems. Meanwhile, synthesizing across forecasts allows for the development of novel theory about the relative predictability of ecological variables across forecast horizons and scales. We envision a future where forecasting is integrated as part of the toolset used in fundamental ecology. By outlining the relevance of forecasting methods to ecological theory, we aim to decrease barriers to entry and broaden the community of researchers using forecasting for fundamental ecological insight.}, - langid = {english}, - keywords = {ecological forecast,ecological theory,forecast cycle,forecast synthesis,hypothesis testing,modelling,predictability,transferability}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13955}, - file = {/Users/renatadiaz/Zotero/storage/6RZLSICS/Lewis et al. - The power of forecasts to advance ecological theor.pdf;/Users/renatadiaz/Zotero/storage/78GZUSJ8/2041-210X.html} -} - -@article{liow2011, - title = {Red {{Queen}}: From Populations to Taxa and Communities}, - shorttitle = {Red {{Queen}}}, - author = {Liow, Lee Hsiang and Van Valen, Leigh and Stenseth, Nils Chr.}, - year = {2011}, - month = jul, - journal = {Trends in Ecology \& Evolution}, - volume = {26}, - number = {7}, - pages = {349--358}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2011.03.016}, - abstract = {Biotic interactions via the struggle for control of energy and the interactive effects of biota with their physical environment characterize Van Valen's Red Queen (VRQ). Here, we review new evidence for and against a VRQ view of the world from studies of increasing temporal and spatial scales. Interactions among biota and with the physical environment are important for generating and maintaining diversity on diverse timescales, but detailed mechanisms remain poorly understood. We recommend directly estimating the effect of biota and the physical environment on ecological and evolutionary processes. Promising approaches for elucidating VRQ include using mathematical modelling, controlled experimental systems, sampling and processes-oriented approaches for analysing data from natural systems, while paying extra attention to biotic interactions discernable from the fossil record.}, - langid = {english}, - keywords = {climate-change,compensatory dynamics,court jester,diversity,drive speciation,eocene thermal maximum,fossil record,species invasions,time-scales,zero-sum}, - file = {/Users/renatadiaz/Zotero/storage/L468HZE6/S0169534711000863.html} -} - -@article{liu2020, - title = {{{DNA}} Metabarcoding Captures Subtle Differences in Forest Beetle Communities Following Disturbance}, - author = {Liu, Mingxin and Baker, Susan C. and Burridge, Christopher P. and Jordan, Gregory J. and Clarke, Laurence J.}, - year = {2020}, - journal = {Restoration Ecology}, - volume = {28}, - number = {6}, - pages = {1475--1484}, - issn = {1526-100X}, - doi = {10.1111/rec.13236}, - abstract = {DNA metabarcoding is an emerging approach for monitoring biodiversity, but uncertainties remain about its capacity to detect subtle differences in invertebrate community composition comparable to those achievable based on conventional morphological identification. In this study, DNA metabarcoding and morphology-based approaches were compared as tools for investigating whether logging history impacted beetle communities in Tasmanian wet eucalypt forests. We compared 12 unlogged mature forest sites with 12 neighboring regeneration sites that had been logged approximately 55 years previously. The number of species identified based on morphology (173) was close to the number of zero-radius operational taxonomic units (ZOTUs) identified by DNA metabarcoding of cytochrome c oxidase subunit I (COI, 176) and 16S ribosomal RNA (16S, 156) markers. Subtle but significant differences in beetle species composition between regeneration and unlogged mature forests were captured by both morphology-based and COI DNA metabarcoding approaches, but not by 16S DNA metabarcoding. Our results support the suitability of mitochondrial COI for studying invertebrate biodiversity. A slight loss of signal compared to the morphology-based approach may be resolved by developing more comprehensive DNA reference databases. While confirming forest recovery of 48\textendash 58 years did not fully restore mature forest beetle communities, we suggest that DNA metabarcoding can be used for monitoring biodiversity and probing subtle differences in community composition.}, - langid = {english}, - keywords = {biodiversity monitoring,Coleoptera,cytochrome c oxidase subunit I (COI),forest restoration,high-throughput sequencing,metabarcoding}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/rec.13236}, - file = {/Users/renatadiaz/Zotero/storage/HXXPMECN/Liu et al. - 2020 - DNA metabarcoding captures subtle differences in f.pdf;/Users/renatadiaz/Zotero/storage/MZXXEQ3J/rec.html} -} - -@article{lloyd-smith2005, - title = {Superspreading and the Effect of Individual Variation on Disease Emergence}, - author = {{Lloyd-Smith}, J. O. and Schreiber, S. J. and Kopp, P. E. and Getz, W. M.}, - year = {2005}, - month = nov, - journal = {Nature}, - volume = {438}, - number = {7066}, - pages = {355--359}, - publisher = {{Nature Publishing Group}}, - issn = {1476-4687}, - doi = {10.1038/nature04153}, - abstract = {From Typhoid Mary to SARS, it has long been known that some people spread disease more than others. But for diseases transmitted via casual contact, contagiousness arises from a plethora of social and physiological factors, so epidemiologists have tended to rely on population averages to assess a disease's potential to spread. A new analysis of outbreak data shows that individual differences in infectiousness exert powerful influences on the epidemiology of ten deadly diseases. SARS and measles (and perhaps avian influenza) show strong tendencies towards `superspreading events' that can ignite explosive epidemics \textemdash{} but this same volatility makes outbreaks more likely to fizzle out. Smallpox and pneumonic plague, two potential bioterrorism agents, show steadier growth but still differ markedly from the traditional average-based view. These findings are relevant to how emerging diseases are detected and controlled.}, - copyright = {2005 Nature Publishing Group}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/GFJYEQQK/Lloyd-Smith et al. - 2005 - Superspreading and the effect of individual variat.pdf;/Users/renatadiaz/Zotero/storage/PBGNEJKF/Lloyd-Smith et al. - 2005 - Superspreading and the effect of individual variat.pdf;/Users/renatadiaz/Zotero/storage/EGTDXG3B/nature04153.html;/Users/renatadiaz/Zotero/storage/ZLKCBJ5T/nature04153.html} -} - -@article{locey2013, - title = {How Species Richness and Total Abundance Constrain the Distribution of Abundance}, - author = {Locey, Kenneth J. and White, Ethan P.}, - year = {2013}, - journal = {Ecology Letters}, - volume = {16}, - number = {9}, - pages = {1177--1185}, - issn = {1461-0248}, - doi = {10.1111/ele.12154}, - abstract = {The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow-curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R2 values {$>$} 75\%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.}, - copyright = {\textcopyright{} 2013 John Wiley \& Sons Ltd/CNRS}, - langid = {english}, - keywords = {constraints,distribution of wealth,feasible set,hollow curve,macroecology,MaxEnt,species abundance distribution}, - file = {/Users/renatadiaz/Zotero/storage/2MBQXGT4/Locey and White - 2013 - How species richness and total abundance constrain.pdf;/Users/renatadiaz/Zotero/storage/BMXG5794/Locey and White - 2013 - How species richness and total abundance constrain.pdf;/Users/renatadiaz/Zotero/storage/GK88F5GZ/Locey and White - 2013 - How species richness and total abundance constrain.pdf;/Users/renatadiaz/Zotero/storage/Z5H7QGN9/Locey and White - 2013 - How species richness and total abundance constrain.pdf;/Users/renatadiaz/Zotero/storage/2MQGWRCK/ele.html;/Users/renatadiaz/Zotero/storage/5DG7WGXK/ele.html;/Users/renatadiaz/Zotero/storage/AB7I7WA7/ele.html;/Users/renatadiaz/Zotero/storage/V5TXC67D/ele.html} -} - -@article{loreau2004, - title = {Does Functional Redundancy Exist?}, - author = {Loreau, Michel}, - year = {2004}, - month = mar, - journal = {Oikos}, - volume = {104}, - number = {3}, - pages = {606--611}, - issn = {00301299, 16000706}, - doi = {10.1111/j.0030-1299.2004.12685.x}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/4G3R34J9/Loreau - 2004 - Does functional redundancy exist.pdf;/Users/renatadiaz/Zotero/storage/ULA2YF5J/Loreau - 2004 - Does functional redundancy exist.pdf} -} - -@techreport{luiselli2021, - type = {Preprint}, - title = {Detecting the Ecological Footprint of Selection}, - author = {Luiselli, Juliette and Overcast, Isaac and Rominger, Andrew and Ruffley, Megan and Morlon, H{\'e}l{\`e}ne and Rosindell, James}, - year = {2021}, - month = may, - institution = {{Ecology}}, - doi = {10.1101/2021.05.11.442553}, - abstract = {The structure of communities is influenced by many processes, both ecological and evolutionary, but the influence of these processes on biodiversity patterns often remains unclear. The aim of this work is to distinguish the ecological footprint of differing formulations of competition and environmental filtering from that of neutral processes that are invariant to species identity. We build our work on ``massive eco-evolutionary synthesis simulations'' (MESS), which uses information from three biodiversity axes \textendash{} species richness and abundance; population genetic diversity; and trait variation in a phylogenetic context \textendash{} to distinguish between processes with a mechanistic model. We add a new form of competition to MESS that explicitly compares the traits of each pair of individuals, allowing us to distinguish between inter- and intra-specific competition. We find that this addition is essential to properly detect and characterise competition, yielding different results than the existing simpler model that only compares species' traits to the community mean. We find from model selection that neutral forces receive much less support from real systems when trait data is available and incorporated into the inference algorithm.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/B6B3L2UF/Luiselli et al. - 2021 - Detecting the ecological footprint of selection.pdf} -} - -@article{macgregor2019, - title = {Moth Biomass Increases and Decreases over 50 Years in {{Britain}}}, - author = {Macgregor, Callum J. and Williams, Jonathan H. and Bell, James R. and Thomas, Chris D.}, - year = {2019}, - month = dec, - journal = {Nature Ecology \& Evolution}, - volume = {3}, - number = {12}, - pages = {1645--1649}, - issn = {2397-334X}, - doi = {10.1038/s41559-019-1028-6}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/35ST2I62/Macgregor et al. - 2019 - Moth biomass increases and decreases over 50 years.pdf} -} - -@article{magurran2003, - title = {Explaining the Excess of Rare Species in Natural Species Abundance Distributions}, - author = {Magurran, Anne E. and Henderson, Peter A.}, - year = {2003}, - month = apr, - journal = {Nature}, - volume = {422}, - number = {6933}, - pages = {714--716}, - publisher = {{Nature Publishing Group}}, - issn = {1476-4687}, - doi = {10.1038/nature01547}, - abstract = {The observation that a few species in ecological communities are exceptionally abundant, whereas most are rare, prompted the development of species abundance models1,2,3. Nevertheless, despite the large literature on the commonness and rarity of species inspired by these pioneering studies, some widespread empirical patterns of species abundance resist easy explanation4. Notable among these is the observation5 that in large assemblages there are more rare species than the log normal model predicts6,7. Here we use a long-term (21-year) data set, from an estuarine fish community, to show how an ecological community can be separated into two components. Core species, which are persistent, abundant and biologically associated with estuarine habitats, are log normally distributed. Occasional species occur infrequently in the record, are typically low in abundance and have different habitat requirements; they follow a log series distribution. These distributions are overlaid, producing the negative skew that characterizes real data sets.}, - copyright = {2003 Macmillan Magazines Ltd.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/DQ785RSR/Magurran and Henderson - 2003 - Explaining the excess of rare species in natural s.pdf;/Users/renatadiaz/Zotero/storage/W43REPQU/nature01547.html} -} - -@article{magurran2005, - title = {Species Abundance Distributions: Pattern or Process?}, - shorttitle = {Species Abundance Distributions}, - author = {Magurran, A. E.}, - year = {2005}, - journal = {Functional Ecology}, - volume = {19}, - number = {1}, - pages = {177--181}, - issn = {1365-2435}, - doi = {10.1111/j.0269-8463.2005.00930.x}, - langid = {english}, - annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.0269-8463.2005.00930.x}, - file = {/Users/renatadiaz/Zotero/storage/BC3WPXRM/Magurran - 2005 - Species abundance distributions pattern or proces.pdf;/Users/renatadiaz/Zotero/storage/PZQ9EU4S/j.0269-8463.2005.00930.html} -} - -@article{magurran2010, - title = {Long-Term Datasets in Biodiversity Research and Monitoring: Assessing Change in Ecological Communities through Time}, - shorttitle = {Long-Term Datasets in Biodiversity Research and Monitoring}, - author = {Magurran, Anne E. and Baillie, Stephen R. and Buckland, Stephen T. and Dick, Jan McP. and Elston, David A. and Scott, E. Marian and Smith, Rognvald I. and Somerfield, Paul J. and Watt, Allan D.}, - year = {2010}, - month = oct, - journal = {Trends in Ecology \& Evolution}, - series = {Special {{Issue}}: {{Long-term}} Ecological Research}, - volume = {25}, - number = {10}, - pages = {574--582}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2010.06.016}, - abstract = {The growing need for baseline data against which efforts to reduce the rate of biodiversity loss can be judged highlights the importance of long-term datasets, some of which are as old as ecology itself. We review methods of evaluating change in biodiversity at the community level using these datasets, and contrast whole-community approaches with those that combine information from different species and habitats. As all communities experience temporal turnover, one of the biggest challenges is distinguishing change that can be attributed to external factors, such as anthropogenic activities, from underlying natural change. We also discuss methodological issues, such as false alerts and modifications in design, of which users of these data sets need to be aware.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/D8AGT9GZ/Magurran et al. - 2010 - Long-term datasets in biodiversity research and mo.pdf;/Users/renatadiaz/Zotero/storage/XUZSGTL2/S0169534710001552.html} -} - -@book{magurran2011, - title = {Biological {{Diversity}}: {{Frontiers}} in {{Measurement}} and {{Assessment}}}, - shorttitle = {Biological {{Diversity}}}, - author = {Magurran, Anne E. and McGill, Brian J.}, - year = {2011}, - publisher = {{Oxford University Press}}, - address = {{Oxford, UNITED KINGDOM}}, - isbn = {978-0-19-157684-3}, - keywords = {Biodiversity -- Monitoring.,Biodiversity conservation.,Biodiversity.}, - file = {/Users/renatadiaz/Zotero/storage/3A66AVNM/reader.html;/Users/renatadiaz/Zotero/storage/ALVZYID6/reader.html;/Users/renatadiaz/Zotero/storage/CF5CBNE2/detail.html} -} - -@article{magurran2019, - title = {Temporal {$\beta$} Diversity\textemdash{{A}} Macroecological Perspective}, - author = {Magurran, Anne E. and Dornelas, Maria and Moyes, Faye and Henderson, Peter A.}, - year = {2019}, - journal = {Global Ecology and Biogeography}, - volume = {28}, - number = {12}, - pages = {1949--1960}, - issn = {1466-8238}, - doi = {10.1111/geb.13026}, - abstract = {Issue Biodiversity change, that is how the taxonomic identities and abundances of species in ecological systems are changing over time, has two facets: temporal {$\alpha$} diversity and temporal {$\beta$} diversity. To date, temporal {$\alpha$} diversity has received most attention even though compositional shifts in assemblages exceed expectations based on ecological theory. Growing concern about the state of the world's biodiversity highlights the need for better understanding of the extent, and consequences, of compositional reorganization in ecological systems. Challenges Most methods of measuring {$\beta$} diversity have been developed in a spatial context. We discuss the additional challenges involved in the assessment of temporal change, summarize existing methodological approaches, highlight the importance of establishing relevant baselines, and identify the need for appropriate null models of temporal {$\beta$} diversity. Given considerable potential for research on the macroecology of temporal {$\beta$} diversity we suggest future directions and challenges. Conclusions Although data availability remains the main impediment to improved quantification of temporal {$\beta$} diversity at macroecological scales, there are substantial opportunities for improved methodology and theory. Taxonomic {$\beta$} diversity has received most attention, but other dimensions of diversity, including functional and phylogenetic, should be part of integrated assessments of biodiversity change. Future approaches need to be ecologically meaningful and interpretable as well as statistically robust.}, - copyright = {\textcopyright{} 2019 John Wiley \& Sons Ltd}, - langid = {english}, - keywords = {Anthropocene,baseline change,biodiversity theory,biogeography,compositional shifts,null models,richness,temporal turnover,temporal α diversity,temporal β diversity}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.13026}, - file = {/Users/renatadiaz/Zotero/storage/8DDCIKPE/Magurran et al. - 2019 - Temporal β diversity—A macroecological perspective.pdf;/Users/renatadiaz/Zotero/storage/SVKKNAHV/geb.html} -} - -@article{malhi2016, - title = {Megafauna and Ecosystem Function from the {{Pleistocene}} to the {{Anthropocene}}}, - author = {Malhi, Yadvinder and Doughty, Christopher E. and Galetti, Mauro and Smith, Felisa A. and Svenning, Jens-Christian and Terborgh, John W.}, - year = {2016}, - month = jan, - journal = {Proceedings of the National Academy of Sciences}, - volume = {113}, - number = {4}, - pages = {838--846}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.1502540113}, - abstract = {Large herbivores and carnivores (the megafauna) have been in a state of decline and extinction since the Late Pleistocene, both on land and more recently in the oceans. Much has been written on the timing and causes of these declines, but only recently has scientific attention focused on the consequences of these declines for ecosystem function. Here, we review progress in our understanding of how megafauna affect ecosystem physical and trophic structure, species composition, biogeochemistry, and climate, drawing on special features of PNAS and Ecography that have been published as a result of an international workshop on this topic held in Oxford in 2014. Insights emerging from this work have consequences for our understanding of changes in biosphere function since the Late Pleistocene and of the functioning of contemporary ecosystems, as well as offering a rationale and framework for scientifically informed restoration of megafaunal function where possible and appropriate.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/942XT436/Malhi et al. - 2016 - Megafauna and ecosystem function from the Pleistoc.pdf} -} - -@article{marquet2017, - title = {Integrating Macroecology through a Statistical Mechanics of Adaptive Matter}, - author = {Marquet, Pablo A.}, - year = {2017}, - month = oct, - journal = {Proceedings of the National Academy of Sciences}, - volume = {114}, - number = {40}, - pages = {10523--10525}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.1713971114}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/4ECPB26E/Marquet - 2017 - Integrating macroecology through a statistical mec.pdf;/Users/renatadiaz/Zotero/storage/TRXJ385W/Marquet - 2017 - Integrating macroecology through a statistical mec.pdf;/Users/renatadiaz/Zotero/storage/DJSPZVQ5/10523.html} -} - -@article{mascarenhas2020, - title = {Integrating {{Computational Methods}} to {{Investigate}} the {{Macroecology}} of {{Microbiomes}}}, - author = {Mascarenhas, Rilquer and Ruziska, Fl{\'a}via M. and Moreira, Eduardo Freitas and Campos, Amanda B. and Loiola, Miguel and Reis, Kaike and {Trindade-Silva}, Amaro E. and Barbosa, Felipe A. S. and Salles, Lucas and Menezes, Rafael and Veiga, Rafael and Coutinho, Felipe H. and Dutilh, Bas E. and Guimar{\~a}es, Paulo R. and Assis, Ana Paula A. and Ara, Anderson and Miranda, Jos{\'e} G. V. and Andrade, Roberto F. S. and Vilela, Bruno and Meirelles, Pedro Milet}, - year = {2020}, - journal = {Frontiers in Genetics}, - volume = {10}, - pages = {1344}, - issn = {1664-8021}, - doi = {10.3389/fgene.2019.01344}, - abstract = {Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as ``everything is everywhere, but the environment selects'') as well as applied ecological problems, such as those posed by human induced global environmental changes.}, - file = {/Users/renatadiaz/Zotero/storage/LI5STCVS/Mascarenhas et al. - 2020 - Integrating Computational Methods to Investigate t.pdf} -} - -@article{masek2006, - title = {A {{Landsat}} Surface Reflectance Dataset for {{North America}}, 1990-2000}, - author = {Masek, J.G. and Vermote, E.F. and Saleous, N.E. and Wolfe, R. and Hall, F.G. and Huemmrich, K.F. and Gao, Feng and Kutler, J. and Lim, Teng-Kui}, - year = {2006}, - month = jan, - journal = {IEEE Geoscience and Remote Sensing Letters}, - volume = {3}, - number = {1}, - pages = {68--72}, - issn = {1558-0571}, - doi = {10.1109/LGRS.2005.857030}, - abstract = {The Landsat Ecosystem Disturbance Adaptive Processing System (LEDAPS) at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center has processed and released 2100 Landsat Thematic Mapper and Enhanced Thematic Mapper Plus surface reflectance scenes, providing 30-m resolution wall-to-wall reflectance coverage for North America for epochs centered on 1990 and 2000. This dataset can support decadal assessments of environmental and land-cover change, production of reflectance-based biophysical products, and applications that merge reflectance data from multiple sensors [e.g., the Advanced Spaceborne Thermal Emission and Reflection Radiometer, Multiangle Imaging Spectroradiometer, Moderate Resolution Imaging Spectroradiometer (MODIS)]. The raw imagery was obtained from the orthorectified Landsat GeoCover dataset, purchased by NASA from the Earth Satellite Corporation. Through the LEDAPS project, these data were calibrated, converted to top-of-atmosphere reflectance, and then atmospherically corrected using the MODIS/6S methodology. Initial comparisons with ground-based optical thickness measurements and simultaneously acquired MODIS imagery indicate comparable uncertainty in Landsat surface reflectance compared to the standard MODIS reflectance product (the greater of 0.5\% absolute reflectance or 5\% of the recorded reflectance value). The rapid automated nature of the processing stream also paves the way for routine high-level products from future Landsat sensors.}, - keywords = {Adaptive systems,Atmospheric correction,Ecosystems,Landsat,Layout,MODIS,NASA,North America,Production,Reflectivity,remote sensing,Remote sensing,Satellites}, - file = {/Users/renatadiaz/Zotero/storage/P3K33ML8/keywords.html} -} - -@article{matthews, - title = {Systematic Variation in {{North American}} Tree Species Abundance Distributions along Macroecological Climatic Gradients}, - author = {Matthews, Thomas J. and Sadler, Jon P. and Kubota, Yasuhiro and Woodall, Christopher W. and Pugh, Thomas A. M.}, - journal = {Global Ecology and Biogeography}, - volume = {0}, - number = {0}, - issn = {1466-8238}, - doi = {10.1111/geb.12879}, - abstract = {Aim The species abundance distribution (SAD) is a fundamental pattern in macroecology. Understanding how SADs vary spatially, and identifying the variables that drive any change, is important from a theoretical perspective because it enables greater understanding of the factors that underpin the relative abundance of species. However, precise knowledge on how the form of SADs varies across large (continental) scales is limited. Here, we use the shape parameter of the gambin distribution to assess how meta-community-scale SAD shape varies spatially as a function of various climatic variables and dataset characteristics. Location Eastern North America (ENA). Time period Present day. Major taxa studied Trees. Methods Using an extensive continental-scale dataset of 863,930 individual trees in plots across ENA sampled using a standardized method, we use a spatial regression framework to examine the effect of temperature and precipitation on the form of the SAD. We also assess whether the prevalence of multimodality in the SAD varies spatially across ENA as a function of temperature and precipitation, in addition to other sample characteristics. Results We found that temperature, precipitation and species richness can explain two-thirds of the variation in tree SAD form across ENA. Temperature had the largest effect on SAD shape, and it was found that increasing temperature resulted in more logseries-like SAD shapes (i.e. SADs with a relatively higher proportion of rarer species). We also found spatial variation in SAD multimodality as a function of temperature and species richness. Main conclusions Our results indicate that temperature is a key environmental driver governing the form of ENA tree meta-community-scale SADs. This finding has implications for our understanding of local-scale variation in tree abundance and suggests that niche factors and environmental filtering are important in the structuring of ENA tree communities at larger scales.}, - copyright = {\textcopyright{} 2019 John Wiley \& Sons Ltd}, - langid = {english}, - keywords = {climate,compound distribution,gambin,macroecology,sampling effects,species abundance distributions}, - file = {/Users/renatadiaz/Zotero/storage/UYEX2GIY/Matthews et al. - Systematic variation in North American tree specie.pdf;/Users/renatadiaz/Zotero/storage/C3VTSIBP/geb.html} -} - -@article{maurer1988, - title = {Distribution of {{Energy Use}} and {{Biomass Among Species}} of {{North American Terrestrial Birds}}}, - author = {Maurer, Brian A. and Brown, James H.}, - year = {1988}, - month = dec, - journal = {Ecology}, - volume = {69}, - number = {6}, - pages = {1923--1932}, - issn = {00129658}, - doi = {10.2307/1941169}, - abstract = {The distribution of biomass and energy use among species with different body sizes provides an empirical basis for studying ecological processes that determine species diversity. Biomass and energy use distributions were determined for North American terrestrial birds from data on population density and body mass of 380 species and data on energy use obtained from the literature. Using these data, several hypotheses regarding the specific form of biomass (summed for all species in a body size category) and energy use distributions were evaluated. Biomass continued to increase in successive log body mass intervals, but this was not due simply to increasing species numbers. Energy use initially increased in these same intervals but leveled off above a body mass of 80 g. Energy used by average populations of individual species was uniformly distributed between the lower and upper bounds of each log body mass interval. In addition, the upper boundaries on biomass and energy use for individual species paralleled closely the biomass and energy use distributions. Qualitatively similar patterns were obtained for plant- and animal-eating birds considered separately, and for birds in 14 arbitrarily defined subregions of the North American continent. There were important quantitative differences among energy use distributions for the 14 subregions. Subregions at lower latitudes had energy use distributions that were nearly an order of magnitude higher than those of regions at higher latitudes. These results imply that previous hypotheses to explain biomass and energy use distributions were not of sufficient generality to account for both similarities among distributions of very different systems (e.g., birds and aquatic plankton) and spatial variation among systems composed of similar species. A more general hypothesis should consider the importance of inherent physiological constraints on energy use and environmental limitations on energy availability. The processes that influence resource allocation in a large assemblage of many species may result in statistical patterns of energy use and biomass that tend to maximize ecological quantities analogous to entropy in statistical physical systems. Key words: biomass; birds; body size; energetics; macroecology; resource allocation; species diversity; statistical distributions.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VIPTZP9G/Maurer and Brown - 1988 - Distribution of Energy Use and Biomass Among Speci.pdf} -} - -@book{maurer1999, - title = {Untangling Ecological Complexity : The Macroscopic Perspective}, - shorttitle = {Untangling Ecological Complexity}, - author = {Maurer, Brian A.}, - year = {1999}, - publisher = {{University of Chicago Press}}, - isbn = {978-0-226-51133-7}, - keywords = {Biotic communities} -} - -@incollection{maurer2011, - title = {Measurement of Species Diversity}, - booktitle = {Biological {{Diversity}}: {{Frontiers}} in {{Measurement}} and {{Assessment}}}, - author = {Maurer, Brian A. and McGill, Brian J.}, - editor = {Magurran, Anne E. and McGill, Brian J.}, - year = {2011}, - pages = {55--61}, - publisher = {{Oxford University Press}}, - address = {{Oxford, UNITED KINGDOM}}, - isbn = {978-0-19-157684-3}, - keywords = {Biodiversity -- Monitoring.,Biodiversity conservation.,Biodiversity.} -} - -@article{mccoy2012, - title = {Connecticut {{Birds}} and {{Climate Change}}: {{Bergmann}}'s {{Rule}} in the {{Fourth Dimension}}}, - shorttitle = {Connecticut {{Birds}} and {{Climate Change}}}, - author = {McCoy, Dakota E.}, - year = {2012}, - month = jun, - journal = {Northeastern Naturalist}, - volume = {19}, - number = {2}, - pages = {323--334}, - publisher = {{Eagle Hill Institute}}, - issn = {1092-6194, 1938-5307}, - doi = {10.1656/045.019.0213}, - abstract = {Bergmann's Rule notes a correlation between animal size reduction and geographical temperature increase in three dimensions. This study examines bird size change in the context of temperature change in a fourth dimension: time. The body size of six passerine bird species found year-round in Connecticut was measured using museum specimens collected between 1874 and 2009, during which time mean temperature in Connecticut increased by 0.94 \textdegree C (SD = 0.71). Mean wing length significantly decreased from a pre-1955 period (1874\textendash 1952) to a post-1955 period (1958\textendash 2010) for all species combined (P {$<$} 0.0025) and for three of the six species (P {$<$} 0.025), suggesting that some Connecticut passerines exhibit an evolved size decrease since 1874. This study joins a growing body of research suggesting a causal relationship between climate change and animal morphological change, and it demonstrates the importance of museum specimens in documenting such global trends.}, - file = {/Users/renatadiaz/Zotero/storage/IBZGID6J/045.019.0213.html} -} - -@article{mccune2013, - title = {Gains in Native Species Promote Biotic Homogenization over Four Decades in a Human-Dominated Landscape}, - author = {McCune, Jenny L. and Vellend, Mark}, - year = {2013}, - journal = {Journal of Ecology}, - volume = {101}, - number = {6}, - pages = {1542--1551}, - issn = {1365-2745}, - doi = {10.1111/1365-2745.12156}, - abstract = {A long-term perspective is needed to understand how disturbance is affecting plant communities in human-dominated landscapes. Increased human disturbance often results in declining local native species richness, gains in exotic species and a decline in beta diversity. However, it is far from certain whether a general decline in plant diversity is occurring across all disturbed landscapes, and knowledge gaps remain concerning how the spread of exotic species influences beta diversity over long time-scales. We resurveyed 184 vegetation plots in three broad vegetation types on southern Vancouver Island, Canada, originally surveyed in the late 1960s. This landscape has experienced a high degree of human disturbance over the past 40 years due to urbanization. We examined changes in total diversity, local diversity and beta diversity over time. We also compiled information on the traits of each species and tested for correlations between traits and plant species success over four decades. We found striking increases in local and total plant species richness driven by both native and exotic species. The most successful species tended to be exotic, disturbance tolerant, shade tolerant and shrubs. Biotic homogenization occurred, but not as a result of exotic species colonization, instead being significantly correlated with gains in native species. The loss in beta diversity has resulted in a shrinking of the gradient of vegetation types, blurring the distinction between them. Synthesis. Our study shows that human-mediated disturbance is the dominant driver of plant community changes, but the net result has actually been an increase in richness, for each plot and for all plots pooled, and for both natives and exotics, despite a decline in variability among plant communities on the landscape. Contrary to conventional definitions of biotic homogenization, this decline in beta diversity was not correlated with the spread of exotic species, but with the colonization of common, disturbance-tolerant natives.}, - langid = {english}, - keywords = {beta diversity,determinants of plant community diversity and structure,exotic species,human disturbance,life-history traits,resurvey,semi-permanent plots,Vancouver Island}, - annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.12156}, - file = {/Users/renatadiaz/Zotero/storage/KLAL8ZCJ/McCune and Vellend - 2013 - Gains in native species promote biotic homogenizat.pdf;/Users/renatadiaz/Zotero/storage/QCK8SHD5/1365-2745.html} -} - -@article{mcgaughran2015, - title = {Integrating a {{Population Genomics Focus}} into {{Biogeographic}} and {{Macroecological Research}}}, - author = {McGaughran, Angela}, - year = {2015}, - month = nov, - journal = {Frontiers in Ecology and Evolution}, - volume = {3}, - issn = {2296-701X}, - doi = {10.3389/fevo.2015.00132}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/HT4L5NVV/McGaughran - 2015 - Integrating a Population Genomics Focus into Bioge.pdf} -} - -@article{mcgill2003, - title = {Strong and Weak Tests of Macroecological Theory}, - author = {McGill, B.}, - year = {2003}, - month = sep, - journal = {Oikos}, - volume = {102}, - number = {3}, - pages = {679--685}, - issn = {00301299}, - doi = {10.1034/j.1600-0706.2003.12617.x}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/LD96C5SH/McGill - 2003 - Strong and weak tests of macroecological theory.pdf} -} - -@article{mcgill2005, - title = {Community Inertia of {{Quaternary}} Small Mammal Assemblages in {{North America}}}, - author = {McGill, B. J. and Hadly, E. A. and Maurer, B. A.}, - year = {2005}, - month = nov, - journal = {Proceedings of the National Academy of Sciences}, - volume = {102}, - number = {46}, - pages = {16701--16706}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.0504225102}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/KA2NG9UW/McGill et al. - 2005 - Community inertia of Quaternary small mammal assem.pdf} -} - -@article{mcgill2006, - title = {Rebuilding Community Ecology from Functional Traits}, - author = {McGill, Brian J. and Enquist, Brian J. and Weiher, Evan and Westoby, Mark}, - year = {2006}, - month = apr, - journal = {Trends in Ecology \& Evolution}, - volume = {21}, - number = {4}, - pages = {178--185}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2006.02.002}, - abstract = {There is considerable debate about whether community ecology will ever produce general principles. We suggest here that this can be achieved but that community ecology has lost its way by focusing on pairwise species interactions independent of the environment. We assert that community ecology should return to an emphasis on four themes that are tied together by a two-step process: how the fundamental niche is governed by functional traits within the context of abiotic environmental gradients; and how the interaction between traits and fundamental niches maps onto the realized niche in the context of a biotic interaction milieu. We suggest this approach can create a more quantitative and predictive science that can more readily address issues of global change.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/DMNHPQAU/McGill et al. - 2006 - Rebuilding community ecology from functional trait.pdf;/Users/renatadiaz/Zotero/storage/6Y7AG55R/S0169534706000334.html} -} - -@article{mcgill2007, - title = {Species Abundance Distributions: Moving beyond Single Prediction Theories to Integration within an Ecological Framework}, - shorttitle = {Species Abundance Distributions}, - author = {McGill, Brian J. and Etienne, Rampal S. and Gray, John S. and Alonso, David and Anderson, Marti J. and Benecha, Habtamu Kassa and Dornelas, Maria and Enquist, Brian J. and Green, Jessica L. and He, Fangliang and Hurlbert, Allen H. and Magurran, Anne E. and Marquet, Pablo A. and Maurer, Brian A. and Ostling, Annette and Soykan, Candan U. and Ugland, Karl I. and White, Ethan P.}, - year = {2007}, - month = oct, - journal = {Ecology Letters}, - volume = {10}, - number = {10}, - pages = {995--1015}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2007.01094.x}, - abstract = {Species abundance distributions (SADs) follow one of ecology's oldest and most universal laws--every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.}, - langid = {english}, - pmid = {17845298}, - keywords = {Animals,Biodiversity,Ecology,Models; Theoretical}, - file = {/Users/renatadiaz/Zotero/storage/QTQVVULA/McGill et al. - 2007 - Species abundance distributions moving beyond sin.pdf;/Users/renatadiaz/Zotero/storage/RNH5VTTB/McGill et al. - 2007 - Species abundance distributions moving beyond sin.pdf} -} - -@article{mcgill2010, - title = {Towards a Unification of Unified Theories of Biodiversity}, - author = {McGill, Brian J.}, - year = {2010}, - journal = {Ecology Letters}, - volume = {13}, - number = {5}, - pages = {627--642}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2010.01449.x}, - abstract = {Ecology Letters (2010) 13: 627\textendash 642 Abstract A unified theory in science is a theory that shows a common underlying set of rules that regulate processes previously thought to be distinct. Unified theories have been important in physics including the unification of electricity and magnetism and the unification of the electromagnetic with the weak nuclear force. Surprisingly, ecology, specifically the subfields of biodiversity and macroecology, also possess not one but at least six unified theories. This is problematic as only one unified theory is desirable. Superficially, the six unified theories seem very different. However, I show that all six theories use the same three rules or assertions to describe a stochastic geometry of biodiversity. The three rules are: (1) intraspecifically individuals are clumped together; (2) interspecifically global or regional abundance varies according to a hollow curve distribution; and (3) interspecifically individuals are placed without regard to individuals of other species. These three rules appear sufficient to explain local species abundance distributions, species\textendash area relationships, decay of similarity of distance and possibly other patterns of biodiversity. This provides a unification of the unified theories. I explore implications of this unified theory for future research.}, - langid = {english}, - keywords = {Biodiversity,continuum theory,fractals,macroecology,MaxEnt,neutral theory,stochastic geometry,unified theory}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2010.01449.x}, - file = {/Users/renatadiaz/Zotero/storage/RZ65EYI8/McGill - 2010 - Towards a unification of unified theories of biodi.pdf;/Users/renatadiaz/Zotero/storage/8BTVEFRU/j.1461-0248.2010.01449.html} -} - -@article{mcgill2015, - title = {Fifteen Forms of Biodiversity Trend in the {{Anthropocene}}}, - author = {McGill, Brian J. and Dornelas, Maria and Gotelli, Nicholas J. and Magurran, Anne E.}, - year = {2015}, - month = feb, - journal = {Trends in Ecology \& Evolution}, - volume = {30}, - number = {2}, - pages = {104--113}, - issn = {01695347}, - doi = {10.1016/j.tree.2014.11.006}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/D56ZYVWQ/McGill et al. - 2015 - Fifteen forms of biodiversity trend in the Anthrop.pdf;/Users/renatadiaz/Zotero/storage/JT3IESFN/McGill et al. - 2015 - Fifteen forms of biodiversity trend in the Anthrop.pdf} -} - -@article{mcgill2019, - title = {The What, How and Why of Doing Macroecology}, - author = {McGill, Brian J.}, - year = {2019}, - journal = {Global Ecology and Biogeography}, - volume = {28}, - number = {1}, - pages = {6--17}, - issn = {1466-8238}, - doi = {10.1111/geb.12855}, - abstract = {Macroecology is a growing and important subdiscipline of ecology, but it is becoming increasingly diffuse, without an organizing principle that is widely agreed upon. I highlight two main current views of macroecology: as the study of large-scale systems and as the study of emergent systems. I trace the history of both these views through the writings of the founders of macroecology. I also highlight the transmutation principle that identifies serious limitations to the study of large-scale systems with reductionist approaches. And I suggest that much of the underlying goal of macroecology is the pursuit of general principles and the escape from contingency. I highlight that there are many intertwined aspects of macroecology, with a number of resulting implications. I propose that returning to a focus on studying assemblages of a large number of particles is a helpful view. I propose defining macroecology as ``the study at the aggregate level of aggregate ecological entities made up of large numbers of particles for the purposes of pursuing generality''.}, - langid = {english}, - keywords = {macroecology,macroevolution,multicausality,philosophy of science,reductionism,transmutation problem}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12855}, - file = {/Users/renatadiaz/Zotero/storage/4MK3WVY5/McGill - 2019 - The what, how and why of doing macroecology.pdf;/Users/renatadiaz/Zotero/storage/U8MN44G5/McGill - 2019 - The what, how and why of doing macroecology.pdf;/Users/renatadiaz/Zotero/storage/937XYHVF/geb.html;/Users/renatadiaz/Zotero/storage/YLK6G34K/geb.html} -} - -@article{mcgill2019a, - title = {Unifying Macroecology and Macroevolution to Answer Fundamental Questions about Biodiversity}, - author = {McGill, Brian J. and Chase, Jonathan M. and Hortal, Joaqu{\'i}n and Overcast, Isaac and Rominger, Andrew J. and Rosindell, James and Borges, Paulo A. V. and Emerson, Brent C. and Etienne, Rampal S. and Hickerson, Michael J. and Mahler, D. Luke and Massol, Francois and McGaughran, Angela and Neves, Pedro and Parent, Christine and Pati{\~n}o, Jairo and Ruffley, Megan and Wagner, Catherine E. and Gillespie, Rosemary}, - editor = {Algar, Adam}, - year = {2019}, - month = dec, - journal = {Global Ecology and Biogeography}, - volume = {28}, - number = {12}, - pages = {1925--1936}, - issn = {1466-822X, 1466-8238}, - doi = {10.1111/geb.13020}, - abstract = {The study of biodiversity started as a single unified field that spanned both ecology and evolution and both macro and micro phenomena. But over the 20th century, major trends drove ecology and evolution apart and pushed an emphasis towards the micro perspective in both disciplines. Macroecology and macroevolution re-emerged as self-consciously distinct fields in the 1970s and 1980s, but they remain largely separated from each other. Here, we argue that despite the challenges, it is worth working to combine macroecology and macroevolution. We present 25 fundamental questions about biodiversity that are answerable only with a mixture of the views and tools of both macroecology and macroevolution.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/4W8UCQZU/McGill et al. - 2019 - Unifying macroecology and macroevolution to answer.pdf;/Users/renatadiaz/Zotero/storage/HFM4Z7NX/McGill et al. - 2019 - Unifying macroecology and macroevolution to answer.pdf;/Users/renatadiaz/Zotero/storage/DIDR82ES/geb.html} -} - -@article{mcgill2021, - title = {You Are Welcome Here: {{A}} Practical Guide to Diversity, Equity, and Inclusion for Undergraduates Embarking on an Ecological Research Experience}, - shorttitle = {You Are Welcome Here}, - author = {McGill, Bonnie M. and Foster, Madison J. and Pruitt, Abagael N. and Thomas, Samantha Gabrielle and Arsenault, Emily R. and Hanschu, Janaye and Wahwahsuck, Kynser and Cortez, Evan and Zarek, Kaci and Loecke, Terrance D. and Burgin, Amy J.}, - year = {2021}, - journal = {Ecology and Evolution}, - volume = {11}, - number = {8}, - pages = {3636--3645}, - issn = {2045-7758}, - doi = {10.1002/ece3.7321}, - abstract = {As we build a more diverse, equitable, and inclusive culture in the ecological research community, we must work to support new ecologists by empowering them with the knowledge, tools, validation, and sense of belonging in ecology to succeed. Undergraduate research experiences (UREs) are critical for a student's professional and interpersonal skill development and key for recruiting and retaining students from diverse groups to ecology. However, few resources exist that speak directly to an undergraduate researcher on the diversity, equity, and inclusion (DEI) dimensions of embarking on a first research experience. Here, we write primarily for undergraduate readers, though a broader audience of readers, especially URE mentors, will also find this useful. We explain many of the ways a URE benefits undergraduate researchers and describe how URE students from different positionalities can contribute to an inclusive research culture. We address three common sources of anxiety for URE students through a DEI lens: imposter syndrome, communicating with mentors, and safety in fieldwork. We discuss the benefits as well as the unique vulnerabilities and risks associated with fieldwork, including the potential for harassment and assault. Imposter syndrome and toxic field experiences are known to drive students, including students from underrepresented minority groups, out of STEM. Our goal is to encourage all students, including those from underrepresented groups, to apply for UREs, build awareness of their contributions to inclusion in ecology research, and provide strategies for overcoming known barriers.}, - langid = {english}, - keywords = {diversity,ecology,equity,inclusion,undergraduate research experience}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.7321}, - file = {/Users/renatadiaz/Zotero/storage/LMU5Y3FE/McGill et al. - 2021 - You are welcome here A practical guide to diversi.pdf;/Users/renatadiaz/Zotero/storage/85LEYKY3/ece3.html} -} - -@article{mcglinn2012, - title = {Scale Dependence in Species Turnover Reflects Variance in Species Occupancy}, - author = {McGlinn, Daniel J. and Hurlbert, Allen H.}, - year = {2012}, - month = feb, - journal = {Ecology}, - volume = {93}, - number = {2}, - pages = {294--302}, - issn = {0012-9658}, - doi = {10.1890/11-0229.1}, - abstract = {Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species\textendash area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90\% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/DI2DAFZS/McGlinn and Hurlbert - 2012 - Scale dependence in species turnover reflects vari.pdf} -} - -@article{mcglinn2019, - title = {Measurement of {{Biodiversity}} ({{MoB}}): {{A}} Method to Separate the Scale-Dependent Effects of Species Abundance Distribution, Density, and Aggregation on Diversity Change}, - shorttitle = {Measurement of {{Biodiversity}} ({{MoB}})}, - author = {McGlinn, Daniel J. and Xiao, Xiao and May, Felix and Gotelli, Nicholas J. and Engel, Thore and Blowes, Shane A. and Knight, Tiffany M. and Purschke, Oliver and Chase, Jonathan M. and McGill, Brian J.}, - year = {2019}, - journal = {Methods in Ecology and Evolution}, - volume = {10}, - number = {2}, - pages = {258--269}, - issn = {2041-210X}, - doi = {10.1111/2041-210X.13102}, - abstract = {Little consensus has emerged regarding how proximate and ultimate drivers such as productivity, disturbance and temperature may affect species richness and other aspects of biodiversity. Part of the confusion is that most studies examine species richness at a single spatial scale and ignore how the underlying components of species richness can vary with spatial scale. We provide an approach for the measurement of biodiversity that decomposes changes in species rarefaction curves into proximate components attributed to: (a) the species abundance distribution, (b) density of individuals and (c) the spatial arrangement of individuals. We decompose species richness by comparing spatial and nonspatial sample- and individual-based species rarefaction curves that differentially capture the influence of these components to estimate the relative importance of each in driving patterns of species richness change. We tested the validity of our method on simulated data, and we demonstrate it on empirical data on plant species richness in invaded and uninvaded woodlands. We integrated these methods into a new r package (mobr). The metrics that mobr provides will allow ecologists to move beyond comparisons of species richness in response to ecological drivers at a single spatial scale toward a dissection of the proximate components that determine species richness across scales.}, - copyright = {\textcopyright{} 2018 The Authors. Methods in Ecology and Evolution \textcopyright{} 2018 British Ecological Society}, - langid = {english}, - keywords = {accumulation curve,community structure,extent,grain,rarefaction curve,spatial scale,species richness,species-area curve}, - file = {/Users/renatadiaz/Zotero/storage/2NZPHR9K/McGlinn et al. - 2019 - Measurement of Biodiversity (MoB) A method to sep.pdf;/Users/renatadiaz/Zotero/storage/R4L5R78K/2041-210X.html} -} - -@article{mcgowan2022, - title = {Design {{Principles}} for {{Data Analysis}}}, - author = {McGowan, Lucy D'Agostino and Peng, Roger D. and Hicks, Stephanie C.}, - year = {2022}, - month = jul, - journal = {Journal of Computational and Graphical Statistics}, - volume = {0}, - number = {0}, - pages = {1--8}, - publisher = {{Taylor \& Francis}}, - issn = {1061-8600}, - doi = {10.1080/10618600.2022.2104290}, - abstract = {The data revolution has led to an increased interest in the practice of data analysis. While much has been written about statistical thinking, a complementary form of thinking that appears in the practice of data analysis is design thinking\textemdash the problem-solving process to understand the people for whom a solution is being designed. For a given problem, there can be significant or subtle differences in how a data analyst (or producer of a data analysis) constructs, creates, or designs a data analysis, including differences in the choice of methods, tooling, and workflow. These choices can affect the data analysis products themselves and the experience of the consumer of the data analysis. Therefore, the role of a producer can be thought of as designing the data analysis with a set of design principles. Here, we introduce design principles for data analysis and describe how they can be mapped to data analyses in a quantitative and informative manner. We also provide data showing variation of principles within and between producers of data analyses. Our work suggests a formal mechanism to describe data analyses based on design principles. These results provide guidance for future work in characterizing the data analytic process. Supplementary materials for this article are available online.}, - keywords = {Data science,Design,Education,Statistics}, - annotation = {\_eprint: https://doi.org/10.1080/10618600.2022.2104290}, - file = {/Users/renatadiaz/Zotero/storage/KHV3LJQY/McGowan et al. - 2022 - Design Principles for Data Analysis.pdf} -} - -@article{mckinney1999, - title = {Biotic Homogenization: A Few Winners Replacing Many Losers in the next Mass Extinction}, - shorttitle = {Biotic Homogenization}, - author = {McKinney, Michael L and Lockwood, Julie L}, - year = {1999}, - month = nov, - journal = {Trends in Ecology \& Evolution}, - volume = {14}, - number = {11}, - pages = {450--453}, - issn = {0169-5347}, - doi = {10.1016/S0169-5347(99)01679-1}, - abstract = {Human activities are not random in their negative and positive impacts on biotas. Emerging evidence shows that most species are declining as a result of human activities (`losers') and are being replaced by a much smaller number of expanding species that thrive in human-altered environments (`winners'). The result will be a more homogenized biosphere with lower diversity at regional and global scales. Recent data also indicate that the many losers and few winners tend to be non-randomly distributed among higher taxa and ecological groups, enhancing homogenization.}, - langid = {english}, - keywords = {Exotic,Extinction,Homogenization,Introduced species,Invasion,Losers,Winners}, - file = {/Users/renatadiaz/Zotero/storage/6Q66YPSF/S0169534799016791.html} -} - -@article{mcloskey1982, - title = {The Principle of Equal Opportunity: A Test with Desert Rodents}, - shorttitle = {The Principle of Equal Opportunity}, - author = {M'Closkey, Robert T.}, - year = {1982}, - month = aug, - journal = {Canadian Journal of Zoology}, - volume = {60}, - number = {8}, - pages = {1968--1972}, - issn = {0008-4301, 1480-3283}, - doi = {10.1139/z82-254}, - abstract = {A basic assumption of the theory of niche overlap and limiting similarity is that the use of limited resources by coexisting species is proportional to resource availability. I provide a test of this assumption with desert rodents using microhabitat structure as a resource. Utilized and available microhabitat frequencies were compared in four desert rodent species. Some rodent species departed significantly in utilized microhabitats from that expected on the basis of availability. However, cumulative utilization frequencies for all four rodent species corresponded closely to the frequency of available microhabitats. Therefore, the assumption of constant ratios of utilization/availability of resources (microhabitats) was not falsified for the entire guild, although individual rodent species used some microhabitats disproportionately.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/NDIMKEY5/M'Closkey - 1982 - The principle of equal opportunity a test with de.pdf} -} - -@article{mcnab2009, - title = {Ecological Factors Affect the Level and Scaling of Avian {{BMR}}}, - author = {McNab, Brian Keith}, - year = {2009}, - month = jan, - journal = {Comparative Biochemistry and Physiology Part A: Molecular \& Integrative Physiology}, - volume = {152}, - number = {1}, - pages = {22--45}, - issn = {1095-6433}, - doi = {10.1016/j.cbpa.2008.08.021}, - abstract = {The basal rate of metabolism (BMR) in 533 species of birds, when examined with ANCOVA, principally correlates with body mass, most of the residual variation correlating with food habits, climate, habitat, a volant or flightless condition, use or not of torpor, and a highland or lowland distribution. Avian BMR also correlates with migratory habits, if climate and a montane distribution is excluded from the analysis, and with an occurrence on small islands if a flightless condition and migration are excluded. Residual variation correlates with membership in avian orders and families principally because these groups are behaviorally and ecologically distinctive. However, the distinction between passerines and other birds remains a significant correlate of avian BMR, even after six ecological factors are included, with other birds having BMRs that averaged 74\% of the passerine mean. This combination of factors accounts for 97.7\% of the variation in avian BMR. Yet, migratory species that belong to Anseriformes, Charadriiformes, Pelecaniformes, and Procellariiformes and breed in temperate or polar environments have mass-independent basal rates equal to those found in passerines. In contrast, penguins belong to an order of polar, aquatic birds that have basal rates lower than passerines because their flightless condition depresses basal rate. Passerines dominate temperate, terrestrial environments and the four orders of aquatic birds dominate temperate and polar aquatic environments because their high BMRs facilitate reproduction and migration. The low BMRs of tropical passerines may reflect a sedentary lifestyle as much as a life in a tropical climate. Birds have BMRs that are 30\textendash 40\% greater than mammals because of the commitment of birds to an expensive and expansive form of flight.}, - langid = {english}, - keywords = {Avian flight,Ecological factors,Energetics,Geography,Mammalian flight,Migration,Non-passerines,Passerines,Phylogeny} -} - -@techreport{mendelsohn2022, - type = {Preprint}, - title = {Global Patterns and Correlates in the Emergence of Antimicrobial Resistance in Humans}, - author = {Mendelsohn, Emma and Ross, Noam and {Zambrana-Torrelio}, Carlos and Van Boeckel, T. P. and Laxminarayan, Ramanan and Daszak, Peter}, - year = {2022}, - month = sep, - institution = {{Public and Global Health}}, - doi = {10.1101/2022.09.29.22280519}, - abstract = {Abstract Antimicrobial resistance (AMR) is a critical global health threat, and drivers of the emergence of novel strains of antibiotic-resistant bacteria in humans are poorly understood at the global scale. We examined correlates of AMR emergence in humans using global data on the origins of novel strains of AMR bacteria from 2006 to 2017, human and livestock antibiotic use, country economic activity, and reporting bias indicators. We found that AMR emergence is positively correlated with antibiotic consumption in humans, whereas the relationship with antibiotic consumption in livestock is modified by gross domestic product (GDP), with only higher GDP countries showing a slight positive association. We also found that human travel may play a role in AMR emergence, likely driving the spread of novel AMR strains into countries where they are subsequently detected for the first time. Finally, we produced predictive models and country-level maps of the global distribution of AMR risk. We assessed these against spatial patterns of reported AMR emergence, to identify gaps in surveillance that can be used to direct prevention and intervention policies.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/9URJCBMN/Mendelsohn et al. - 2022 - Global patterns and correlates in the emergence of.pdf} -} - -@misc{meyer2019, - title = {E1071: {{Misc Functions}} of the {{Department}} of {{Statistics}}, {{Probability Theory Group}} ({{Formerly}}: {{E1071}}), {{TU Wien}}}, - author = {Meyer, David and Dimitriadou, Evgenia and Hornik, Kurt and Weingessel, Andreas and Leisch, Friedrich}, - year = {2019} -} - -@article{micheli1999, - title = {The {{Dual Nature}} of {{Community Variability}}}, - author = {Micheli, F. and Cottingham, K. L. and Bascompte, J. and Bj{\o}rnstad, O. N. and Eckert, G. L. and Fischer, J. M. and Keitt, T. H. and Kendall, B. E. and Klug, J. L. and Rusak, J. A.}, - year = {1999}, - journal = {Oikos}, - volume = {85}, - number = {1}, - pages = {161--169}, - publisher = {{[Nordic Society Oikos, Wiley]}}, - issn = {0030-1299}, - doi = {10.2307/3546802}, - abstract = {Community variability has a dual nature. On the one hand, there is compositional variability, changes in the relative abundance of component species. On the other hand, there is aggregate variability, changes in summary properties such as total abundance, biomass, or production. Although these two aspects of variability have received much individual attention, few studies have explicitly related the compositional and aggregate variability of natural communities. In this paper, we show how simultaneous consideration of both aspects of community variability might advance our understanding of ecological communities. We use the distinction between compositional and aggregate variability to develop an organizational framework for describing patterns of community variability. At their extremes, compositional and aggregate variability combine in four different ways: (1) stasis, low compositional and low aggregate variability; (2) synchrony, low compositional and high aggregate variability; (3) asynchrony, high compositional and high aggregate variability; and (4) compensation, high compositional and low aggregate variability. Each of these patterns has been observed in natural communities, and can be linked to a suite of abiotic and biotic mechanisms. We give examples of the potential relevance of variability patterns to applied ecology, and describe the methodological developments needed to make meaningful comparisons of aggregate and compositional variability across communities. Finally, we provide two numerical examples of how our approach can be applied to natural communities.}, - file = {/Users/renatadiaz/Zotero/storage/F88R7FYX/Micheli et al. - 1999 - The Dual Nature of Community Variability.pdf} -} - -@article{monnet2014, - title = {Asynchrony of Taxonomic, Functional and Phylogenetic Diversity in Birds}, - author = {Monnet, Anne-Christine and Jiguet, Fr{\'e}d{\'e}ric and Meynard, Christine N. and Mouillot, David and Mouquet, Nicolas and Thuiller, Wilfried and Devictor, Vincent}, - year = {2014}, - journal = {Global Ecology and Biogeography}, - volume = {23}, - number = {7}, - pages = {780--788}, - issn = {1466-8238}, - doi = {10.1111/geb.12179}, - abstract = {Aim We assessed the temporal trends of taxonomic, functional and phylogenetic diversities in the French avifauna over the last two decades. Additionally, we investigated whether and how this multifaceted approach to biodiversity dynamics can reveal an increasing similarity of local assemblages in terms of species, traits and/or lineages. Location France. Methods We analysed a large-scale dataset that recorded annual changes in the abundance of 116 breeding birds in France between 1989 and 2012. We decomposed and analysed the spatio-temporal dynamics of taxonomic, phylogenetic and functional diversities and each of their {$\alpha$}-, {$\beta$}- and {$\gamma$}-components. We also calculated the trend in the mean specialization of bird communities to track the relative success of specialist versus generalist species within communities during the same period. Results We found large variation within and among the temporal trends of each biodiversity facet. On average, we found a marked increase in species and phylogenetic diversity over the period considered, but no particular trend was found for functional diversity. Conversely, changes in {$\beta$}-diversities for the three facets were characterized by independent and nonlinear trends. We also found a general increase in the local occurrence and abundance of generalist species within local communities. Main conclusions These results highlight a relative asynchrony of the different biodiversity facets occurring at large spatial scales. We show why a multifaceted approach to biodiversity dynamics is needed to better describe and understand changes in community composition in macroecology and conservation biogeography.}, - langid = {english}, - keywords = {Beta diversity,breeding bird survey,functional traits,homogenization,Rao,species turnover,temporal dynamics}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12179}, - file = {/Users/renatadiaz/Zotero/storage/YE9H2LVY/Monnet et al. - 2014 - Asynchrony of taxonomic, functional and phylogenet.pdf;/Users/renatadiaz/Zotero/storage/Q79RRT7F/geb.html} -} - -@article{moore2020, - title = {On Mutualism, Models, and Masting: {{The}} Effects of Seed-dispersing Animals on the Plants They Disperse}, - shorttitle = {On Mutualism, Models, and Masting}, - author = {Moore, Christopher M. and Dittel, Jacob W.}, - editor = {Shefferson, Richard}, - year = {2020}, - month = sep, - journal = {Journal of Ecology}, - volume = {108}, - number = {5}, - pages = {1775--1783}, - issn = {0022-0477, 1365-2745}, - doi = {10.1111/1365-2745.13414}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2TXNIYYF/Moore and Dittel - 2020 - On mutualism, models, and masting The effects of .pdf} -} - -@article{morlon2009, - title = {Taking Species Abundance Distributions beyond Individuals}, - author = {Morlon, H{\'e}l{\`e}ne and White, Ethan P. and Etienne, Rampal S. and Green, Jessica L. and Ostling, Annette and Alonso, David and Enquist, Brian J. and He, Fangliang and Hurlbert, Allen and Magurran, Anne E. and Maurer, Brian A. and McGill, Brian J. and Olff, Han and Storch, David and Zillio, Tommaso}, - year = {2009}, - journal = {Ecology Letters}, - volume = {12}, - number = {6}, - pages = {488--501}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2009.01318.x}, - abstract = {The species abundance distribution (SAD) is one of the few universal patterns in ecology. Research on this fundamental distribution has primarily focused on the study of numerical counts, irrespective of the traits of individuals. Here we show that considering a set of Generalized Species Abundance Distributions (GSADs) encompassing several abundance measures, such as numerical abundance, biomass and resource use, can provide novel insights into the structure of ecological communities and the forces that organize them. We use a taxonomically diverse combination of macroecological data sets to investigate the similarities and differences between GSADs. We then use probability theory to explore, under parsimonious assumptions, theoretical linkages among them. Our study suggests that examining different GSADs simultaneously in natural systems may help with assessing determinants of community structure. Broadening SADs to encompass multiple abundance measures opens novel perspectives in biodiversity research and warrants future empirical and theoretical developments.}, - langid = {english}, - keywords = {biomass,body-size,energy use,macroecology,metabolic theory,resource partitioning,size distribution,size–density relationship,size–energy relationship,Species abundance distribution}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2009.01318.x}, - file = {/Users/renatadiaz/Zotero/storage/WD8BPWHJ/Morlon et al. - 2009 - Taking species abundance distributions beyond indi.pdf;/Users/renatadiaz/Zotero/storage/H9WD4D6K/j.1461-0248.2009.01318.html} -} - -@article{morton2022, - title = {Merging Theory and Experiments to Predict and Understand Coextinctions}, - author = {Morton, Dana N. and Keyes, Aislyn and Barner, Allison K. and Dee, Laura E.}, - year = {2022}, - month = oct, - journal = {Trends in Ecology \& Evolution}, - volume = {37}, - number = {10}, - pages = {886--898}, - publisher = {{Elsevier}}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2022.06.004}, - langid = {english}, - pmid = {35798612}, - keywords = {cascading extinctions,coextinction,ecological network,food web,rewiring,robustness}, - file = {/Users/renatadiaz/Zotero/storage/QZ99QXWM/Morton et al. - 2022 - Merging theory and experiments to predict and unde.pdf;/Users/renatadiaz/Zotero/storage/7Z7Y3V99/S0169-5347(22)00137-9.html} -} - -@article{mullin, - title = {First Large-Scale Quantification Study of {{DNA}} Preservation in Insects from Natural History Collections Using Genome-Wide Sequencing}, - author = {Mullin, Victoria E. and Stephen, William and Arce, Andres N. and Nash, Will and Raine, Calum and Notton, David G. and Whiffin, Ashleigh and Blagderov, Vladimir and Gharbi, Karim and Hogan, James and Hunter, Tony and Irish, Naomi and Jackson, Simon and Judd, Steve and Watkins, Chris and Haerty, Wilfried and Ollerton, Jeff and Brace, Selina and Gill, Richard J. and Barnes, Ian}, - journal = {Methods in Ecology and Evolution}, - volume = {n/a}, - number = {n/a}, - issn = {2041-210X}, - doi = {10.1111/2041-210X.13945}, - abstract = {Insect declines are a global issue with significant ecological and economic ramifications. Yet, we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens have the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses is to understand how molecular preservation varies between specimens. Here, we highlight how Next-Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee Bombus lapidarius specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research, we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9 bp per decade. The proportion of quality filtered reads mapping to our assembled reference genome was around 50\%, and decreased by 1.1\% per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population-level analyses\textemdash for example for conservation or evolutionary studies\textemdash are entirely feasible, as long as the degraded nature of DNA is accounted for.}, - langid = {english}, - keywords = {aDNA,Bombus,collection genomics,DNA degradation,entomological collections,historical DNA,museum specimen,pollinators}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13945}, - file = {/Users/renatadiaz/Zotero/storage/Y62SLICA/Mullin et al. - First large-scale quantification study of DNA pres.pdf;/Users/renatadiaz/Zotero/storage/XZVC9UN9/2041-210X.html} -} - -@article{munger1981, - title = {Competition in {{Desert Rodents}}: {{An Experiment}} with {{Semipermeable Exclosures}}}, - shorttitle = {Competition in {{Desert Rodents}}}, - author = {Munger, J. C. and Brown, J. H.}, - year = {1981}, - month = jan, - journal = {Science}, - volume = {211}, - number = {4481}, - pages = {510--512}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.211.4481.510}, - abstract = {Larger species of seed-eating desert rodents were excludedfrom experimental plots while smaller, potentially competing species were allowed to enter. Density of small granivores on these plots increased to nearly 3.5 times that on control plots but only after 8 months. These results indicate that interspecific competition aKfects the abundance of desert rodents; they also support indirect evidence that competition for seeds infiuences the organization of desert rodent communities.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/JG3DAVT3/Munger and Brown - 1981 - Competition in Desert Rodents An Experiment with .pdf} -} - -@article{murali2022, - title = {Emphasizing Declining Populations in the {{Living Planet Report}}}, - author = {Murali, Gopal and {de Oliveira Caetano}, Gabriel Henrique and Barki, Goni and Meiri, Shai and Roll, Uri}, - year = {2022}, - month = jan, - journal = {Nature}, - volume = {601}, - number = {7894}, - pages = {E20-E24}, - publisher = {{Nature Publishing Group}}, - issn = {1476-4687}, - doi = {10.1038/s41586-021-04165-z}, - copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited}, - langid = {english}, - keywords = {Conservation biology,Macroecology,Population dynamics}, - file = {/Users/renatadiaz/Zotero/storage/PM6U8QGB/Murali et al. - 2022 - Emphasizing declining populations in the Living Pl.pdf;/Users/renatadiaz/Zotero/storage/I725VHIJ/s41586-021-04165-z.html} -} - -@article{nagy1999, - title = {Energetics of {{Free-Ranging Mammals}}, {{Reptiles}}, and {{Birds}}}, - author = {Nagy, K. A. and Girard, I. A. and Brown, T. K.}, - year = {1999}, - journal = {Annual Review of Nutrition}, - volume = {19}, - number = {1}, - pages = {247--277}, - doi = {10.1146/annurev.nutr.19.1.247}, - abstract = {We summarize the recent information on field metabolic rates (FMR) of wild terrestrial vertebrates as determined by the doubly labeled water technique. Allometric (scaling) relationships are calculated for mammals (79 species), reptiles (55 species), and birds (95 species) and for various taxonomic, dietary, and habitat groups within these categories. Exponential equations based on body mass are offered for predicting rates of daily energy expenditure and daily food requirements of free-ranging mammals, reptiles, and birds. Significant scaling differences between various taxa, dietary, and habitat groups (detected by analysis of covariance with P {$\leq$} 0.05) include the following: (a) The allometric slope for reptiles (0.889) is greater than that for mammals (0.734), which is greater than that for birds (0.681); (b) the slope for eutherian mammals (0.772) is greater than that for marsupial mammals (0.590); (c) among families of birds, slopes do not differ but elevations (intercepts) do, with passerine and procellariid birds having relatively high FMRs and gallinaceous birds having low FMRs; (d) Scleroglossan lizards have a higher slope (0.949) than do Iguanian lizards (0.793); (e) desert mammals have a higher slope (0.785) than do nondesert mammals; (f) marine birds have relatively high FMRs and desert birds have low FMRs; and (g) carnivorous mammals have a relatively high slope and carnivorous, insectivorous, and nectarivorous birds have relatively higher FMRs than do omnivores and granivores. The difference detected between passerine and nonpasserine birds reported in earlier reviews is not evident in the larger data set analyzed here. When the results are adjusted for phylogenetic effects using independent contrasts analysis, the difference between allometric slopes for marsupials and eutherians is no longer significant and the slope difference between Scleroglossan and Iguanian lizards disappears as well, but other taxonomic differences remain significant. Possible causes of the unexplained variations in FMR that could improve our currently inaccurate FMR prediction capabilities should be evaluated, including many important groups of terrestrial vertebrates that remain under- or unstudied and such factors as reproductive, thermoregulatory, social, and predator-avoidance behavior.}, - pmid = {10448524}, - keywords = {allometric scaling,bioenergetics,doubly labeled water,field metabolic rate,food requirement}, - annotation = {\_eprint: https://doi.org/10.1146/annurev.nutr.19.1.247}, - file = {/Users/renatadiaz/Zotero/storage/2HGGZI5F/Nagy et al. - 1999 - Energetics of Free-Ranging Mammals, Reptiles, and .pdf} -} - -@article{nagy2005, - title = {Field Metabolic Rate and Body Size}, - author = {Nagy, Kenneth A.}, - year = {2005}, - month = may, - journal = {Journal of Experimental Biology}, - volume = {208}, - number = {9}, - pages = {1621--1625}, - issn = {0022-0949}, - doi = {10.1242/jeb.01553}, - abstract = {The field metabolic rates (FMRs) of 229 species of terrestrial vertebrates,all measured using the doubly labeled water method in free-living individuals,were evaluated. Daily rates of energy expenditure were as low as 0.23 kJ per day in a small reptile (gecko), to as high as 52 500 kJ per day in a marine mammal (seal). This is a range of nearly six orders of magnitude. More than 70\% of the variation in log-transformed data is due to variation in body size(expressed as body mass). Much of the remaining variation is accounted for by thermal physiology, with the endothermic mammals and birds having FMRs that are about 12 and 20 times higher, respectively, than FMRs of equivalent-sized,but ectothermic, reptiles. Variation in log(body mass) within each of these three taxonomic classes accounts for over 94\% of the variation in log(FMR),and results from nonlinear regression analyses using untransformed data support this conclusion. However, the range of residual variation in mass-adjusted FMR within classes is still more than sixfold (ratio of highest over lowest). Some of this variation is associated with affiliations with lower taxonomic levels (Infraclass: eutherian vs metatherian mammals;Family: passerine, procellariform and galliform birds vs other birds), some is associated with habitat (especially desert vsnondesert), and some with differences in basic diet preference and foraging mode and season. The scaling slopes for FMR often differ from BMR slopes for the same Class of animals, and most differ from the theoretical slope of 0.75. Differences among slopes and intercepts that were detected using conventional regression analyses were largely confirmed upon reanalysis using Independent Contrasts Analysis to adjust for phylogenetic biases.}, - file = {/Users/renatadiaz/Zotero/storage/U3PSJXIU/Nagy - 2005 - Field metabolic rate and body size.pdf;/Users/renatadiaz/Zotero/storage/AV5ULJYF/Field-metabolic-rate-and-body-size.html} -} - -@article{nee1991, - title = {Lifting the Veil on Abundance Patterns}, - author = {Nee, Sean and Harvey, Paul H. and May, Robert Mccredie and Krebs, John Richard}, - year = {1991}, - month = feb, - journal = {Proceedings of the Royal Society of London. Series B: Biological Sciences}, - volume = {243}, - number = {1307}, - pages = {161--163}, - publisher = {{Royal Society}}, - doi = {10.1098/rspb.1991.0026}, - abstract = {The distribution of species abundances in samples from large species assemblages appears to follow a lognormal distribution truncated on the left at what Preston called the `veil line'. MacArthur suggested that if we could see the entire, unveiled distribution of abundances in the assemblage, we would discover that the distribution is left-skewed. This suggestion takes on a particular interest because, as we will show, Sugihara's so-far successful model of abundance patterns predicts that abundance distributions are more likely to be left- than right-skewed. Recently published estimates of the population sizes of British bird species allow us to observe the completely unveiled distribution of a natural assemblage. This data set is, perhaps, uniquely informative because of the accuracy of the population size estimates of rare British bird species. The distribution is indeed left-skewed and the degree of left-skewness is quantitatively compatible with Sugihara's model.}, - file = {/Users/renatadiaz/Zotero/storage/BVT3YZ7P/rspb.1991.html} -} - -@article{nekola2007, - title = {The Wealth of Species: Ecological Communities, Complex Systems and the Legacy of {{Frank Preston}}}, - shorttitle = {The Wealth of Species}, - author = {Nekola, Jeffrey C. and Brown, James H.}, - year = {2007}, - journal = {Ecology Letters}, - volume = {10}, - number = {3}, - pages = {188--196}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2006.01003.x}, - abstract = {General statistical patterns in community ecology have attracted considerable recent debate. Difficulties in discriminating among mathematical models and the ecological mechanisms underlying them are likely related to a phenomenon first described by Frank Preston. He noted that the frequency distribution of abundances among species was uncannily similar to the Boltzmann distribution of kinetic energies among gas molecules and the Pareto distribution of incomes among wage earners. We provide additional examples to show that four different `distributions of wealth' (species abundance distributions, species\textendash area and species\textendash time relations, and distance decay of compositional similarity) are not unique to ecology, but have analogues in other physical, geological, economic and cultural systems. Because these appear to be general statistical patterns characteristic of many complex dynamical systems they are likely not generated by uniquely ecological mechanistic processes.}, - langid = {english}, - keywords = {Community ecology,competitive sorting,complexity science,distance decay,ecological theory,neutral models,species–abundance distribution,species–area relationship,species–time relationship,statistical mechanics}, - file = {/Users/renatadiaz/Zotero/storage/5XAZBFLE/Nekola and Brown - 2007 - The wealth of species ecological communities, com.pdf;/Users/renatadiaz/Zotero/storage/LA8EQH6Z/Nekola and Brown - 2007 - The wealth of species ecological communities, com.pdf;/Users/renatadiaz/Zotero/storage/XHUPSQ4M/Nekola and Brown - 2007 - The wealth of species ecological communities, com.pdf;/Users/renatadiaz/Zotero/storage/7EVJZST2/j.1461-0248.2006.01003.html;/Users/renatadiaz/Zotero/storage/LHRUPH6F/j.1461-0248.2006.01003.html} -} - -@article{newberry2020, - title = {Genome-Resolved Metagenomics to Study Co-Occurrence Patterns and Intraspecific Heterogeneity among Plant Pathogen Metapopulations}, - author = {Newberry, Eric and Bhandari, Rishi and Kemble, Joseph and Sikora, Edward and Potnis, Neha}, - year = {2020}, - journal = {Environmental Microbiology}, - volume = {22}, - number = {7}, - pages = {2693--2708}, - issn = {1462-2920}, - doi = {10.1111/1462-2920.14989}, - abstract = {Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture-based approaches that do not provide quantitative assessment of pathogen populations at the field-level or the associated host microbiome. Here, we applied whole-genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co-occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co-occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co-occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non-random association of several other human and plant opportunists.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.14989}, - file = {/Users/renatadiaz/Zotero/storage/WXTDLTL2/Newberry et al. - 2020 - Genome-resolved metagenomics to study co-occurrenc.pdf;/Users/renatadiaz/Zotero/storage/K8XN598G/1462-2920.html} -} - -@article{newman2019, - title = {Disturbance {{Ecology}} in the {{Anthropocene}}}, - author = {Newman, Erica A.}, - year = {2019}, - journal = {Frontiers in Ecology and Evolution}, - volume = {7}, - pages = {147}, - issn = {2296-701X}, - doi = {10.3389/fevo.2019.00147}, - abstract = {With the accumulating evidence of changing disturbance regimes becoming increasingly obvious, there is potential for disturbance ecology to become the most valuable lens through which climate-related disturbance events are interpreted. In this paper, I revisit some of the central themes of disturbance ecology and argue that the knowledge established in the field of disturbance ecology continues to be relevant to ecosystem management, even with rapid changes to disturbance regimes and changing disturbance types in local ecosystems. Disturbance ecology has been tremendously successful over the past several decades at elucidating the interactions between disturbances, biodiversity, and ecosystems, and this knowledge can be leveraged in different contexts. Primarily, management in changing and uncertain conditions should be focused primarily on the long-term persistence of that native biodiversity that has evolved within the local disturbance regime and is likely to go extinct with rapid changes to disturbance intensity, frequency, and type. Where possible, conserving aspects of natural disturbance regimes will be vital to preserving functioning ecosystems and to that native biodiversity that requires disturbance for its continued existence, though these situations may become more limited over time. Finally, scientists must actively propose management policies that incorporate knowledge of disturbance ecology. Successful policies regarding changing disturbance regimes for biodiversity will not merely be reactive, and will recognize that for natural ecosystems as for human society, not all desired outcomes are simultaneously possible.}, - file = {/Users/renatadiaz/Zotero/storage/SMJN5AF4/Newman - 2019 - Disturbance Ecology in the Anthropocene.pdf} -} - -@article{newman2019a, - title = {Scaling and {{Complexity}} in {{Landscape Ecology}}}, - author = {Newman, Erica A. and Kennedy, Maureen C. and Falk, Donald A. and McKenzie, Donald}, - year = {2019}, - journal = {Frontiers in Ecology and Evolution}, - volume = {7}, - pages = {293}, - issn = {2296-701X}, - doi = {10.3389/fevo.2019.00293}, - abstract = {Landscapes and the ecological processes they support are inherently complex systems, in that they have large numbers of heterogeneous components that interact in multiple ways, and exhibit scale dependence, non-linear dynamics, and emergent properties. The emergent properties of landscapes encompass a broad range of processes that influence biodiversity and human environments. These properties, such as hydrologic and biogeochemical cycling, dispersal, evolutionary adaptation of organisms to their environments, and the focus of this article, ecological disturbance regimes (including wildfire), operate at scales that are relevant to human societies. These scales often tend to be the ones at which ecosystem dynamics are most difficult to understand and predict. We identify three intrinsic limitations to progress in landscape ecology, and ecology in general: (1) the problem of coarse-graining, or how to aggregate fine-scale information to larger scales in a statistically unbiased manner; (2) the middle-number problem, which describes systems with elements that are too few and too varied to be amenable to global averaging, but too numerous and varied to be computationally tractable; and (3) non-stationarity, in which modeled relationships or parameter choices are valid in one environment but may not hold when projected onto future environments, such as a warming climate. Modeling processes and interactions at the landscape scale, including future states of biological communities and their interactions with each other and with processes such as landscape fire, requires quantitative metrics and algorithms that minimize error propagation across scales. We illustrate these challenges with examples drawn from the context of landscape ecology and wildfire, and review recent progress and paths to developing scaling laws in landscape ecology, and relatedly, macroecology. We incorporate concepts of compression of state spaces from complexity theory to suggest ways to overcome the problems presented by coarse-graining, the middle-number domain, and non-stationarity.}, - file = {/Users/renatadiaz/Zotero/storage/LHKUH7UT/Newman et al. - 2019 - Scaling and Complexity in Landscape Ecology.pdf;/Users/renatadiaz/Zotero/storage/XFE82PPU/Newman et al. - 2019 - Scaling and Complexity in Landscape Ecology.pdf} -} - -@article{newman2020, - title = {Disturbance Macroecology: A Comparative Study of Community Structure Metrics in a High-Severity Disturbance Regime}, - shorttitle = {Disturbance Macroecology}, - author = {Newman, Erica A. and Wilber, Mark Q. and Kopper, Karen E. and Moritz, Max A. and Falk, Donald A. and McKenzie, Don and Harte, John}, - year = {2020}, - journal = {Ecosphere}, - volume = {11}, - number = {1}, - pages = {e03022}, - issn = {2150-8925}, - doi = {10.1002/ecs2.3022}, - abstract = {Macroecological studies have established widespread patterns of species diversity and abundance in ecosystems but have generally restricted their scope to relatively steady-state systems. As a result, how macroecological metrics are expected to scale in ecosystems that experience natural disturbance regimes is unknown. We examine macroecological patterns in a fire-dependent forest of Bishop pine (Pinus muricata). We target two different-aged stands in a stand-replacing fire regime: a mature stand with a diverse understory and with no history of major disturbance for at least 40 yr, and one disturbed by a stand-replacing fire 17 yr prior to measurement. We compare properties of these stands with macroecological predictions from the Maximum Entropy Theory of Ecology (METE), an information entropy-based theory that has proven highly successful in predicting macroecological metrics in multiple ecosystems and taxa. Ecological patterns in the mature stand more closely match METE predictions than do data from the more recently disturbed, mid-seral stage stand. This suggests METE's predictions are more robust in late-successional, slowly changing, or steady-state systems than those in rapid flux with respect to species composition, abundances, and organisms' sizes. Our findings highlight the need for a macroecological theory that incorporates natural disturbance, perturbations, and ecological dynamics into its predictive capabilities, because most natural systems are not in a steady state.}, - copyright = {\textcopyright{} 2020 The Authors. This article has been contributed to by US Government employees and their work is in the public domain in the USA.}, - langid = {english}, - keywords = {Bishop pine (Pinus muricata),California Floristic Province,closed-cone pine forest,macroecology,Maximum Entropy Theory of Ecology (METE),natural disturbance,species abundance distribution,species–area relationship,wildfire}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3022}, - file = {/Users/renatadiaz/Zotero/storage/MLI4PNIJ/Newman et al. - 2020 - Disturbance macroecology a comparative study of c.pdf;/Users/renatadiaz/Zotero/storage/7S8JLNS9/ecs2.html} -} - -@article{niedballa, - title = {Imageseg: {{An R}} Package for Deep Learning-Based Image Segmentation}, - shorttitle = {Imageseg}, - author = {Niedballa, J{\"u}rgen and Axtner, Jan and D{\"o}bert, Timm Fabian and Tilker, Andrew and Nguyen, An and Wong, Seth T. and Fiderer, Christian and Heurich, Marco and Wilting, Andreas}, - journal = {Methods in Ecology and Evolution}, - volume = {n/a}, - number = {n/a}, - issn = {2041-210X}, - doi = {10.1111/2041-210X.13984}, - abstract = {Convolutional neural networks (CNNs) and deep learning are powerful and robust tools for ecological applications, and are particularly suited for image data. Image segmentation (the classification of all pixels in images) is one such application and can, for example, be used to assess forest structural metrics. While CNN-based image segmentation methods for such applications have been suggested, widespread adoption in ecological research has been slow, likely due to technical difficulties in implementation of CNNs and lack of toolboxes for ecologists. Here, we present R package imageseg which implements a CNN-based workflow for general purpose image segmentation using the U-Net and U-Net++ architectures in R. The workflow covers data (pre)processing, model training and predictions. We illustrate the utility of the package with image recognition models for two forest structural metrics: tree canopy density and understorey vegetation density. We trained the models using large and diverse training datasets from a variety of forest types and biomes, consisting of 2877 canopy images (both canopy cover and hemispherical canopy closure photographs) and 1285 understorey vegetation images. Overall segmentation accuracy of the models was high with a Dice score of 0.91 for the canopy model and 0.89 for the understorey vegetation model (assessed with 821 and 367 images respectively). The image segmentation models performed significantly better than commonly used thresholding methods, and generalized well to data from study areas not included in training. This indicates robustness to variation in input images and good generalization strength across forest types and biomes. The package and its workflow allow simple yet powerful assessments of forest structural metrics using pretrained models. Furthermore, the package facilitates custom image segmentation with single or multiple classes and based on colour or grayscale images, for example, for applications in cell biology or for medical images. Our package is free, open source and available from CRAN. It will enable easier and faster implementation of deep learning-based image segmentation within R for ecological applications and beyond.}, - langid = {english}, - keywords = {canopy density,canopy hemispherical photography,computer vision,convolutional neural network,forest monitoring,machine learning,UNet,vegetation density}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13984}, - file = {/Users/renatadiaz/Zotero/storage/EIMW5EEI/Niedballa et al. - imageseg An R package for deep learning-based ima.pdf;/Users/renatadiaz/Zotero/storage/G7RPZD3P/2041-210X.html} -} - -@incollection{nordborg2019, - title = {Coalescent {{Theory}}}, - booktitle = {Handbook of {{Statistical Genomics}}}, - author = {Nordborg, Magnus}, - year = {2019}, - pages = {145--30}, - publisher = {{John Wiley \& Sons, Ltd}}, - doi = {10.1002/9781119487845.ch5}, - abstract = {Whereas most of classical population genetics considers the future of a population given a starting point, the coalescent considers the present, while taking the past into account. The pattern of polymorphism, that is, the allelic states of all homologous gene copies in a population, is determined by the genealogical and mutational history of these copies. The coalescent is based on the realization that the genealogy is usually easier to model backwards in time, and that selectively neutral mutations can then be superimposed afterwards. This leads to extremely efficient algorithms for simulating data under a wide variety of models \textemdash{} data that can then be compared with actual observations in order to understand the process that gave rise to the latter.}, - chapter = {5}, - isbn = {978-1-119-48784-5}, - langid = {english}, - keywords = {coalescent theory,genealogical process,geographic structure,Kingman's coalescent,matrix migration,neutral mutation process,Wright-Fisher model}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119487845.ch5}, - file = {/Users/renatadiaz/Zotero/storage/553EK34S/9781119487845.html} -} - -@article{odwyer2017, - title = {Reinterpreting Maximum Entropy in Ecology: A Null Hypothesis Constrained by Ecological Mechanism}, - shorttitle = {Reinterpreting Maximum Entropy in Ecology}, - author = {O'Dwyer, James P. and Rominger, Andrew and Xiao, Xiao}, - year = {2017}, - journal = {Ecology Letters}, - volume = {20}, - number = {7}, - pages = {832--841}, - issn = {1461-0248}, - doi = {10.1111/ele.12788}, - abstract = {Simplified mechanistic models in ecology have been criticised for the fact that a good fit to data does not imply the mechanism is true: pattern does not equal process. In parallel, the maximum entropy principle (MaxEnt) has been applied in ecology to make predictions constrained by just a handful of state variables, like total abundance or species richness. But an outstanding question remains: what principle tells us which state variables to constrain? Here we attempt to solve both problems simultaneously, by translating a given set of mechanisms into the state variables to be used in MaxEnt, and then using this MaxEnt theory as a null model against which to compare mechanistic predictions. In particular, we identify the sufficient statistics needed to parametrise a given mechanistic model from data and use them as MaxEnt constraints. Our approach isolates exactly what mechanism is telling us over and above the state variables alone.}, - langid = {english}, - keywords = {Macroecology,maximum entropy,neutral ecology}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12788}, - file = {/Users/renatadiaz/Zotero/storage/95ESGT7V/O’Dwyer et al. - 2017 - Reinterpreting maximum entropy in ecology a null .pdf;/Users/renatadiaz/Zotero/storage/4UB26K3G/ele.html} -} - -@article{odwyer2018, - title = {Cross-Scale Ecological Theory Sheds Light on the Maintenance of Biodiversity}, - author = {O'Dwyer, James P. and Cornell, Stephen J.}, - year = {2018}, - month = jul, - journal = {arXiv:1705.07856 [q-bio]}, - eprint = {1705.07856}, - eprinttype = {arxiv}, - primaryclass = {q-bio}, - abstract = {One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances changes with spatial scale, and this gap has hampered attempts to use observed species abundances as a way to quantify what non-neutral processes are needed to fully explain observed patterns. To address this, we introduce a new formulation of spatial neutral biodiversity theory and derive analytical predictions for the way abundance distributions change with scale. For tropical forest data where neutrality has been extensively tested before now, we apply this approach and identify an incompatibility between neutral fits at regional and local scales. We use this approach derive a sharp quantification of what remains to be explained by non-neutral processes at the local scale, setting a quantitative target for more general models for the maintenance of biodiversity.}, - archiveprefix = {arXiv}, - keywords = {Quantitative Biology - Populations and Evolution}, - file = {/Users/renatadiaz/Zotero/storage/QY3HLEIU/O'Dwyer and Cornell - 2018 - Cross-scale ecological theory sheds light on the m.pdf;/Users/renatadiaz/Zotero/storage/ITK6HCE9/1705.html} -} - -@article{ohara2005, - title = {Species Richness Estimators: How Many Species Can Dance on the Head of a Pin?}, - shorttitle = {Species Richness Estimators}, - author = {O'hara, R. B.}, - year = {2005}, - journal = {Journal of Animal Ecology}, - volume = {74}, - number = {2}, - pages = {375--386}, - issn = {1365-2656}, - doi = {10.1111/j.1365-2656.2005.00940.x}, - abstract = {1 Several species richness estimators (two non-parametric, four based on rarefaction curves and two from fitting of abundance distributions) were compared by examining their performance in estimating the species richness for two moth data sets from the United Kingdom. Comparisons were also made using data simulated from the fitted abundance distributions. 2 The different species richness estimators gave different estimates. The non-parametric estimates and the rarefaction estimates were similar, but were smaller than the parametric estimates. When the simulated data were used, the only methods to give estimates near the true value was the parametric method using the distribution from which the data were simulated. 3 At present it is impossible to decide whether any of the estimation methods will give a realistic estimate, as not enough is known about the true numbers of species in communities. Until this is rectified, the most that can be hoped for is to obtain upper and lower bounds on species richness.}, - langid = {english}, - keywords = {ACE,Chao1,negative binomial,Poisson log-normal,taxon sampling curve}, - annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2656.2005.00940.x}, - file = {/Users/renatadiaz/Zotero/storage/SAFDJ6VN/O'hara - 2005 - Species richness estimators how many species can .pdf;/Users/renatadiaz/Zotero/storage/G5CHIMPG/j.1365-2656.2005.00940.html} -} - -@misc{oksanen2020, - title = {Vegan: {{Community Ecology Package}}}, - author = {Oksanen, Jari and Blanchet, F. Guillaume and Friendly, Michael and Kindt, Roeland and Legendre, Pierre and McGlinn, Dan and Minchin, Peter R and O'Hara, R.B. and Simpson, Gavin L. and Solymos, Peter and Stevens, M. Henry H. and Szoecs, Eduard and Wagner, Helene}, - year = {2020} -} - -@article{olden2004, - title = {Ecological and Evolutionary Consequences of Biotic Homogenization}, - author = {Olden, Julian D. and LeRoy Poff, N. and Douglas, Marlis R. and Douglas, Michael E. and Fausch, Kurt D.}, - year = {2004}, - month = jan, - journal = {Trends in Ecology \& Evolution}, - volume = {19}, - number = {1}, - pages = {18--24}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2003.09.010}, - abstract = {Biotic homogenization, the gradual replacement of native biotas by locally expanding non-natives, is a global process that diminishes floral and faunal distinctions among regions. Although patterns of homogenization have been well studied, their specific ecological and evolutionary consequences remain unexplored. We argue that our current perspective on biotic homogenization should be expanded beyond a simple recognition of species diversity loss, towards a synthesis of higher order effects. Here, we explore three distinct forms of homogenization (genetic, taxonomic and functional), and discuss their immediate and future impacts on ecological and evolutionary processes. Our goal is to initiate future research that investigates the broader conservation implications of homogenization and to promote a proactive style of adaptive management that engages the human component of the anthropogenic blender that is currently mixing the biota on Earth.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/JSNWCAYJ/S016953470300288X.html} -} - -@article{olden2006, - title = {On Defining and Quantifying Biotic Homogenization}, - author = {Olden, Julian D. and Rooney, Thomas P.}, - year = {2006}, - journal = {Global Ecology and Biogeography}, - volume = {15}, - number = {2}, - pages = {113--120}, - issn = {1466-8238}, - doi = {10.1111/j.1466-822X.2006.00214.x}, - abstract = {Ongoing species invasions and extinctions are changing biological diversity in different ways at different spatial scales. Biotic homogenization (or BH) refers to the process by which the genetic, taxonomic or functional similarities of regional biotas increase over time. It is a multifaceted process that encompasses species invasions, extinctions and environmental alterations, focusing on how the identities of species (or their genetic or functional attributes) change over space and time. Despite the increasing use of the term BH in conservation biology, it is often used erroneously as a synonym for patterns of species invasions, loss of native species or changes in species richness through time. This reflects the absence of an agreed-upon, cogent definition of BH. Here, we offer an operational definition for BH and review the various methodologies used to study this process. We identify the strengths and weaknesses of these approaches, and make explicit recommendations for future studies. We conclude by citing the need for researchers to: (1) consider carefully the definition of BH by recognizing the genetic, taxonomic and functional realms of this process; (2) recognize that documenting taxonomic homogenization requires tracking the identity of species (not species richness) comprising biotas through space and time; and (3) employ more rigorous methods for quantifying BH.}, - langid = {english}, - keywords = {Beta-diversity,biological impoverishment,community change,extinction,invasion,species richness,taxonomic homogenization}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1466-822X.2006.00214.x}, - file = {/Users/renatadiaz/Zotero/storage/28UYBS5D/Olden and Rooney - 2006 - On defining and quantifying biotic homogenization.pdf;/Users/renatadiaz/Zotero/storage/4J93NBTD/j.1466-822X.2006.00214.html} -} - -@book{oneill1986, - title = {A {{Hierarchical Concept}} of {{Ecosystems}}}, - author = {O'Neill, R.V. and University, Princeton and Press, Princeton University and Waide, J.B. and Deangelis, D.L. and Allen, T.F.H.}, - year = {1986}, - series = {Monographs in Population Biology}, - publisher = {{Princeton University Press}}, - isbn = {978-0-691-08436-7}, - lccn = {86009423} -} - -@article{osullivan2019, - title = {Metacommunity-Scale Biodiversity Regulation and the Self-Organised Emergence of Macroecological Patterns}, - author = {O'Sullivan, Jacob D. and Knell, Robert J. and Rossberg, Axel G.}, - year = {2019}, - journal = {Ecology Letters}, - volume = {22}, - number = {9}, - pages = {1428--1438}, - issn = {1461-0248}, - doi = {10.1111/ele.13294}, - abstract = {There exist a number of key macroecological patterns whose ubiquity suggests that the spatio-temporal structure of ecological communities is governed by some universal mechanisms. The nature of these mechanisms, however, remains poorly understood. Here, we probe spatio-temporal patterns in species richness and community composition using a simple metacommunity assembly model. Despite making no a priori assumptions regarding biotic spatial structure or the distribution of biomass across species, model metacommunities self-organise to reproduce well-documented patterns including characteristic species abundance distributions, range size distributions and species area relations. Also in agreement with observations, species richness in our model attains an equilibrium despite continuous species turnover. Crucially, it is in the neighbourhood of the equilibrium that we observe the emergence of these key macroecological patterns. Biodiversity equilibria in models occur due to the onset of ecological structural instability, a population-dynamical mechanism. This strongly suggests a causal link between local community processes and macroecological phenomena.}, - copyright = {\textcopyright{} 2019 John Wiley \& Sons Ltd/CNRS}, - langid = {english}, - keywords = {biodiversity,ecological structural stability,macroecology,metacommunity,spatial ecology}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13294}, - file = {/Users/renatadiaz/Zotero/storage/5KUKQTZF/O’Sullivan et al. - 2019 - Metacommunity-scale biodiversity regulation and th.pdf;/Users/renatadiaz/Zotero/storage/CRR66KTZ/ele.html} -} - -@article{overcast2019, - title = {An Integrated Model of Population Genetics and Community Ecology}, - author = {Overcast, Isaac and Emerson, Brent C. and Hickerson, Michael J.}, - year = {2019}, - journal = {Journal of Biogeography}, - volume = {46}, - number = {4}, - pages = {816--829}, - doi = {10.1111/jbi.13541}, - abstract = {Abstract Aim Quantifying abundance distributions is critical for understanding both how communities assemble, and how community structure varies through time and space, yet estimating abundances requires considerable investment in fieldwork. Community-level population genetic data potentially offer a powerful way to indirectly infer richness, abundance and the history of accumulation of biodiversity within a community. Here we introduce a joint model linking neutral community assembly and comparative phylogeography to generate both community-level richness, abundance and genetic variation under a neutral model, capturing both equilibrium and non-equilibrium dynamics. Location Global. Methods Our model combines a forward-time individual-based community assembly process with a rescaled backward-time neutral coalescent model of multi-taxa population genetics. We explore general dynamics of genetic and abundance-based summary statistics and use approximate Bayesian computation (ABC) to estimate parameters underlying the model of island community assembly. Finally, we demonstrate two applications of the model using community-scale mtDNA sequence data and densely sampled abundances of an arachnid community on La R\'eunion. First, we use genetic data alone to estimate a summary of the abundance distribution, ground-truthing this against the observed abundances. Then, we jointly use the observed genetic data and abundances to estimate the proximity of the community to equilibrium. Results Simulation experiments of our ABC procedure demonstrate that coupling abundance with genetic data leads to improved accuracy and precision of model parameter estimates compared with using abundance-only data. We further demonstrate reasonable precision and accuracy in estimating a metric underlying the shape of the abundance distribution, temporal progress towards local equilibrium and several key parameters of the community assembly process. For the insular arachnid assemblage, we find the joint distribution of genetic diversity and abundance approaches equilibrium expectations, and that the Shannon entropy of the observed abundances can be estimated using genetic data alone. Main conclusions The framework that we present unifies neutral community assembly and comparative phylogeography to characterize the community-level distribution of both abundance and genetic variation through time, providing a resource that should greatly enhance understanding of both the processes structuring ecological communities and the associated aggregate demographic histories.}, - keywords = {community genetic diversity,comparative phylogeography,ecological neutral theory,island biogeography,non-equilibrium dynamics,species abundance distributions}, - file = {/Users/renatadiaz/Zotero/storage/TCQLW68H/Overcast et al. - 2019 - An integrated model of population genetics and com.pdf;/Users/renatadiaz/Zotero/storage/DQZ332SY/jbi.html} -} - -@article{overcast2021, - title = {A Unified Model of Species Abundance, Genetic Diversity, and Functional Diversity Reveals the Mechanisms Structuring Ecological Communities}, - author = {Overcast, Isaac and Ruffley, Megan and Rosindell, James and Harmon, Luke and Borges, Paulo A. V. and Emerson, Brent C. and Etienne, Rampal S. and Gillespie, Rosemary and Krehenwinkel, Henrik and Mahler, D. Luke and Massol, Francois and Parent, Christine E. and Pati{\~n}o, Jairo and Peter, Ben and Week, Bob and Wagner, Catherine and Hickerson, Michael J. and Rominger, Andrew}, - year = {2021}, - journal = {Molecular Ecology Resources}, - volume = {21}, - number = {8}, - pages = {2782--2800}, - issn = {1755-0998}, - doi = {10.1111/1755-0998.13514}, - abstract = {Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce massive ecoevolutionary synthesis simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: (i) species richness and abundances, (ii) population genetic diversities, and (iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community-scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multidimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine MESS with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales.}, - langid = {english}, - keywords = {community ecology,community genetic diversity,community phylogenetics,comparative phylogeography,population genetics}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13514}, - file = {/Users/renatadiaz/Zotero/storage/JAH6C35W/Overcast et al. - 2021 - A unified model of species abundance, genetic dive.pdf;/Users/renatadiaz/Zotero/storage/JK4PQKJF/1755-0998.html} -} - -@article{paine2018, - title = {Towards the General Mechanistic Prediction of Community Dynamics}, - author = {Paine, C. E. Timothy and Deasey, Anna and Duthie, A. Bradley}, - year = {2018}, - journal = {Functional Ecology}, - volume = {32}, - number = {7}, - pages = {1681--1692}, - issn = {1365-2435}, - doi = {10.1111/1365-2435.13096}, - abstract = {``What controls the distribution and abundance of organisms''? This question, at the heart of the dynamics of ecological communities, would have been familiar to the earliest ecologists. Having lain effectively abandoned for many years, community dynamics today is a vibrant research topic of great conceptual interest with practical import for conservation, ecological management, ecosystem services and the responses of ecological communities to climate change. We describe how modern coexistence theory can be used to predict community dynamics through the use of demography. We explore the challenges that limit the deployment of this demographic framework, and the tools from phylogenetic and functional ecology that have been used to surmount them. Finding existing tools not altogether sufficient, we propose the use of ``hard'' functional traits and physiological tolerances of environmental conditions and low resource availability to extend the demographic framework so that the dynamics of a broader range of ecological communities can be accurately predicted. We illustrate these new approaches with two case studies. Given the urgent need to accurately forecast the dynamics of ecological communities, we hope that many ecologists will adopt these tools. A plain language summary is available for this article.}, - copyright = {\textcopyright{} 2018 The Authors. Functional Ecology\textcopyright{} 2018 British Ecological Society}, - langid = {english}, - keywords = {competition,context dependence,demography,ecological forecasting,interspecific interactions,relative abundance,species composition}, - annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2435.13096}, - file = {/Users/renatadiaz/Zotero/storage/NF4FZANR/Paine et al. - 2018 - Towards the general mechanistic prediction of comm.pdf;/Users/renatadiaz/Zotero/storage/4YH7DTN6/1365-2435.html} -} - -@article{papadopoulou2011, - title = {Testing the {{Species}}\textendash{{Genetic Diversity Correlation}} in the {{Aegean Archipelago}}: {{Toward}} a {{Haplotype-Based Macroecology}}?}, - shorttitle = {Testing the {{Species}}\textendash{{Genetic Diversity Correlation}} in the {{Aegean Archipelago}}}, - author = {Papadopoulou, Anna and Anastasiou, Ioannis and Spagopoulou, Foteini and Stalimerou, Malda and Terzopoulou, Sofia and Legakis, Anastasios and Vogler, Alfried P.}, - year = {2011}, - month = aug, - journal = {The American Naturalist}, - volume = {178}, - number = {2}, - pages = {241--255}, - issn = {0003-0147, 1537-5323}, - doi = {10.1086/660828}, - abstract = {A positive correlation between species diversity and genetic diversity has been proposed, consistent with neutral predictions in macroecology. We assessed the species\textendash genetic diversity correlation in tenebrionid beetle communities of the Aegean archipelago on 15 islands of different sizes, distances to mainland, and ages of isolation. Alpha and beta diversity of species and haplotypes were assessed using sequences of 11,000 individuals (mitochondrial cytochrome oxidase 1 and nuclear muscular protein 20). We show that (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland is factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated on the basis of species, nuclear, and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sanddwelling lineages compared with less dispersive lineages that are not sand obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting largescale biodiversity patterns based on genetic inventories of local samples.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/QSML7CZX/Papadopoulou et al. - 2011 - Testing the Species–Genetic Diversity Correlation .pdf} -} - -@misc{pardieck2019, - title = {North {{American Breeding Bird Survey Dataset}} 1966 - 2018, Version 2018.0}, - author = {Pardieck, Keith L. and Ziolkowski, David J. and Lutmerding, Michael and Aponte, Veronica and Hudson, Marie-Anne}, - year = {2019}, - publisher = {{U.S. Geological Survey}}, - doi = {10.5066/P9HE8XYJ}, - abstract = {The 1966-2018 North American Breeding Bird Survey dataset contains avian point count data for more than 700 North American bird taxa (primarily species, but also some races and unidentified species groupings). These data are collected annually during the breeding season, primarily June and May, along thousands of randomly established roadside survey routes in the United States and Canada. Routes are about 24.5 miles (39.2 km) long with counting locations placed at regular intervals, for a total of 50 stops. At each stop, a person highly skilled in avian identification conducts a 3-minute point count, recording every bird seen within a quarter-mile (400-m) radius and every bird heard. Surveys begin 30 minutes before local sunrise and take approximately 5 hours to complete. A route is sampled once per year, with the total number of routes sampled per year growing over time; about 600 routes were sampled in 1966, while in recent decades approximately 3000 routes have been sampled annually. In addition to avian count data, this dataset also contains date route sampled, survey start and end times, start and end weather conditions, a unique observer identification number, route identification information, route location information including geographic coordinates of route start point, and an indicator of sample quality.}, - keywords = {avian population data; bird counts; relative abundance; BBS} -} - -@misc{pardieck2019a, - title = {North {{American Breeding Bird Survey Dataset}} 1966 - 2018, Version 2018.0}, - author = {Pardieck, Keith L. and Ziolkowski, David J. and Lutmerding, Michael and Aponte, Veronica and Hudson, Marie-Anne}, - year = {2019}, - publisher = {{U.S. Geological Survey}}, - doi = {10.5066/P9HE8XYJ}, - abstract = {The 1966-2018 North American Breeding Bird Survey dataset contains avian point count data for more than 700 North American bird taxa (primarily species, but also some races and unidentified species groupings). These data are collected annually during the breeding season, primarily June and May, along thousands of randomly established roadside survey routes in the United States and Canada. Routes are about 24.5 miles (39.2 km) long with counting locations placed at regular intervals, for a total of 50 stops. At each stop, a person highly skilled in avian identification conducts a 3-minute point count, recording every bird seen within a quarter-mile (400-m) radius and every bird heard. Surveys begin 30 minutes before local sunrise and take approximately 5 hours to complete. A route is sampled once per year, with the total number of routes sampled per year growing over time; about 600 routes were sampled in 1966, while in recent decades approximately 3000 routes have been sampled annually. In addition to avian count data, this dataset also contains date route sampled, survey start and end times, start and end weather conditions, a unique observer identification number, route identification information, route location information including geographic coordinates of route start point, and an indicator of sample quality.}, - keywords = {avian population data; bird counts; relative abundance; BBS} -} - -@article{pedersen2017, - title = {Shallow Size-Density Relations within Mammal Clades Suggest Greater Intra-Guild Ecological Impact of Large-Bodied Species}, - author = {Pedersen, Rasmus {\O}stergaard and Faurby, S{\o}ren and Svenning, Jens-Christian}, - editor = {Meiri, Shai}, - year = {2017}, - month = sep, - journal = {Journal of Animal Ecology}, - volume = {86}, - number = {5}, - pages = {1205--1213}, - issn = {00218790}, - doi = {10.1111/1365-2656.12701}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/UU5KTZHE/Pedersen et al. - 2017 - Shallow size-density relations within mammal clade.pdf} -} - -@article{perez-garcia2021, - title = {Nonlinear Science against the {{COVID-19}} Pandemic}, - author = {{P{\'e}rez-Garc{\'i}a}, V{\'i}ctor M.}, - year = {2021}, - month = oct, - journal = {Physica D: Nonlinear Phenomena}, - volume = {424}, - pages = {132946}, - issn = {0167-2789}, - doi = {10.1016/j.physd.2021.132946}, - abstract = {This special issue showcases recent uses of mathematical and nonlinear science methods in the study of different problems arising in the context of the COVID-19 pandemic. The sixteen original research papers included in this collection span a wide spectrum of studies including classical epidemiological models, new models accounting for COVID-19 specificities, non-pharmaceutical control measures, network models and other problems related to the pandemic.}, - langid = {english}, - keywords = {Dynamical systems in epidemics,Mathematical epidemiology,SARS-COV-19 mathematical studies}, - file = {/Users/renatadiaz/Zotero/storage/KI8JCK4U/Pérez-García - 2021 - Nonlinear science against the COVID-19 pandemic.pdf;/Users/renatadiaz/Zotero/storage/KY7XNWYX/S0167278921001044.html} -} - -@article{perez-riverol2016, - title = {Ten {{Simple Rules}} for {{Taking Advantage}} of {{Git}} and {{GitHub}}}, - author = {{Perez-Riverol}, Yasset and Gatto, Laurent and Wang, Rui and Sachsenberg, Timo and Uszkoreit, Julian and Leprevost, Felipe da Veiga and Fufezan, Christian and Ternent, Tobias and Eglen, Stephen J. and Katz, Daniel S. and Pollard, Tom J. and Konovalov, Alexander and Flight, Robert M. and Blin, Kai and Vizca{\'i}no, Juan Antonio}, - editor = {Markel, Scott}, - year = {2016}, - month = jul, - journal = {PLOS Computational Biology}, - volume = {12}, - number = {7}, - pages = {e1004947}, - issn = {1553-7358}, - doi = {10.1371/journal.pcbi.1004947}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/9DT68368/Perez-Riverol et al. - 2016 - Ten Simple Rules for Taking Advantage of Git and G.pdf} -} - -@article{perez-riverol2016a, - title = {Ten {{Simple Rules}} for {{Taking Advantage}} of {{Git}} and {{GitHub}}}, - author = {{Perez-Riverol}, Yasset and Gatto, Laurent and Wang, Rui and Sachsenberg, Timo and Uszkoreit, Julian and Leprevost, Felipe da Veiga and Fufezan, Christian and Ternent, Tobias and Eglen, Stephen J. and Katz, Daniel S. and Pollard, Tom J. and Konovalov, Alexander and Flight, Robert M. and Blin, Kai and Vizca{\'i}no, Juan Antonio}, - year = {2016}, - month = jul, - journal = {PLOS Computational Biology}, - volume = {12}, - number = {7}, - pages = {e1004947}, - publisher = {{Public Library of Science}}, - issn = {1553-7358}, - doi = {10.1371/journal.pcbi.1004947}, - langid = {english}, - keywords = {Bioinformatics,Computer software,Control systems,Open source software,Scientific publishing,Software development,Source code,Web-based applications}, - file = {/Users/renatadiaz/Zotero/storage/4RDA28MR/Perez-Riverol et al. - 2016 - Ten Simple Rules for Taking Advantage of Git and G.pdf;/Users/renatadiaz/Zotero/storage/FC76A78P/article.html} -} - -@article{perkins2019, - title = {Energetic Equivalence Underpins the Size Structure of Tree and Phytoplankton Communities}, - author = {Perkins, Daniel M. and Perna, Andrea and Adrian, Rita and Cerme{\~n}o, Pedro and Gaedke, Ursula and {Huete-Ortega}, Maria and White, Ethan P. and {Yvon-Durocher}, Gabriel}, - year = {2019}, - month = dec, - journal = {Nature Communications}, - volume = {10}, - number = {1}, - pages = {255}, - issn = {2041-1723}, - doi = {10.1038/s41467-018-08039-3}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/6AUGV3YU/Perkins et al. - 2019 - Energetic equivalence underpins the size structure.pdf} -} - -@article{petchey2007, - title = {Low Functional Diversity and No Redundancy in {{British}} Avian Assemblages}, - author = {Petchey, Owen L. and Evans, Karl L. and Fishburn, Isla S. and Gaston, Kevin J.}, - year = {2007}, - journal = {Journal of Animal Ecology}, - volume = {76}, - number = {5}, - pages = {977--985}, - issn = {1365-2656}, - doi = {10.1111/j.1365-2656.2007.01271.x}, - abstract = {1 Spatial and temporal patterns in functional diversity can reveal the patterns and processes behind community assembly and whether ecological redundancy exists. Here, we analyse functional diversity in British avian assemblages over a period of about 20 years. 2 Functional diversity is generally lower than expected by chance, indicating that assemblages contain species with relatively similar functional traits. One potential explanation is filtering for traits suitable to particular habitats, though other explanations exist. 3 There was no evidence of ecological redundancy over the 20 years. In fact, changes in functional diversity were almost exactly proportional to changes in species richness. 4 The absence of functional redundancy results from little redundancy intrinsic to the species' functional relationships and also because compositional change was nonrandom. Observed extinction and colonization events caused greater changes in functional diversity than if these events were random. 5 Our findings suggest that community assembly is influenced by the traits of species and that observed changes in functional diversity provide no reason to believe that the functioning of natural systems is buffered against change by ecological redundancy.}, - langid = {english}, - annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2656.2007.01271.x}, - file = {/Users/renatadiaz/Zotero/storage/536MMJV9/Petchey et al. - 2007 - Low functional diversity and no redundancy in Brit.pdf;/Users/renatadiaz/Zotero/storage/YZN4D4A9/Petchey et al. - 2007 - Low functional diversity and no redundancy in Brit.pdf;/Users/renatadiaz/Zotero/storage/9N7U7L6D/j.1365-2656.2007.01271.html} -} - -@article{petchey2010, - title = {Body-Size Distributions and Size-Spectra: Universal Indicators of Ecological Status?}, - shorttitle = {Body-Size Distributions and Size-Spectra}, - author = {Petchey, Owen L. and Belgrano, Andrea}, - year = {2010}, - month = aug, - journal = {Biology Letters}, - volume = {6}, - number = {4}, - pages = {434--437}, - publisher = {{Royal Society}}, - doi = {10.1098/rsbl.2010.0240}, - abstract = {The sizes of individual organisms, rather than their taxonomy, are used to inform management and conservation in some aquatic ecosystems. The European Science Foundation Research Network, SIZEMIC, facilitates integration of such approaches with the more taxonomic approaches used in terrestrial ecology. During its 4-year tenure, the Network is bringing together researchers from disciplines including theorists, empiricists, government employees, and practitioners, via a series of meetings, working groups and research visits. The research conducted suggests that organismal size, with a generous helping of taxonomy, provides the most probable route to universal indicators of ecological status.}, - keywords = {allometry,ecosystem assessment,taxonomy}, - file = {/Users/renatadiaz/Zotero/storage/44RGIATR/Petchey and Belgrano - 2010 - Body-size distributions and size-spectra universa.pdf;/Users/renatadiaz/Zotero/storage/BL6PCR7Q/Petchey and Belgrano - 2010 - Body-size distributions and size-spectra universa.pdf;/Users/renatadiaz/Zotero/storage/27GCR3Z6/rsbl.2010.html} -} - -@article{pfeiffer2018, - title = {Partitioning Genetic and Species Diversity Refines Our Understanding of Species\textendash Genetic Diversity Relationships}, - author = {Pfeiffer, Vera Wilder and Ford, Brett Michael and Housset, Johann and McCombs, Audrey and {Blanco-Pastor}, Jos{\'e} Luis and Gouin, Nicolas and Manel, St{\'e}phanie and Bertin, Ang{\'e}line}, - year = {2018}, - journal = {Ecology and Evolution}, - volume = {8}, - number = {24}, - pages = {12351--12364}, - issn = {2045-7758}, - doi = {10.1002/ece3.4530}, - abstract = {Disentangling the origin of species\textendash genetic diversity correlations (SGDCs) is a challenging task that provides insight into the way that neutral and adaptive processes influence diversity at multiple levels. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high-elevation Andean wetland system, where previous evidence identified neutral processes as major determinants of the strong and positive covariation between plant species richness and AFLP genetic diversity of the common sedge Carex gayana. To tease apart putative neutral and non-neutral genetic variation of C. gayana, we identified loci putatively under selection from a dataset of 1,709 SNPs produced using restriction site-associated DNA sequencing (RAD-seq). Significant and positive relationships between local estimates of genetic and species diversities ({$\alpha$}-SGDCs) were only found with the putatively neutral loci datasets and with species richness, confirming that neutral processes were primarily driving the correlations and that the involved processes differentially influenced local species diversity components (i.e., richness and evenness). In contrast, SGDCs based on genetic and community dissimilarities ({$\beta$}-SGDCs) were only significant with the putative non-neutral datasets. This suggests that selective processes influencing C. gayana genetic diversity were involved in the detected correlations. Together, our results demonstrate that analyzing distinct components of genetic and species diversity simultaneously is useful to determine the mechanisms behind species\textendash genetic diversity relationships.}, - langid = {english}, - keywords = {genetic outlier,high Andean wetlands,SNP,species–genetic diversity correlation}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4530}, - file = {/Users/renatadiaz/Zotero/storage/CS2DJIDN/Pfeiffer et al. - 2018 - Partitioning genetic and species diversity refines.pdf;/Users/renatadiaz/Zotero/storage/GJDT7XY8/ece3.html} -} - -@book{phillips2002, - title = {Global Patterns of Plant Diversity: {{Alwyn H}}. {{Gentry}}'s Forest Transect Data Set}, - shorttitle = {Global Patterns of Plant Diversity}, - author = {Phillips, Oliver and Miller, James Stuart}, - year = {2002}, - volume = {89}, - publisher = {{Missouri Botanical Press}} -} - -@misc{pinheiro2020, - title = {Nlme: {{Linear}} and {{Nonlinear Mixed Effects Models}}}, - author = {Pinheiro, Jose and Bates, Douglas and DebRoy, Saikat and Sarkar, Deepayan and {R Core Team}}, - year = {2020} -} - -@article{poisot2016, - title = {Synthetic Datasets and Community Tools for the Rapid Testing of Ecological Hypotheses}, - author = {Poisot, Timoth{\'e}e and Gravel, Dominique and Leroux, Shawn and Wood, Spencer A. and Fortin, Marie-Jos{\'e}e and Baiser, Benjamin and Cirtwill, Alyssa R. and Ara{\'u}jo, Miguel B. and Stouffer, Daniel B.}, - year = {2016}, - journal = {Ecography}, - volume = {39}, - number = {4}, - pages = {402--408}, - issn = {1600-0587}, - doi = {10.1111/ecog.01941}, - abstract = {The increased availability of both open ecological data, and software to interact with it, allows the fast collection and integration of information at all spatial and taxonomic scales. This offers the opportunity to address macroecological questions in a cost-effective way. In this contribution, we illustrate this approach by forecasting the structure of a stream food web at the global scale. In so doing, we highlight the most salient issues needing to be addressed before this approach can be used with a high degree of confidence.}, - copyright = {\textcopyright{} 2015 The Authors}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/WWAGQNUK/Poisot et al. - 2016 - Synthetic datasets and community tools for the rap.pdf;/Users/renatadiaz/Zotero/storage/7Y77FBKA/ecog.html;/Users/renatadiaz/Zotero/storage/BYTU5I2G/ecog.html} -} - -@article{poisot2018, - title = {Data-Based, Synthesis-Driven: Setting the Agenda for Computational Ecology}, - shorttitle = {Data-Based, Synthesis-Driven}, - author = {Poisot, Timothee and Labrie, Richard and Larson, Erin and Rahlin, Anastasia}, - year = {2018}, - month = jul, - journal = {bioRxiv}, - doi = {10.1101/150128}, - abstract = {Computational ecology, defined as the application of computational thinking to ecological problems, has the potential to transform the way ecologists think about the integration of data and models. As the practice is gaining prominence as a way to conduct ecological research, it is important to reflect on what its agenda could be, and how it fits within the broader landscape. In this contribution, we suggest areas in which empirical ecologists, modellers, and the emerging community of computational ecologists could engage in a constructive dialogue to build on one another expertise. We discuss how training can be amended to improve the computational literacy of ecologists can be improved.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/6HPWDU39/Poisot et al. - 2018 - Data-based, synthesis-driven setting the agenda f.pdf} -} - -@misc{poisot2022, - title = {Network Embedding Unveils the Hidden Interactions in the Mammalian Virome}, - author = {Poisot, Timoth{\'e}e and Ouellet, Marie-Andr{\'e}e and Mollentze, Nardus and Farrell, Maxwell J. and Becker, Daniel J. and Brierly, Liam and Albery, Gregory F. and Gibb, Rory J. and Seifert, Stephanie N. and Carlson, Colin J.}, - year = {2022}, - month = mar, - number = {arXiv:2105.14973}, - eprint = {2105.14973}, - eprinttype = {arxiv}, - primaryclass = {q-bio}, - publisher = {{arXiv}}, - doi = {10.48550/arXiv.2105.14973}, - abstract = {At most 1-2\% of the global virome has been sampled to date. Recent work has shown that predicting which host-virus interactions are possible but undiscovered or unrealized is, fundamentally, a network science problem. Here, we develop a novel method that combines a coarse recommender system (Linear Filtering; LF) with an imputation algorithm based on low-rank graph embedding (Singular Value Decomposition; SVD) to infer host-virus associations. This combination of techniques results in informed initial guesses based on directly measurable network properties (density, degree distribution) that are refined through SVD (which is able to leverage emerging features). Using this method, we recovered highly plausible undiscovered interactions with a strong signal of viral coevolutionary history, and revealed a global hotspot of unusually unique but unsampled (or unrealized) host-virus interactions in the Amazon rainforest. We develop several tests for quantifying the bias and realism of these predictions, and show that the LF-SVD method is robust in each aspect. We finally show that graph embedding of the imputed network can be used to improve predictions of human infection from viral genome features, showing that the global structure of the mammal-virus network provides additional insights into human disease emergence.}, - archiveprefix = {arXiv}, - keywords = {Quantitative Biology - Quantitative Methods}, - file = {/Users/renatadiaz/Zotero/storage/XHMUBIAY/Poisot et al. - 2022 - Network embedding unveils the hidden interactions .pdf;/Users/renatadiaz/Zotero/storage/UXT5IDVS/2105.html} -} - -@article{ponisio2019, - title = {A {{Network Perspective}} for {{Community Assembly}}}, - author = {Ponisio, Lauren C. and Valdovinos, Fernanda S. and Allhoff, Korinna T. and Gaiarsa, Mar{\'i}lia P. and Barner, Allison and Guimar{\~a}es, Paulo R. Jr and Hembry, David H. and Morrison, Beth and Gillespie, Rosemary}, - year = {2019}, - journal = {Frontiers in Ecology and Evolution}, - volume = {7}, - publisher = {{Frontiers}}, - issn = {2296-701X}, - doi = {10.3389/fevo.2019.00103}, - abstract = {Species interactions are responsible for many key mechanisms that govern the dynamics of ecological communities. Variation in the way interactions are organized among species results in different network structures, which translates into a community's ability to resist collapse and change. To better understand the factors involved in dictating ongoing dynamics in a community at a given time, we must unravel how interactions affect the assembly process. Here, we build a novel, integrative conceptual model for understanding how ecological communities assemble that combines ecological networks and island biogeography theory, as well as the principles of niche theory. Through our conceptual model, we show how the rate of species turnover and gene flow within communities will influence the structure of ecological networks. We conduct a preliminary test of our predictions using plant-herbivore networks from differently-aged sites in the Hawaiian archipelago. Our approach will allow future modeling and empirical studies to develop a better understanding of the role of the assembly process in shaping patterns of biodiversity.}, - langid = {english}, - keywords = {Coevolution,evolution,Island,island biogeography,network,succession,turnover}, - file = {/Users/renatadiaz/Zotero/storage/I6NYTDRZ/Ponisio et al. - 2019 - A Network Perspective for Community Assembly.pdf} -} - -@article{pontarp2019, - title = {The {{Latitudinal Diversity Gradient}}: {{Novel Understanding}} through {{Mechanistic Eco-evolutionary Models}}}, - shorttitle = {The {{Latitudinal Diversity Gradient}}}, - author = {Pontarp, Mikael and Bunnefeld, Lynsey and Cabral, Juliano Sarmento and Etienne, Rampal S. and Fritz, Susanne A. and Gillespie, Rosemary and Graham, Catherine H. and Hagen, Oskar and Hartig, Florian and Huang, Shan and Jansson, Roland and Maliet, Odile and M{\"u}nkem{\"u}ller, Tamara and Pellissier, Lo{\"i}c and Rangel, Thiago F. and Storch, David and Wiegand, Thorsten and Hurlbert, Allen H.}, - year = {2019}, - month = mar, - journal = {Trends in Ecology \& Evolution}, - volume = {34}, - number = {3}, - pages = {211--223}, - issn = {01695347}, - doi = {10.1016/j.tree.2018.11.009}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/EAINHVBD/Pontarp et al. - 2019 - The Latitudinal Diversity Gradient Novel Understa.pdf} -} - -@article{portet2020, - title = {A Primer on Model Selection Using the {{Akaike Information Criterion}}}, - author = {Portet, St{\'e}phanie}, - year = {2020}, - month = jan, - journal = {Infectious Disease Modelling}, - volume = {5}, - pages = {111--128}, - issn = {2468-0427}, - doi = {10.1016/j.idm.2019.12.010}, - abstract = {A powerful investigative tool in biology is to consider not a single mathematical model but a collection of models designed to explore different working hypotheses and select the best model in that collection. In these lecture notes, the usual workflow of the use of mathematical models to investigate a biological problem is described and the use of a collection of model is motivated. Models depend on parameters that must be estimated using observations; and when a collection of models is considered, the best model has then to be identified based on available observations. Hence, model calibration and selection, which are intrinsically linked, are essential steps of the workflow. Here, some procedures for model calibration and a criterion, the Akaike Information Criterion, of model selection based on experimental data are described. Rough derivation, practical technique of computation and use of this criterion are detailed.}, - langid = {english}, - keywords = {Akaike information criterion,Collection of models,Model calibration,Model selection}, - file = {/Users/renatadiaz/Zotero/storage/EF52SUW8/Portet - 2020 - A primer on model selection using the Akaike Infor.pdf} -} - -@article{potapov2019, - title = {Linking Size Spectrum, Energy Flux and Trophic Multifunctionality in Soil Food Webs of Tropical Land-Use Systems}, - author = {Potapov, Anton M. and Klarner, Bernhard and Sandmann, Dorothee and Widyastuti, Rahayu and Scheu, Stefan}, - year = {2019}, - journal = {Journal of Animal Ecology}, - volume = {88}, - number = {12}, - pages = {1845--1859}, - issn = {1365-2656}, - doi = {10.1111/1365-2656.13027}, - abstract = {Many ecosystem functions depend on the structure of food webs, which heavily relies on the body size spectrum of the community. Despite that, little is known on how the size spectrum of soil animals responds to agricultural practices in tropical land-use systems and how these responses affect ecosystem functioning. We studied land-use-induced changes in below-ground communities in tropical lowland ecosystems in Sumatra (Jambi province, Indonesia), a hot spot of tropical rainforest conversion into rubber and oil palm plantations. The study included ca. 30,000 measured individuals from 33 high-order taxa of meso- and macrofauna spanning eight orders of magnitude in body mass. Using individual body masses, we calculated the metabolism of trophic guilds and used food web models to calculate energy fluxes and infer ecosystem functions, such as decomposition, herbivory, primary and intraguild predation. Land-use change was associated with reduced abundance and taxonomic diversity of soil invertebrates, but strong increase in total biomass and moderate changes in total energy flux. These changes were due to increased biomass of large-sized decomposers in soil, in particular earthworms, with their share in community metabolism increasing from 11\% in rainforest to 59\%\textendash 76\% in jungle rubber, and rubber and oil palm plantations. Decomposition, that is the energy flux to decomposers, stayed unchanged, but herbivory, primary and intraguild predation decreased by an order of magnitude in plantation systems. Intraguild predation was very important, being responsible for 38\% of the energy flux in rainforest according to our model. Conversion of rainforest into monoculture plantations is associated by an uneven loss of size classes and trophic levels of soil invertebrates resulting in sequestration of energy in large-sized primary consumers and restricted flux of energy to higher trophic levels. Pronounced differences between rainforest and jungle rubber reflect sensitivity of rainforest soil animal communities to moderate land-use changes. Soil communities in plantation systems sustained high total energy flux despite reduced biodiversity. The high energy flux into large decomposers but low energy fluxes into other trophic guilds suggests that trophic multifunctionality of below-ground communities is compromised in plantation systems.}, - copyright = {\textcopyright{} 2019 The Authors. Journal of Animal Ecology \textcopyright{} 2019 British Ecological Society}, - langid = {english}, - keywords = {biodiversity,biomass,body mass,ecosystem functioning,intraguild predation,oil palm,rainforest,trophic guilds}, - annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2656.13027}, - file = {/Users/renatadiaz/Zotero/storage/MEKR23IR/Potapov et al. - 2019 - Linking size spectrum, energy flux and trophic mul.pdf;/Users/renatadiaz/Zotero/storage/CKQKW3K4/1365-2656.html} -} - -@article{preston1948, - title = {The {{Commonness}}, {{And Rarity}}, of {{Species}}}, - author = {Preston, F. W.}, - year = {1948}, - month = jul, - journal = {Ecology}, - volume = {29}, - number = {3}, - pages = {254--283}, - issn = {00129658}, - doi = {10.2307/1930989}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/PS4UQBGN/Preston - 1948 - The Commonness, And Rarity, of Species.pdf;/Users/renatadiaz/Zotero/storage/7DK84HEJ/1930989.html} -} - -@article{preston1950, - title = {Gas {{Laws}} and {{Wealth Laws}}}, - author = {Preston, Frank W.}, - year = {1950}, - journal = {The Scientific Monthly}, - volume = {71}, - number = {5}, - pages = {309--311}, - publisher = {{American Association for the Advancement of Science}}, - issn = {0096-3771} -} - -@article{preston1962, - title = {The {{Canonical Distribution}} of {{Commonness}} and {{Rarity}}: {{Part II}}}, - shorttitle = {The {{Canonical Distribution}} of {{Commonness}} and {{Rarity}}}, - author = {Preston, F. W.}, - year = {1962}, - journal = {Ecology}, - volume = {43}, - number = {3}, - pages = {410--432}, - issn = {1939-9170}, - doi = {10.2307/1933371}, - copyright = {\textcopyright{} 1962 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1933371}, - file = {/Users/renatadiaz/Zotero/storage/DX4NHBKH/Preston - 1962 - The Canonical Distribution of Commonness and Rarit.pdf;/Users/renatadiaz/Zotero/storage/ND2E3E8Z/1933371.html} -} - -@article{preston1962a, - title = {The {{Canonical Distribution}} of {{Commonness}} and {{Rarity}}: {{Part I}}}, - shorttitle = {The {{Canonical Distribution}} of {{Commonness}} and {{Rarity}}}, - author = {Preston, F. W.}, - year = {1962}, - journal = {Ecology}, - volume = {43}, - number = {2}, - pages = {185--215}, - issn = {1939-9170}, - doi = {10.2307/1931976}, - copyright = {\textcopyright{} 1962 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1931976}, - file = {/Users/renatadiaz/Zotero/storage/XGI2PMC3/1931976.html} -} - -@article{preston1980, - title = {Noncanonical {{Distributions}} of {{Commonness}} and {{Rarity}}}, - author = {Preston, Frank W.}, - year = {1980}, - journal = {Ecology}, - volume = {61}, - number = {1}, - pages = {88--97}, - issn = {1939-9170}, - doi = {10.2307/1937159}, - abstract = {Some reported counts of species abundances, when tallied by octaves or other appropriate intervals, do not conform at all well to the expected normal (lognormal) distribution, but the departures therefrom seem to be by no means systematic or consistent. In the present paper we examine briefly two examples: The Audubon Christmas Bird Counts, and the counts of diatoms in freshwater streams. In some cases the departure may be due to defective, nonrandom, sampling; in others to using more than one method of sampling and then confounding the samples; in still others the sampling may be satisfactory, but the 'universe' that is sampled may itself be a hybrid one, two universes (or more than two) interpenetrating one another. In the tropics the distribution of birds is lognormal but not canonical. Here the explanation must be different. The sigma values are far too low. I call these 'congested' distributions. Biologically it may mean that there are more species than niches, a presumably unstable situation, possibly arising from recent (Pleistocene?) excessive speciation. Apparently some problems exist that deserve examination.}, - copyright = {\textcopyright{} 1980 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1937159}, - file = {/Users/renatadiaz/Zotero/storage/4KUTN9CC/1937159.html} -} - -@article{price1978, - title = {The {{Role}} of {{Microhabitat}} in {{Structuring Desert Rodent Communities}}}, - author = {Price, Mary V}, - year = {1978}, - journal = {Ecology}, - pages = {13}, - abstract = {Interspecific competition is thought to be important in determining patterns of r use and species abundances in natural communities. However, there have been few field t competition-based models of community structure. In this study, experiments were conduct 4 coexisting desert rodent species to see whether competition is a sufficient explanation f resource use and abundance patterns. Results were consistent with 3 predictions from compe theory. (1) The 4 species differed in their use of a resource, foraging microhabitat, which is pote limiting to their populations. (2) Each species shifted its use of microhabitats in predicted dir when competitors were removed from or added to outdoor enclosures. (3) Each species was dense where its preferred microhabitat was abundant, and augmentation of 1 microhabitat l increase in the density of the appropriate microhabitat specialist. These results suggest that tition maintains interspecific differences in foraging microhabitat, and that the availability o priate microhabitats determines species abundances on a local scale.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/HZZ72K2M/Price - 1978 - The Role of Microhabitat in Structuring Desert Rod.pdf} -} - -@article{prokosch2019, - title = {Are Animals Shrinking Due to Climate Change? {{Temperature-mediated}} Selection on Body Mass in Mountain Wagtails}, - shorttitle = {Are Animals Shrinking Due to Climate Change?}, - author = {Prokosch, Jorinde and Bernitz, Zephne and Bernitz, Herman and Erni, Birgit and Altwegg, Res}, - year = {2019}, - month = mar, - journal = {Oecologia}, - volume = {189}, - number = {3}, - pages = {841--849}, - issn = {1432-1939}, - doi = {10.1007/s00442-019-04368-2}, - abstract = {Climate change appears to affect body size of animals whose optimal size in part depends on temperature. However, attribution of observed body size changes to climate change requires an understanding of the selective pressures acting on body size under different temperatures. We examined the link between temperature and body mass in a population of mountain wagtails (Motacilla clara) in KwaZulu-Natal, South Africa, between 1976 and 1999, where temperature increased by 0.18~\$\$\^\textbackslash circ \$\$C. The wagtails became lighter by 0.035~g per year. Partitioning this trend, we found that only a small part of the effect (0.009~g/year) was due to individuals losing weight and a large part (0.027~g/year) was due to lighter individuals replacing heavier ones. Only the latter component was statistically significant. Apparently, the wagtails were reacting to selection for reduced weight. Examining survival, we found that selection was temperature-mediated, i.e., lighter individuals survived better under high temperatures, whereas heavier individuals survived better under low temperatures. Our results thus support the hypothesis that temperature drove the decline in body mass in this wagtail population and provides one of the first demonstrations of the selective forces underlying such trends.}, - langid = {english}, - keywords = {Bergmann’s rule,Body mass,Climate change,Motacilla clara,Survival} -} - -@article{prugh2012, - title = {Partitioning the Effects of an Ecosystem Engineer: Kangaroo Rats Control Community Structure via Multiple Pathways}, - shorttitle = {Partitioning the Effects of an Ecosystem Engineer}, - author = {Prugh, Laura R. and Brashares, Justin S.}, - year = {2012}, - journal = {Journal of Animal Ecology}, - volume = {81}, - number = {3}, - pages = {667--678}, - publisher = {{British Ecological Society}}, - issn = {0021-8790}, - abstract = {1. Ecosystem engineers impact communities by altering habitat conditions, but they can also have strong effects through consumptive, competitive and other non-engineering pathways. 2. Engineering effects can lead to fundamentally different community dynamics than non-engineering effects, but the relative strengths of these interactions are seldom quantified. 3. We combined structural equation modelling and exclosure experiments to partition the effects of a keystone engineer, the giant kangaroo rat (Dipodomys ingens), on plants, invertebrates and vertebrates in a semi-arid California grassland. 4. We separated the effects of burrow creation from kangaroo rat density and found that kangaroo rats increased the diversity and abundance of other species via both engineering and non-engineering pathways. 5. Engineering was the primary factor structuring plant and small mammal communities, whereas non-engineering effects structured invertebrate communities and increased lizard abundance. 6. These results highlight the importance of the non-engineering effects of ecosystem engineers and shed new light on the multiple pathways by which strong-interactors shape communities.} -} - -@misc{qubes, - title = {{{QUBES}} - {{Home}}}, - author = {QUBES}, - journal = {https://qubeshub.org/}, - howpublished = {https://qubeshub.org/}, - file = {/Users/renatadiaz/Zotero/storage/9MWZY3L3/qubeshub.org.html} -} - -@article{raup1994, - title = {The Role of Extinction in Evolution.}, - author = {Raup, D M}, - year = {1994}, - month = jul, - journal = {Proceedings of the National Academy of Sciences}, - volume = {91}, - number = {15}, - pages = {6758--6763}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.91.15.6758}, - abstract = {The extinction of species is not normally consideed an important element of neodarwinian theory, in contrast to the opposite phenomenon, specatlon. This is surprising in view of the special importance Darwin attced to extinction, and because the number of species extinctions in the history of life is almost the same as the number of originations; present-day biodiversity Is the result of a trivial surplus of tions, cumulated over millions of years. For an evolutionary biologist to ignore extinction is probably as foolhardy as for a demographer to ignore mortality. The past decade has seen a resurgence of interest in extinction, yet research on the topic Is stifl at a reconnaissance level, and our present undernding of its role in evolution is weak. Despite uncertainties, extinction probably contains three important elements. (a) For geographically wide d species, extinction is likely only if the killing stress is one so rare as to be beyond the experience of the species, and thus outside the reach of natural selection. (is) The largest mass extinctions produce major ruc g of the biosphere wherein some successful groups are elmited, allowing previously minor groups to expand and diversify. (iih) Except for a few cases, there is little evidence that extinction is selective in the positive sense argued by Darwin. It has generally been possible to predict, before the fact, which species will be victims of an extinction event.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VBIB93YL/Raup - 1994 - The role of extinction in evolution..pdf} -} - -@misc{rcoreteam2020, - title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}}, - author = {{R Core Team}}, - year = {2020}, - address = {{Vienna, Austria}}, - howpublished = {R Foundation for Statistical Computing} -} - -@article{read2018, - title = {Among-Species Overlap in Rodent Body Size Distributions Predicts Species Richness along a Temperature Gradient}, - author = {Read, Quentin D. and Grady, John M. and Zarnetske, Phoebe L. and Record, Sydne and Baiser, Benjamin and Belmaker, Jonathan and Tuanmu, Mao-Ning and Strecker, Angela and Beaudrot, Lydia and Thibault, Katherine M.}, - year = {2018}, - journal = {Ecography}, - volume = {41}, - number = {10}, - pages = {1718--1727}, - issn = {1600-0587}, - doi = {10.1111/ecog.03641}, - abstract = {Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Here, we use individual-level trait data from a long-term monitoring network spanning a large geographic extent to test niche-based theory of community assembly in small mammals. We examined variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantified body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.}, - langid = {english}, - keywords = {body size,niche,rodents}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.03641}, - file = {/Users/renatadiaz/Zotero/storage/DJ8LMQPQ/Read et al. - 2018 - Among-species overlap in rodent body size distribu.pdf;/Users/renatadiaz/Zotero/storage/UJ3LZELN/Read et al. - 2018 - Among-species overlap in rodent body size distribu.pdf;/Users/renatadiaz/Zotero/storage/AUCTVF5Z/ecog.html;/Users/renatadiaz/Zotero/storage/BVPRZ6HE/ecog.html} -} - -@misc{reich2018, - title = {Plant Density: {{Effect}} of {{Burning Patterns}} on {{Vegetation}} in the {{Fish Lake Burn Compartments}}}, - shorttitle = {Plant Density}, - author = {Reich, Peter}, - year = {2018}, - publisher = {{Environmental Data Initiative}}, - doi = {10.6073/PASTA/FE139ACF2F45E75FCBE684284952D93B}, - langid = {english} -} - -@article{reichman1975, - title = {Relation of {{Desert Rodent Diets}} to {{Available Resources}}}, - author = {Reichman, O. J.}, - year = {1975}, - month = nov, - journal = {Journal of Mammalogy}, - volume = {56}, - number = {4}, - pages = {731--751}, - issn = {0022-2372}, - doi = {10.2307/1379649}, - abstract = {This study was designed to determine the diets of four species of Sonoran Desert rodents (Dipodomys merriami, Perognathus ampins, Perognathus baileyi, and Perognathus intermedins) and compare the diets to available food resources. Items ingested and their relative frequencies were determined by microscopic examination of stomach contents. Contents of cheek pouches of these heteromyid rodents also were analyzed and the relative density of each item was calculated. Seeds, especially those of forbs were the primary food of all species, but insects were important in diets of D. merriami and P. intermedins. Green vegetation was eaten infrequently. Soil samples taken at the capture sites of the rodents were analyzed for seeds to determine their relative density. It was found that availability of resources generally determined the pattern of food utilization, but that the preferences of the various species determined the exact quantities used. Cheek pouch contents were found to be consistently different from stomach contents and poor indicators of how much and when specific items were ingested.}, - file = {/Users/renatadiaz/Zotero/storage/HZ8LGFFH/841134.html} -} - -@article{renaut2018, - title = {Management, {{Archiving}}, and {{Sharing}} for {{Biologists}} and the {{Role}} of {{Research Institutions}} in the {{Technology-Oriented Age}}}, - author = {Renaut, S{\'e}bastien and Budden, Amber E. and Gravel, Dominique and Poisot, Timoth{\'e}e and {Peres-Neto}, Pedro}, - year = {2018}, - month = jun, - journal = {BioScience}, - volume = {68}, - number = {6}, - pages = {400--411}, - issn = {0006-3568}, - doi = {10.1093/biosci/biy038}, - abstract = {Abstract. Data are one of the primary outputs of science. Although certain subdisciplines of biology have pioneered efforts to ensure their long-term preservat}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/QU56N3YK/Renaut et al. - 2018 - Management, Archiving, and Sharing for Biologists .pdf;/Users/renatadiaz/Zotero/storage/55N7EMWL/4983937.html} -} - -@article{reuman2014, - title = {The Marine Diversity Spectrum}, - author = {Reuman, Daniel C. and Gislason, Henrik and Barnes, Carolyn and M{\'e}lin, Fr{\'e}d{\'e}ric and Jennings, Simon}, - year = {2014}, - journal = {Journal of Animal Ecology}, - volume = {83}, - number = {4}, - pages = {963--979}, - issn = {1365-2656}, - doi = {10.1111/1365-2656.12194}, - abstract = {Distributions of species body sizes within a taxonomic group, for example, mammals, are widely studied and important because they help illuminate the evolutionary processes that produced these distributions. Distributions of the sizes of species within an assemblage delineated by geography instead of taxonomy (all the species in a region regardless of clade) are much less studied but are equally important and will illuminate a different set of ecological and evolutionary processes. We develop and test a mechanistic model of how diversity varies with body mass in marine ecosystems. The model predicts the form of the `diversity spectrum', which quantifies the distribution of species' asymptotic body masses, is a species analogue of the classic size spectrum of individuals, and which we have found to be a new and widely applicable description of diversity patterns. The marine diversity spectrum is predicted to be approximately linear across an asymptotic mass range spanning seven orders of magnitude. Slope -0{$\cdot$}5 is predicted for the global marine diversity spectrum for all combined pelagic zones of continental shelf seas, and slopes for large regions are predicted to lie between -0{$\cdot$}5 and -0{$\cdot$}1. Slopes of -0{$\cdot$}5 and -0{$\cdot$}1 represent markedly different communities: a slope of -0{$\cdot$}5 depicts a 10-fold reduction in diversity for every 100-fold increase in asymptotic mass; a slope of -0{$\cdot$}1 depicts a 1{$\cdot$}6-fold reduction. Steeper slopes are predicted for larger or colder regions, meaning fewer large species per small species for such regions. Predictions were largely validated by a global empirical analysis. Results explain for the first time a new and widespread phenomenon of biodiversity. Results have implications for estimating numbers of species of small asymptotic mass, where taxonomic inventories are far from complete. Results show that the relationship between diversity and body mass can be explained from the dependence of predation behaviour, dispersal, and life history on body mass, and a neutral assumption about speciation and extinction.}, - langid = {english}, - keywords = {biodiversity,body mass,community,neutral theory,power law,size spectrum}, - file = {/Users/renatadiaz/Zotero/storage/HAHS6TZV/Reuman et al. - 2014 - The marine diversity spectrum.pdf;/Users/renatadiaz/Zotero/storage/BNIK45MI/1365-2656.html} -} - -@article{riouxpaquette2014, - title = {Severe Recent Decrease of Adult Body Mass in a Declining Insectivorous Bird Population}, - author = {Rioux Paquette, S{\'e}bastien and Pelletier, Fanie and Garant, Dany and B{\'e}lisle, Marc}, - year = {2014}, - month = jul, - journal = {Proceedings of the Royal Society B: Biological Sciences}, - volume = {281}, - number = {1786}, - pages = {20140649}, - publisher = {{Royal Society}}, - doi = {10.1098/rspb.2014.0649}, - abstract = {Migratory bird species that feed on air-borne insects are experiencing widespread regional declines, but these remain poorly understood. Agricultural intensification in the breeding range is often regarded as one of the main drivers of these declines. Here, we tested the hypothesis that body mass in breeding individuals should reflect habitat quality in an aerial insectivore, the tree swallow (Tachycineta bicolor), along a gradient of agricultural intensity. Our dataset was collected over 7 years (2005\textendash 2011) and included 2918 swallow captures and 1483 broods. Analyses revealed a substantial decline of the population over the course of the study (-19\% occupancy rate), mirrored by decreasing body mass. This trend was especially severe in females, representing a total loss of 8\% of their mass. Reproductive success was negatively influenced by intensive agriculture, but did not decrease over time. Interestingly, variation in body mass was independent of breeding habitat quality, leading us to suggest that this decline in body mass may result from carry-over effects from non-breeding areas and affect population dynamics through reduced survival. This work contributes to the growing body of evidence suggesting that declines in migratory aerial insectivores are driven by multiple, complex factors requiring better knowledge of year-round habitat use.}, - keywords = {aerial insectivores,agricultural intensification,body mass,breeding success,phenotypic plasticity,tree swallow}, - file = {/Users/renatadiaz/Zotero/storage/26CXHD9P/Rioux Paquette et al. - 2014 - Severe recent decrease of adult body mass in a dec.pdf} -} - -@article{rittenhouse2010, - title = {Conservation of {{Forest Birds}}: {{Evidence}} of a {{Shifting Baseline}} in {{Community Structure}}}, - shorttitle = {Conservation of {{Forest Birds}}}, - author = {Rittenhouse, Chadwick D. and Pidgeon, Anna M. and Albright, Thomas P. and Culbert, Patrick D. and Clayton, Murray K. and Flather, Curtis H. and Huang, Chengquan and Masek, Jeffrey G. and Stewart, Susan I. and Radeloff, Volker C.}, - year = {2010}, - month = aug, - journal = {PLOS ONE}, - volume = {5}, - number = {8}, - pages = {e11938}, - publisher = {{Public Library of Science}}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0011938}, - abstract = {Background Quantifying changes in forest bird diversity is an essential task for developing effective conservation actions. When subtle changes in diversity accumulate over time, annual comparisons may offer an incomplete perspective of changes in diversity. In this case, progressive change, the comparison of changes in diversity from a baseline condition, may offer greater insight because changes in diversity are assessed over longer periods of times. Our objectives were to determine how forest bird diversity has changed over time and whether those changes were associated with forest disturbance. Methodology/Principal Findings We used North American Breeding Bird Survey data, a time series of Landsat images classified with respect to land cover change, and mixed-effects models to associate changes in forest bird community structure with forest disturbance, latitude, and longitude in the conterminous United States for the years 1985 to 2006. We document a significant divergence from the baseline structure for all birds of similar migratory habit and nest location, and all forest birds as a group from 1985 to 2006. Unexpectedly, decreases in progressive similarity resulted from small changes in richness ({$<$}1 species per route for the 22-year study period) and modest losses in abundance (-28.7\textendash -10.2 individuals per route) that varied by migratory habit and nest location. Forest disturbance increased progressive similarity for Neotropical migrants, permanent residents, ground nesting, and cavity nesting species. We also documented highest progressive similarity in the eastern United States. Conclusions/Significance Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., {$\sim$}22 years). Forest disturbance and forest regeneration are primary factors associated with contemporary forest bird community structure, longitude and latitude are secondary factors, and forest loss is a tertiary factor. Importantly, these findings suggest some regions of the United States may already fall below the habitat amount threshold where fragmentation effects become important predictors of forest bird community structure.}, - langid = {english}, - keywords = {Birds,Community structure,Forests,Latitude,Longitude,Nesting habits,Species diversity,Temperate forests}, - file = {/Users/renatadiaz/Zotero/storage/ATZ2W4J6/Rittenhouse et al. - 2010 - Conservation of Forest Birds Evidence of a Shifti.pdf;/Users/renatadiaz/Zotero/storage/PKP3ITCD/Rittenhouse et al. - 2010 - Conservation of Forest Birds Evidence of a Shifti.pdf;/Users/renatadiaz/Zotero/storage/C84IVMJD/article.html;/Users/renatadiaz/Zotero/storage/Z4A2E6GZ/article.html} -} - -@misc{rmontdiaz2017, - title = {From Field to Repo \textendash{} {{Portal}} Data}, - author = {{Rmontdiaz}}, - year = {2017}, - month = dec, - journal = {The Portal Project}, - abstract = {Whenever we get new Portal data, we want to update our database as quickly as we can, without sacrificing data quality by adding data with errors or messing up the existing database when we try to \ldots}, - langid = {english} -} - -@manual{rominger2014, - type = {Manual}, - title = {{{meteR}}: {{Analysis}} with the Maximum Entropy Theory of Ecology}, - author = {Rominger, Andy and {Merow, Cory} and {Harte, John}}, - year = {2014} -} - -@article{rominger2016, - title = {Community Assembly on Isolated Islands: Macroecology Meets Evolution}, - shorttitle = {Community Assembly on Isolated Islands}, - author = {Rominger, A. J. and Goodman, K. R. and Lim, J. Y. and Armstrong, E. E. and Becking, L. E. and Bennett, G. M and Brewer, M. S. and Cotoras, D. D. and Ewing, C. P. and Harte, J. and Martinez, N. D. and O'Grady, P. M. and Percy, D. M. and Price, D. K. and Roderick, G. K. and Shaw, K. L. and Valdovinos, F. S. and Gruner, D. S. and Gillespie, R. G. and Ricklefs, Robert}, - year = {2016}, - month = jul, - journal = {Global Ecology and Biogeography}, - volume = {25}, - number = {7}, - pages = {769--780}, - issn = {1466-822X, 1466-8238}, - doi = {10.1111/geb.12341}, - abstract = {Aim Understanding how ecological and evolutionary processes together determine patterns of biodiversity remains a central aim in biology. Guided by ecological theory, we use data from multiple arthropod lineages across the Hawaiian archipelago to explore the interplay between ecological (population dynamics, dispersal, trophic interactions) and evolutionary (genetic structuring, adaptation, speciation, extinction) processes. Our goal is to show how communities develop from the dynamic feedbacks that operate at different temporal and spatial scales.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2GKT45C7/Rominger et al. - 2016 - Community assembly on isolated islands macroecolo.pdf} -} - -@article{rominger2017, - title = {Linking Evolutionary and Ecological Theory Illuminates Non-Equilibrium Biodiversity}, - author = {Rominger, A. J. and Overcast, I. and Krehenwinkel, H. and Gillespie, R. G. and Harte, J. and Hickerson, M. J.}, - year = {2017}, - month = may, - journal = {arXiv:1705.04725 [q-bio]}, - eprint = {1705.04725}, - eprinttype = {arxiv}, - primaryclass = {q-bio}, - abstract = {Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models and macroecological theory represent two primary lenses through which we view biodiversity. While phylo/population genetics provide an averaged view of changes in demography and diversity over timescales of generations to geological epochs, macroecology provides an ahistorical description of commonness and rarity across contemporary co-occurring species. Our goal is to combine these two approaches to gain novel insights into the non-equilibrium nature of biodiversity. We help guide near future research with a call for bioinformatic advances and an outline of quantitative predictions made possible by our approach.}, - archiveprefix = {arXiv}, - langid = {english}, - keywords = {Quantitative Biology - Populations and Evolution}, - file = {/Users/renatadiaz/Zotero/storage/LY9M85QN/Rominger et al. - 2017 - Linking evolutionary and ecological theory illumin.pdf} -} - -@misc{rominger2017a, - title = {Linking Evolutionary and Ecological Theory Illuminates Non-Equilibrium Biodiversity}, - author = {Rominger, A. J. and Overcast, I. and Krehenwinkel, H. and Gillespie, R. G. and Harte, J. and Hickerson, M. J.}, - year = {2017}, - month = may, - number = {arXiv:1705.04725}, - eprint = {1705.04725}, - eprinttype = {arxiv}, - primaryclass = {q-bio}, - publisher = {{arXiv}}, - abstract = {Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models and macroecological theory represent two primary lenses through which we view biodiversity. While phylo/population genetics provide an averaged view of changes in demography and diversity over timescales of generations to geological epochs, macroecology provides an ahistorical description of commonness and rarity across contemporary co-occurring species. Our goal is to combine these two approaches to gain novel insights into the non-equilibrium nature of biodiversity. We help guide near future research with a call for bioinformatic advances and an outline of quantitative predictions made possible by our approach.}, - archiveprefix = {arXiv}, - langid = {english}, - keywords = {Quantitative Biology - Populations and Evolution}, - file = {/Users/renatadiaz/Zotero/storage/IWCCAGBK/Rominger et al. - 2017 - Linking evolutionary and ecological theory illumin.pdf} -} - -@article{rominger2019, - title = {Nonequilibrium Evolution of Volatility in Origination and Extinction Explains Fat-Tailed Fluctuations in {{Phanerozoic}} Biodiversity}, - author = {Rominger, Andrew J. and Fuentes, Miguel A. and Marquet, Pablo A.}, - year = {2019}, - month = jun, - journal = {Science Advances}, - publisher = {{American Association for the Advancement of Science}}, - doi = {10.1126/sciadv.aat0122}, - abstract = {Phanerozoic marine invertebrate richness fluctuates out of equilibrium due to pulsed adaptive evolution.}, - copyright = {Copyright \textcopyright{} 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/C3WCZTRB/Rominger et al. - 2019 - Nonequilibrium evolution of volatility in originat.pdf;/Users/renatadiaz/Zotero/storage/FWJDDL44/sciadv.html} -} - -@article{rooney2012, - title = {Integrating Food Web Diversity, Structure and Stability}, - author = {Rooney, Neil and McCann, Kevin S.}, - year = {2012}, - month = jan, - journal = {Trends in Ecology \& Evolution}, - volume = {27}, - number = {1}, - pages = {40--46}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2011.09.001}, - abstract = {Given the unprecedented rate of species extinctions facing the planet, understanding the causes and consequences of species diversity in ecosystems is of paramount importance. Ecologists have investigated both the influence of environmental variables on species diversity and the influence of species diversity on ecosystem function and stability. These investigations have largely been carried out without taking into account the overarching stabilizing structures of food webs that arise from evolutionary and successional processes and that are maintained through species interactions. Here, we argue that the same large-scale structures that have been purported to convey stability to food webs can also help to understand both the distribution of species diversity in nature and the relationship between species diversity and food web stability. Specifically, the allocation of species diversity to slow energy channels within food webs results in the skewed distribution of interactions strengths that has been shown to confer stability to complex food webs. We end by discussing the processes that might generate and maintain the structured, stable and diverse food webs observed in nature.}, - file = {/Users/renatadiaz/Zotero/storage/VLFKJZNL/Rooney and McCann - 2012 - Integrating food web diversity, structure and stab.pdf;/Users/renatadiaz/Zotero/storage/V685VIK7/S016953471100259X.html} -} - -@article{rosenberg2019, - title = {Decline of the {{North American}} Avifauna}, - author = {Rosenberg, Kenneth V. and Dokter, Adriaan M. and Blancher, Peter J. and Sauer, John R. and Smith, Adam C. and Smith, Paul A. and Stanton, Jessica C. and Panjabi, Arvind and Helft, Laura and Parr, Michael and Marra, Peter P.}, - year = {2019}, - month = oct, - journal = {Science}, - volume = {366}, - number = {6461}, - pages = {120--124}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.aaw1313}, - abstract = {Species extinctions have defined the global biodiversity crisis, but extinction begins with loss in abundance of individuals that can result in compositional and functional changes of ecosystems. Using multiple and independent monitoring networks, we report population losses across much of the North American avifauna over 48 years, including once-common species and from most biomes. Integration of range-wide population trajectories and size estimates indicates a net loss approaching 3 billion birds, or 29\% of 1970 abundance. A continent-wide weather radar network also reveals a similarly steep decline in biomass passage of migrating birds over a recent 10-year period. This loss of bird abundance signals an urgent need to address threats to avert future avifaunal collapse and associated loss of ecosystem integrity, function, and services.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/7922NSHK/Rosenberg et al. - 2019 - Decline of the North American avifauna.pdf} -} - -@article{rosenberg2019a, - title = {Decline of the {{North American}} Avifauna}, - author = {Rosenberg, Kenneth V. and Dokter, Adriaan M. and Blancher, Peter J. and Sauer, John R. and Smith, Adam C. and Smith, Paul A. and Stanton, Jessica C. and Panjabi, Arvind and Helft, Laura and Parr, Michael and Marra, Peter P.}, - year = {2019}, - month = oct, - journal = {Science}, - volume = {366}, - number = {6461}, - pages = {120--124}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.aaw1313}, - abstract = {Staggering decline of bird populations Because birds are conspicuous and easy to identify and count, reliable records of their occurrence have been gathered over many decades in many parts of the world. Drawing on such data for North America, Rosenberg et al. report wide-spread population declines of birds over the past half-century, resulting in the cumulative loss of billions of breeding individuals across a wide range of species and habitats. They show that declines are not restricted to rare and threatened species\textemdash those once considered common and wide-spread are also diminished. These results have major implications for ecosystem integrity, the conservation of wildlife more broadly, and policies associated with the protection of birds and native ecosystems on which they depend. Science , this issue p. 120 , The cumulative loss of nearly 3 billion birds since 1970 across North American biomes signals a continuing avifaunal crisis. , Species extinctions have defined the global biodiversity crisis, but extinction begins with loss in abundance of individuals that can result in compositional and functional changes of ecosystems. Using multiple and independent monitoring networks, we report population losses across much of the North American avifauna over 48 years, including once-common species and from most biomes. Integration of range-wide population trajectories and size estimates indicates a net loss approaching 3 billion birds, or 29\% of 1970 abundance. A continent-wide weather radar network also reveals a similarly steep decline in biomass passage of migrating birds over a recent 10-year period. This loss of bird abundance signals an urgent need to address threats to avert future avifaunal collapse and associated loss of ecosystem integrity, function, and services.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/E8N77YB2/Rosenberg et al. - 2019 - Decline of the North American avifauna.pdf} -} - -@article{rosenfeld2002, - title = {Functional Redundancy in Ecology and Conservation}, - author = {Rosenfeld, Jordan S.}, - year = {2002}, - journal = {Oikos}, - volume = {98}, - number = {1}, - pages = {156--162}, - issn = {1600-0706}, - doi = {10.1034/j.1600-0706.2002.980116.x}, - abstract = {Multiple studies have shown that biodiversity loss can impair ecosystem processes, providing a sound basis for the general application of a precautionary approach to managing biodiversity. However, mechanistic details of species loss effects and the generality of impacts across ecosystem types are poorly understood. The functional niche is a useful conceptual tool for understanding redundancy, where the functional niche is defined as the area occupied by a species in an n-dimensional functional space. Experiments to assess redundancy based on a single functional attribute are biased towards finding redundancy, because species are more likely to have non-overlapping functional niches in a multi-dimensional functional space. The effect of species loss in any particular ecosystem will depend on i) the range of function and diversity of species within a functional group, ii) the relative partitioning of variance in functional space between and within functional groups, and iii) the potential for functional compensation (degree of functional niche overlap) of the species within a functional group. Future research on functional impairment with species loss should focus on identifying which species, functional groups, and ecosystems are most vulnerable to functional impairment from species loss, so that these can be prioritized for management activities directed at maintaining ecosystem function. This will require a better understanding of how the organization of diversity into discrete functional groups differs between different communities and ecosystems.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1600-0706.2002.980116.x}, - file = {/Users/renatadiaz/Zotero/storage/7M2CNRU8/Rosenfeld - 2002 - Functional redundancy in ecology and conservation.pdf;/Users/renatadiaz/Zotero/storage/S9ER3R4N/j.1600-0706.2002.980116.html} -} - -@article{rosenzweig1969, - title = {Population {{Ecology}} of {{Desert Rodent Communities}}: {{Habitats}} and {{Environmental Complexity}}}, - shorttitle = {Population {{Ecology}} of {{Desert Rodent Communities}}}, - author = {Rosenzweig, Michael L. and Winakur, Jerald}, - year = {1969}, - journal = {Ecology}, - volume = {50}, - number = {4}, - pages = {558--572}, - issn = {1939-9170}, - doi = {10.2307/1936246}, - abstract = {We investigated the relative densities of granivorous, nocturnal desert rodents in small plots within two arid regions of Arizona to study how sympatric species avoid competitive extinction. The most common rodents were kangaroo rats, Dipodomys spp., and pocket mice, Perognathus spp. We attempted correlating the density of each species with several environmental measurements, derived from the soil's i) depth; ii) texture or iii) resistance to sheer stress; or from the plant's i) species diversity; ii) growth forms or iii) foliage density. Successful variables were derived from plant growth form and foliage density. The soil's resistance to sheer stress also seemed important for a few species. In general, kangaroo rats were associated with sparseness of vegetation; pocket mice with denseness. One group of mice, which we term bush mice, seemed to require bushes and included two Perognathus spp., three Peromyscus spp., and probably a harvest mouse (Reithrodontomys fulvescens). Two other Perognathus spp. were taken in grassy habitats. Some suitable habitats tended to be complementary to others, suggesting that species associated with them are competitors. Comparisons of the density and distribution of D. merriami, present in both regions but under different biotic circumstances, reinforces the opinion that competition is responsible for the complementariness of habitats. In some cases the evidence suggests that competitive coexistence is accounted for by the fact that different specializations are needed to escape predation in different environments. We use variables which correlate with the relative density of various species to construct a model of habitat complexity. The rodent species diversities obtained in our plots can be approximately accounted for by this model. The model is based on the premises that the rodents collectively discriminate four qualities of soil surface, and three heights and two densities of vegetation. In general, specializations based on biotic variables appear most important.}, - copyright = {\textcopyright{} 1969 by the Ecological Society of America}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1936246}, - file = {/Users/renatadiaz/Zotero/storage/IYDRIGVA/Rosenzweig and Winakur - 1969 - Population Ecology of Desert Rodent Communities H.pdf;/Users/renatadiaz/Zotero/storage/RZUTUV9S/1936246.html} -} - -@article{rosindell2011, - title = {The {{Unified Neutral Theory}} of {{Biodiversity}} and {{Biogeography}} at {{Age Ten}}}, - author = {Rosindell, James and Hubbell, Stephen P. and Etienne, Rampal S.}, - year = {2011}, - month = jul, - journal = {Trends in Ecology \& Evolution}, - volume = {26}, - number = {7}, - pages = {340--348}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2011.03.024}, - abstract = {A decade has now passed since Hubbell published The Unified Neutral Theory of Biodiversity and Biogeography. Neutral theory highlights the importance of dispersal limitation, speciation and ecological drift in the natural world and provides quantitative null models for assessing the role of adaptation and natural selection. Significant advances have been made in providing methods for understanding neutral predictions and comparing them with empirical data. In this review, we describe the current state-of-the-art techniques and ideas in neutral theory and how these are of relevance to ecology. The future of neutral theory is promising, but its concepts must be applied more broadly beyond the current focus on species\textendash abundance distributions.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/75BKL8TD/S0169534711000942.html} -} - -@article{rosindell2015, - title = {Unifying Ecology and Macroevolution with Individual-Based Theory}, - author = {Rosindell, James and Harmon, Luke J. and Etienne, Rampal S.}, - year = {2015}, - journal = {Ecology Letters}, - volume = {18}, - number = {5}, - pages = {472--482}, - issn = {1461-0248}, - doi = {10.1111/ele.12430}, - abstract = {A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage-based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual-based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology.}, - langid = {english}, - keywords = {Ecology,fitness,individual-based model,lineages-through-time,macroevolution,neutral,phylogeny,selection,species abundance,theory}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12430}, - file = {/Users/renatadiaz/Zotero/storage/AX2949UW/Rosindell et al. - 2015 - Unifying ecology and macroevolution with individua.pdf;/Users/renatadiaz/Zotero/storage/DBMD9QXE/ele.html} -} - -@article{saint-germain2007, - title = {Should Biomass Be Considered More Frequently as a Currency in Terrestrial Arthropod Community Analyses?}, - author = {{Saint-Germain}, Michel and Buddle, Christopher M. and Larriv{\'e}e, Maxim and Mercado, Alida and Motchula, Tania and Reichert, Elisabeth and Sackett, Tara E. and Sylvain, Zachary and Webb, Annie}, - year = {2007}, - journal = {Journal of Applied Ecology}, - volume = {44}, - number = {2}, - pages = {330--339}, - issn = {1365-2664}, - doi = {10.1111/j.1365-2664.2006.01269.x}, - abstract = {1 Community structure involving large taxonomical groups is frequently used to assess changes in ecosystems along environmental gradients or in response to disturbance. For terrestrial arthropods, abundance is generally used as the response variable in community data analyses; biomass, however, is generally a better indicator of the functionality of a species within a community, as it is strongly correlated with metabolism. 2 In this study, we considered whether biomass should be used more often in community analyses with terrestrial arthropod biodiversity data, particularly when asking questions involving strong functional components. We selected 10 previously published and five unpublished Coleoptera abundance data sets, and produced biomass species-by-sample matrices using body length to body mass conversion equations, and then compared the results obtained using commonly used ecological analyses. 3 Correlations between species abundance and biomass varied from strong to poor, depending on the taxa considered and on the sampling method used. We show that abundance and biomass can produce different results in community data analysis and lead to alternative interpretations for data sets with poor abundance to biomass correlations. 4 Synthesis and applications. When dealing with databases showing poor abundance to biomass relationships, the question of the relevance of using biomass instead of abundance emerges, and the choice of the response variable to be used in analyses should be considered carefully. At the very least, when studying terrestrial arthropod biodiversity, one should consider the use of biomass with simple conversion equations that do not require obtaining the mass of individual specimens. This approach may lead to different interpretations. For research questions in which trophic interactions may play an important role, biomass may provide a broader and more accurate picture of the processes driving changes in community structure.}, - langid = {english}, - keywords = {abundance,biodiversity studies,body mass,energetic equivalence rule,species functionality}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2664.2006.01269.x}, - file = {/Users/renatadiaz/Zotero/storage/TMRX6NRD/Saint-Germain et al. - 2007 - Should biomass be considered more frequently as a .pdf;/Users/renatadiaz/Zotero/storage/4N2JJPLV/j.1365-2664.2006.01269.html} -} - -@article{salewski2014, - title = {Morphological {{Change}} to {{Birds}} over 120 {{Years Is Not Explained}} by {{Thermal Adaptation}} to {{Climate Change}}}, - author = {Salewski, Volker and Siebenrock, Karl-Heinz and Hochachka, Wesley M. and Woog, Friederike and Fiedler, Wolfgang}, - year = {2014}, - month = jul, - journal = {PLOS ONE}, - volume = {9}, - number = {7}, - pages = {e101927}, - publisher = {{Public Library of Science}}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0101927}, - abstract = {Changes in morphology have been postulated as one of the responses of animals to global warming, with increasing ambient temperatures leading to decreasing body size. However, the results of previous studies are inconsistent. Problems related to the analyses of trends in body size may be related to the short-term nature of data sets, to the selection of surrogates for body size, to the appropriate models for data analyses, and to the interpretation as morphology may change in response to ecological drivers other than climate and irrespective of size. Using generalized additive models, we analysed trends in three morphological traits of 4529 specimens of eleven bird species collected between 1889 and 2010 in southern Germany and adjacent areas. Changes and trends in morphology over time were not consistent when all species and traits were considered. Six of the eleven species displayed a significant association of tarsus length with time but the direction of the association varied. Wing length decreased in the majority of species but there were few significant trends in wing pointedness. Few of the traits were significantly associated with mean ambient temperatures. We argue that although there are significant changes in morphology over time there is no consistent trend for decreasing body size and therefore no support for the hypothesis of decreasing body size because of climate change. Non-consistent trends of change in surrogates for size within species indicate that fluctuations are influenced by factors other than temperature, and that not all surrogates may represent size appropriately. Future analyses should carefully select measures of body size and consider alternative hypotheses for change.}, - langid = {english}, - keywords = {Animal migration,Animal wings,Birds,Climate change,Global warming,Physiological parameters,Starlings,Woodpeckers}, - file = {/Users/renatadiaz/Zotero/storage/XZZQCTCY/Salewski et al. - 2014 - Morphological Change to Birds over 120 Years Is No.pdf} -} - -@article{sauer2013, - title = {The {{North American Breeding Bird Survey}} 1966\textendash 2011: {{Summary Analysis}} and {{Species Accounts}}}, - shorttitle = {The {{North American Breeding Bird Survey}} 1966\textendash 2011}, - author = {Sauer, John R. and Link, William A. and Fallon, Jane E. and Pardieck, Keith L. and Ziolkowski, David J.}, - year = {2013}, - month = dec, - journal = {North American Fauna}, - number = {79 (79)}, - pages = {1--32}, - publisher = {{Allen Press}}, - issn = {0078-1304}, - doi = {10.3996/nafa.79.0001}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/QMIMFBP4/Sauer et al. - 2013 - The North American Breeding Bird Survey 1966–2011.pdf;/Users/renatadiaz/Zotero/storage/ENLVMEEI/The-North-American-Breeding-Bird-Survey-1966-2011.html} -} - -@article{scheffer2006, - title = {Self-Organized Similarity, the Evolutionary Emergence of Groups of Similar Species}, - author = {Scheffer, M. and {van Nes}, E. H.}, - year = {2006}, - month = apr, - journal = {Proceedings of the National Academy of Sciences}, - volume = {103}, - number = {16}, - pages = {6230--6235}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.0508024103}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/LJW46Q3G/Scheffer and van Nes - 2006 - Self-organized similarity, the evolutionary emerge.pdf} -} - -@article{schipper2016, - title = {Contrasting Changes in the Abundance and Diversity of {{North American}} Bird Assemblages from 1971 to 2010}, - author = {Schipper, Aafke M. and Belmaker, Jonathan and {de Miranda}, Murilo Dantas and Navarro, Laetitia M. and {B{\"o}hning-Gaese}, Katrin and Costello, Mark J. and Dornelas, Maria and Foppen, Ruud and Hortal, Joaqu{\'i}n and Huijbregts, Mark A. J. and {Mart{\'i}n-L{\'o}pez}, Berta and Pettorelli, Nathalie and Queiroz, Cibele and Rossberg, Axel G. and Santini, Luca and Schiffers, Katja and Steinmann, Zoran J. N. and Visconti, Piero and Rondinini, Carlo and Pereira, Henrique M.}, - year = {2016}, - journal = {Global Change Biology}, - volume = {22}, - number = {12}, - pages = {3948--3959}, - issn = {1365-2486}, - doi = {10.1111/gcb.13292}, - abstract = {Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5-year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.}, - langid = {english}, - keywords = {biodiversity change,biodiversity metrics,functional diversity (FD),phylogenetic diversity (PD),species abundance,taxonomic diversity (TD)}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.13292}, - file = {/Users/renatadiaz/Zotero/storage/2FLDBRW6/Schipper et al. - 2016 - Contrasting changes in the abundance and diversity.pdf;/Users/renatadiaz/Zotero/storage/AKQE2UG9/Schipper et al. - 2016 - Contrasting changes in the abundance and diversity.pdf;/Users/renatadiaz/Zotero/storage/I94GG9M5/Schipper et al. - 2016 - Contrasting changes in the abundance and diversity.pdf;/Users/renatadiaz/Zotero/storage/9GNYPFQD/gcb.html;/Users/renatadiaz/Zotero/storage/CQX6STIT/gcb.html;/Users/renatadiaz/Zotero/storage/JMDPUBKZ/gcb.html} -} - -@article{schmitz2018, - title = {Animals and the Zoogeochemistry of the Carbon Cycle}, - author = {Schmitz, Oswald J. and Wilmers, Christopher C. and Leroux, Shawn J. and Doughty, Christopher E. and Atwood, Trisha B. and Galetti, Mauro and Davies, Andrew B. and Goetz, Scott J.}, - year = {2018}, - month = dec, - journal = {Science}, - publisher = {{American Association for the Advancement of Science}}, - abstract = {Flux across the carbon cycle is generally characterized by contributions from plants, microbes, and abiotic systems. Animals, however, move vast amounts of carbon, both through ecosystem webs and across the landscape. Schmitz et al. review ...}, - copyright = {Copyright \textcopyright{} 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/6B7EP6YA/science.html} -} - -@article{schooley2018, - title = {Shrub Encroachment, Productivity Pulses, and Core-Transient Dynamics of {{Chihuahuan Desert}} Rodents}, - author = {Schooley, Robert L. and Bestelmeyer, Brandon T. and Campanella, Andrea}, - year = {2018}, - month = jul, - journal = {Ecosphere}, - volume = {9}, - number = {7}, - pages = {e02330}, - publisher = {{Wiley}}, - address = {{Hoboken}}, - issn = {2150-8925}, - doi = {10.1002/ecs2.2330}, - abstract = {Drylands worldwide are experiencing shrub encroachment into grasslands with potential consequences for biodiversity and ecosystem services. Climate change could increase the rate of shrub encroachment, amplify precipitation variability, and thus alter bottom-up processes for animal communities. Desert rodents are important biodiversity elements of arid grasslands and shrublands that exert strong effects on soil, vegetation, and other animal species. We used long-term data from the Jornada Basin Long Term Ecological Research site in the Chihuahuan Desert of southern New Mexico to ask whether bottom-up control of desert rodents changes across shrub encroachment gradients. Our design included spatial blocks with replicated ecological states representing transitions from black grama (Bouteloua eriopoda) to honey mesquite (Prosopis glandulosa). Grassland-to-shrubland transitions did not produce degraded ecosystems, on average, with reduced net primary production or decreased rodent biomass. However, more rodent biomass was supported on unencroached grasslands following droughts whose frequency and severity may increase in southwestern United States. Hence, the observed evenness in rodent biomass across ecological states should be sensitive to climate change. The best predictors of rodent biomass also differed markedly for two trophic groups. This outcome was explained by considering core-transient dynamics. Granivores were mostly core species that regularly occurred on sites and responded to lagged net primary production at local scales, whereas folivores included transient species (especially Sigmodon hispidus) that responded to lagged precipitation at broader scales via spillover dynamics. Bottom-up processes for desert rodents across shrub invasion gradients were understood by integrating lagged responses to productivity pulses with core-transient structuring of communities.}, - langid = {english}, - keywords = {bottom-up control,bottom-up regulation,Chihuahuan Desert,climate-change,community structure,land-use,long-term,missing link,net primary production,precipitation variability,Prosopis glandulosa,rodent communities,shrub encroachment,small mammal populations,spatial ecology,Special Feature: Dynamic Deserts,temporal dynamics,top-down}, - annotation = {WOS:000441526900034}, - file = {/Users/renatadiaz/Zotero/storage/I2LBV44M/Schooley et al. - 2018 - Shrub encroachment, productivity pulses, and core-.pdf} -} - -@book{schrodinger2013, - title = {Statistical {{Thermodynamics}}}, - author = {Schrodinger, Erwin}, - year = {2013}, - month = apr, - publisher = {{Courier Corporation}}, - abstract = {In this concise volume, one of the founder of quantum mechanics and one of the greatest theoretical physicists of the century (Nobel laureate, 1933) attempts to develop a simple, unified standard method of dealing with all cases of statistical thermodynamics (classical, quantum, Bose-Einstein, Fermi-Dirac, etc.)The level of discussion is relatively advanced. As Professor Schr\"odinger remarks in the Introduction: \"It is not a first introduction for newcomers to the subject, but rather a \&\#39;repetitorium.\&\#39; The treatment of those topics which are to be found in every one of a hundred text-books is severely condensed; on the other hand, vital points which are usually passed over in all but the large monographs (such as Fowler\&\#39;s and Tolman\&\#39;s) are dealt with at greater level.\"}, - googlebooks = {gHHCAgAAQBAJ}, - isbn = {978-0-486-31860-8}, - langid = {english}, - keywords = {Science / Physics / General} -} - -@article{senyondo2017, - title = {Retriever: {{Data Retrieval Tool}}}, - shorttitle = {Retriever}, - author = {Senyondo, Henry and Morris, Benjamin D. and Goel, Akash and Zhang, Andrew and Narasimha, Akshay and Negi, Shivam and Harris, David J. and Digges, Deborah Gertrude and Kumar, Kapil and Jain, Amritanshu and Pal, Kunal and Amipara, Kevinkumar and White, Ethan P.}, - year = {2017}, - month = nov, - journal = {Journal of Open Source Software}, - volume = {2}, - number = {19}, - pages = {451}, - issn = {2475-9066}, - doi = {10.21105/joss.00451}, - abstract = {Senyondo et al., (2017). Retriever: Data Retrieval Tool. Journal of Open Source Software, 2(19), 451, doi:10.21105/joss.00451}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/ZISAFNKN/Senyondo et al. - 2017 - Retriever Data Retrieval Tool.pdf} -} - -@article{sewall2013, - title = {Size-{{Energy Relationships}} in {{Ecological Communities}}}, - author = {Sewall, Brent J. and Freestone, Amy L. and Hawes, Joseph E. and Andriamanarina, Ernest}, - editor = {White, Ethan P.}, - year = {2013}, - month = aug, - journal = {PLoS ONE}, - volume = {8}, - number = {8}, - pages = {e68657}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0068657}, - abstract = {Hypotheses that relate body size to energy use are of particular interest in community ecology and macroecology because of their potential to facilitate quantitative predictions about species interactions and to clarify complex ecological patterns. One prominent size-energy hypothesis, the energetic equivalence hypothesis, proposes that energy use from shared, limiting resources by populations or size classes of foragers will be independent of body size. Alternative hypotheses propose that energy use will increase with body size, decrease with body size, or peak at an intermediate body size. Despite extensive study, however, size-energy hypotheses remain controversial, due to a lack of directly-measured data on energy use, a tendency to confound distinct scaling relationships, and insufficient attention to the ecological contexts in which predicted relationships are likely to occur. Our goal, therefore, was to directly evaluate size-energy hypotheses while clarifying how results would differ with alternate methods and assumptions. We comprehensively tested size-energy hypotheses in a vertebrate frugivore guild in a tropical forest in Madagascar. Our test of size-energy hypotheses, which is the first to examine energy intake directly, was consistent with the energetic equivalence hypothesis. This finding corresponds with predictions of metabolic theory and models of energy distribution in ecological communities, which imply that body size does not confer an advantage in competition for energy among populations or size classes of foragers. This result was robust to different assumptions about energy regulation. Our results from direct energy measurement, however, contrasted with those obtained with conventional methods of indirect inference from size-density relationships, suggesting that size-density relationships do not provide an appropriate proxy for size-energy relationships as has commonly been assumed. Our research also provides insights into mechanisms underlying local size-energy relationships and has important implications for predicting species interactions and for understanding the structure and dynamics of ecological communities.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/NMMRXDAH/Sewall et al. - 2013 - Size-Energy Relationships in Ecological Communitie.PDF} -} - -@article{shade2012, - title = {Lake Microbial Communities Are Resilient after a Whole-Ecosystem Disturbance}, - author = {Shade, Ashley and Read, Jordan S. and Youngblut, Nicholas D. and Fierer, Noah and Knight, Rob and Kratz, Timothy K. and Lottig, Noah R. and Roden, Eric E. and Stanley, Emily H. and Stombaugh, Jesse and Whitaker, Rachel J. and Wu, Chin H. and McMahon, Katherine D.}, - year = {2012}, - month = dec, - journal = {The ISME Journal}, - volume = {6}, - number = {12}, - pages = {2153--2167}, - publisher = {{Nature Publishing Group}}, - issn = {1751-7370}, - doi = {10.1038/ismej.2012.56}, - abstract = {Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted a whole-ecosystem manipulation, during which we imposed an intense disturbance on freshwater microbial communities by artificially mixing a temperate lake during peak summer thermal stratification. We employed environmental sensors and water chemistry analyses to evaluate the physical and chemical responses of the lake, and bar-coded 16S ribosomal RNA gene pyrosequencing and automated ribosomal intergenic spacer analysis (ARISA) to assess the bacterial community responses. The artificial mixing increased mean lake temperature from 14 to 20\,\textdegree C for seven weeks after mixing ended, and exposed the microorganisms to very different environmental conditions, including increased hypolimnion oxygen and increased epilimnion carbon dioxide concentrations. Though overall ecosystem conditions remained altered (with hypolimnion temperatures elevated from 6 to 20\,\textdegree C), bacterial communities returned to their pre-manipulation state as some environmental conditions, such as oxygen concentration, recovered. Recovery to pre-disturbance community composition and diversity was observed within 7 (epilimnion) and 11 (hypolimnion) days after mixing. Our results suggest that some microbial communities have capacity to recover after a major disturbance.}, - copyright = {2012 The Author(s)}, - langid = {english}, - keywords = {Ecosystem ecology,Limnology,Microbial ecology,Population dynamics}, - annotation = {Bandiera\_abtest: a Cg\_type: Nature Research Journals Primary\_atype: Research Subject\_term: Ecosystem ecology;Limnology;Microbial ecology;Population dynamics Subject\_term\_id: ecosystem-ecology;limnology;microbial-ecology;population-dynamics}, - file = {/Users/renatadiaz/Zotero/storage/NYJ8VRCG/Shade et al. - 2012 - Lake microbial communities are resilient after a w.pdf;/Users/renatadiaz/Zotero/storage/3BKU5J62/ismej201256.html} -} - -@article{shade2018, - title = {Macroecology to {{Unite All Life}}, {{Large}} and {{Small}}}, - author = {Shade, Ashley and Dunn, Robert R. and Blowes, Shane A. and Keil, Petr and Bohannan, Brendan J. M. and Herrmann, Martina and K{\"u}sel, Kirsten and Lennon, Jay T. and Sanders, Nathan J. and Storch, David and Chase, Jonathan}, - year = {2018}, - month = oct, - journal = {Trends in Ecology \& Evolution}, - volume = {33}, - number = {10}, - pages = {731--744}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2018.08.005}, - abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.}, - langid = {english}, - keywords = {abundance occupancy,distance decay,diversity gradient,metabolic theory of ecology,metagenomics,microbiome,rarefaction,species abundance distribution,species–area relationship}, - file = {/Users/renatadiaz/Zotero/storage/HW4S9EWH/S0169534718301861.html} -} - -@article{shipley2006, - title = {From {{Plant Traits}} to {{Plant Communities}}: {{A Statistical Mechanistic Approach}} to {{Biodiversity}}}, - shorttitle = {From {{Plant Traits}} to {{Plant Communities}}}, - author = {Shipley, B. and Vile, D. and Garnier, E.}, - year = {2006}, - month = nov, - journal = {Science}, - volume = {314}, - number = {5800}, - pages = {812--814}, - issn = {0036-8075, 1095-9203}, - doi = {10.1126/science.1131344}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/D7UTUTJH/Shipley et al. - 2006 - From Plant Traits to Plant Communities A Statisti.pdf} -} - -@article{shipley2009, - title = {Limitations of Entropy Maximization in Ecology: A Reply to {{Haegeman}} and {{Loreau}}}, - shorttitle = {Limitations of Entropy Maximization in Ecology}, - author = {Shipley, Bill}, - year = {2009}, - journal = {Oikos}, - volume = {118}, - number = {1}, - pages = {152--159}, - issn = {1600-0706}, - doi = {10.1111/j.1600-0706.2008.17179.x}, - abstract = {Haegeman and Loreau published a paper that is primarily a criticism of a maximum entropy model of trait-based community assembly (by Shipley et al.) and purports to show the limitations of this method in ecology. However, they misunderstood the basic purpose, logic and justification of the maximum entropy formalism and, because of this, leveled criticisms of Shipley et al. that are unfounded. Part of the confusion can be traced to sloppy presentation of the underlying approach in Shipley et al. The confusion arises because maximum entropy models are justified based on information theory and Bayesian logic while the interpretation that Haegeman and Loreau present is based on substantive empirical assumptions about microstate allocations and a combinatorial argument that do not apply to maximum entropy models and which I do not apply to my model in particular.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0706.2008.17179.x}, - file = {/Users/renatadiaz/Zotero/storage/N85YKMFY/Shipley - 2009 - Limitations of entropy maximization in ecology a .pdf;/Users/renatadiaz/Zotero/storage/CSK85Q4X/j.1600-0706.2008.17179.html} -} - -@article{shockley1957, - title = {On the {{Statistics}} of {{Individual Variations}} of {{Productivity}} in {{Research Laboratories}}}, - author = {Shockley, William}, - year = {1957}, - journal = {Proceedings of the IRE}, - volume = {45}, - number = {3}, - pages = {279--290}, - issn = {0096-8390}, - doi = {10.1109/JRPROC.1957.278364}, - abstract = {It is well-known that some workers in scientific research laboratories are enormously more creative than others. If the number of scientific publications is used as a measure of productivity, it is found that some individuals create new science at a rate at least fifty times greater than others. Thus differences in rates of scientific production are much bigger than differences in the rates of performing simpler acts, such as the rate of running the mile, or the number of words a man can speak per minute.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/WPNWU3DT/Shockley - 1957 - On the Statistics of Individual Variations of Prod.pdf} -} - -@article{shoemaker2017, - title = {A Macroecological Theory of Microbial Biodiversity}, - author = {Shoemaker, William R. and Locey, Kenneth J. and Lennon, Jay T.}, - year = {2017}, - month = apr, - journal = {Nature Ecology \& Evolution}, - volume = {1}, - number = {5}, - pages = {1--6}, - publisher = {{Nature Publishing Group}}, - issn = {2397-334X}, - doi = {10.1038/s41559-017-0107}, - abstract = {Microorganisms are the most abundant, diverse and functionally important organisms on Earth. Over the past decade, microbial ecologists have produced the largest ever community datasets. However, these data are rarely used to uncover law-like patterns of commonness and rarity, test theories of biodiversity, or explore unifying explanations for the structure of microbial communities. Using a global scale compilation of {$>$}20,000 samples from environmental, engineered and host-related ecosystems, we test the power of competing theories to predict distributions of microbial abundance and diversity\textendash abundance scaling laws. We show that these patterns are best explained by the synergistic interaction of stochastic processes that are captured by lognormal dynamics. We demonstrate that lognormal dynamics have predictive power across scales of abundance, a criterion that is essential to biodiversity theory. By understanding the multiplicative and stochastic nature of ecological processes, scientists can better understand the structure and dynamics of Earth's largest and most diverse ecological systems.}, - copyright = {2017 Macmillan Publishers Limited, part of Springer Nature.}, - langid = {english}, - keywords = {Biodiversity,Community ecology,Macroecology,Microbial ecology}, - annotation = {Bandiera\_abtest: a Cg\_type: Nature Research Journals Primary\_atype: Research Subject\_term: Biodiversity;Community ecology;Macroecology;Microbial ecology Subject\_term\_id: biodiversity;community-ecology;macroecology;microbial-ecology}, - file = {/Users/renatadiaz/Zotero/storage/ZQZDDUSE/Shoemaker et al. - 2017 - A macroecological theory of microbial biodiversity.pdf;/Users/renatadiaz/Zotero/storage/ZWJWEYBG/s41559-017-0107.html} -} - -@article{siefert2013, - title = {Functional Beta-Diversity Patterns Reveal Deterministic Community Assembly Processes in Eastern {{North American}} Trees}, - author = {Siefert, Andrew and Ravenscroft, Catherine and Weiser, Michael D. and Swenson, Nathan G.}, - year = {2013}, - journal = {Global Ecology and Biogeography}, - volume = {22}, - number = {6}, - pages = {682--691}, - issn = {1466-8238}, - doi = {10.1111/geb.12030}, - abstract = {Aim Determining the relative influence of niche-based and neutral processes in driving the spatial turnover of community composition is a central challenge in community ecology. Spatial patterns of functional turnover, or functional beta diversity, may capture important signals of niche-based assembly processes, but these patterns have not been quantified for communities across broad geographic and environmental gradients. Here, we analyse continental-scale patterns of species and functional beta diversity in relation to space and the environment to assess the relative importance of niche-based and neutral community assembly mechanisms. Location Eastern North America. Methods We use a continental-scale forest plot dataset and functional trait data to quantify spatial patterns of species and functional beta diversity. We use redundancy analysis-based variance partitioning to evaluate the influence of space, soil and climate on beta-diversity metrics. We use a null model approach to test for non-random functional beta diversity given the observed patterns of species turnover across spatial scales. Results Species and functional beta diversity increased with increasing geographic distance (i.e. distance decay of community similarity). Results of variance partitioning analysis show that species and functional beta diversity were spatially structured and significantly related to environmental, particularly climatic, variation. Results of null model analysis show that functional beta diversity was lower than expected based on species turnover at fine scales ({$<$} 600 km) and higher than expected at broad scales ({$>$} 1800 km). Main conclusions The observed patterns of functional beta diversity support a niche-based model of community assembly, driven by the deterministic filtering of species across environmental gradients based on their functional traits.}, - langid = {english}, - keywords = {Beta diversity,community assembly,eastern North America,environmental filtering,functional traits,species turnover,temperate forest,trees}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12030}, - file = {/Users/renatadiaz/Zotero/storage/XI24TZQA/Siefert et al. - 2013 - Functional beta-diversity patterns reveal determin.pdf;/Users/renatadiaz/Zotero/storage/ASZMSD8Y/geb.html} -} - -@article{siegert1949, - title = {On the {{Approach}} to {{Statistical Equilibrium}}}, - author = {Siegert, Arnold J. F.}, - year = {1949}, - month = dec, - journal = {Physical Review}, - volume = {76}, - number = {11}, - pages = {1708--1714}, - issn = {0031-899X}, - doi = {10.1103/PhysRev.76.1708}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/ZRQ4R9GP/Siegert - 1949 - On the Approach to Statistical Equilibrium.pdf} -} - -@article{silvertown2009, - title = {Community Genetics: Resource Addition Has Opposing Effects on Genetic and Species Diversity in a 150-Year Experiment}, - shorttitle = {Community Genetics}, - author = {Silvertown, Jonathan and Biss, Pamela M. and Freeland, Joanna}, - year = {2009}, - journal = {Ecology Letters}, - volume = {12}, - number = {2}, - pages = {165--170}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2008.01273.x}, - abstract = {We used the Park Grass Experiment, begun in 1856, to test alternative hypotheses about the relationship between genetic diversity and plant species diversity. The niche variation hypothesis predicts that populations with few interspecific competitors and hence broader niches are expected to contain greater genetic diversity. The coexistence hypothesis predicts that genetic diversity within species favours coexistence among species and therefore species and genetic diversity should be positively correlated. Amplified Fragment Length Polymorphism (AFLP) markers were used to measure the genetic diversity of populations of Anthoxanthum odoratum growing in 10 plots of differing species richness that lie along resource and soil pH gradients. Genetic diversity in A. odoratum was positively correlated with the number of resources added to a plot, but not correlated with species richness. However, separate analyses have shown a negative correlation between resource addition and species richness at Park Grass and elsewhere, so genetic and species diversity appear to respond in opposite directions.}, - langid = {english}, - keywords = {AFLP,Anthoxanthum odoratum,coexistence,community genetics,genetic diversity,niche variation hypothesis,Park Grass Experiment,resource limitation,species diversity}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2008.01273.x}, - file = {/Users/renatadiaz/Zotero/storage/RZW3YIDD/Silvertown et al. - 2009 - Community genetics resource addition has opposing.pdf;/Users/renatadiaz/Zotero/storage/WUEV28KC/j.1461-0248.2008.01273.html} -} - -@article{simberloff2004, - title = {Community {{Ecology}}: {{Is It Time}} to {{Move On}}?: ({{An American Society}} of {{Naturalists Presidential Address}})}, - shorttitle = {Community {{Ecology}}}, - author = {Simberloff, Daniel}, - year = {2004}, - month = jun, - journal = {The American Naturalist}, - volume = {163}, - number = {6}, - pages = {787--799}, - issn = {0003-0147, 1537-5323}, - doi = {10.1086/420777}, - abstract = {Because of the contingency and complexity of its subject matter, community ecology has few general laws. Laws and models in community ecology are highly contingent, and their domain is usually very local. This fact does not mean that community ecology is a weak science; in fact, it is the locus of exciting advances, with growing mechanistic understanding of causes, patterns, and processes. Further, traditional community ecological research, often local, experimental, and reductionist, is crucial in understanding and responding to many environmental problems, including those posed by global changes. For both scientific and societal reasons, it is not time to abandon community ecology.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/6YWBSE39/Simberloff - 2004 - Community Ecology Is It Time to Move On (An Ame.pdf} -} - -@misc{simonis2020, - title = {Latent {{Dirichlet Allocation Coupled}} with {{Bayesian Time Series Analyses}}}, - author = {Simonis, Juniper L. and Christensen, Erica M. and Harris, David J. and Diaz, Renata and Ye, Hao and White, Ethan P. and Ernest, S. K. Morgan}, - year = {2020}, - month = mar, - doi = {10.5281/zenodo.3715386}, - abstract = {Combines Latent Dirichlet Allocation and Bayesian Multinomial Time Series methods in a two-stage analysis to quantify dynamics in high-dimensional temporal data.}, - howpublished = {Zenodo}, - keywords = {ecology,lda,long-term,parallel-tempering,softmax,time-series}, - file = {/Users/renatadiaz/Zotero/storage/863T4ZEZ/3715386.html} -} - -@misc{simonis2020a, - title = {{{LDATS}}: {{Latent Dirichlet Allocation Coupled}} with {{Time Series Analyses}}}, - author = {Simonis, Juniper L. and Christensen, Erica M. and Harris, David J. and Diaz, Renata M. and Ye, Hao and White, Ethan P. and Ernest, S. K. Morgan}, - year = {2020} -} - -@article{slette2019, - title = {How Ecologists Define Drought, and Why We Should Do Better}, - author = {Slette, Ingrid J. and Post, Alison K. and Awad, Mai and Even, Trevor and Punzalan, Arianna and Williams, Sere and Smith, Melinda D. and Knapp, Alan K.}, - year = {2019}, - month = oct, - journal = {Global Change Biology}, - volume = {25}, - number = {10}, - pages = {3193--3200}, - issn = {1354-1013, 1365-2486}, - doi = {10.1111/gcb.14747}, - langid = {english}, - keywords = {climate,drought,literature review,precipitation,SPEI}, - file = {/Users/renatadiaz/Zotero/storage/949HYWW3/Slette et al. - 2019 - How ecologists define drought, and why we should d.pdf;/Users/renatadiaz/Zotero/storage/X23WWZY9/Slette et al. - 2019 - How ecologists define drought, and why we should d.pdf;/Users/renatadiaz/Zotero/storage/JDL7T9FF/gcb.html} -} - -@article{smith2018, - title = {Body Size Downgrading of Mammals over the Late {{Quaternary}}}, - author = {Smith, Felisa A. and Elliott Smith, Rosemary E. and Lyons, S. Kathleen and Payne, Jonathan L.}, - year = {2018}, - month = apr, - journal = {Science}, - volume = {360}, - number = {6386}, - pages = {310--313}, - publisher = {{American Association for the Advancement of Science}}, - doi = {10.1126/science.aao5987}, - file = {/Users/renatadiaz/Zotero/storage/X5P8VRJG/Smith et al. - 2018 - Body size downgrading of mammals over the late Qua.pdf} -} - -@misc{smith2020, - title = {{{KKE01 The Konza-Kruger Experiment}}: {{A}} Cross-Continental Fire and Grazing Experiment at {{Konza Prairie}}}, - shorttitle = {{{KKE01 The Konza-Kruger Experiment}}}, - author = {Smith, Melinda and Koerner, Sally}, - year = {2020}, - publisher = {{Environmental Data Initiative}}, - doi = {10.6073/PASTA/02BBDC00F35AF065D9BB366042F13E5B}, - abstract = {For more than a decade, we have compared responses of mesic (subhumid) savanna grasslands (\>500 mm MAP in the tropics and \>600 mm MAP outside the tropics) in North America and South Africa to alterations in both fire and grazing regimes. The long-term, comparative experiment that forms the centerpiece of this cross-continental research program is located in tallgrass prairie at the Konza Prairie Biological Station (Kansas, USA) and in knob-thorn marula savanna at the Kruger National Park (Limpopo and Mpumalanga provinces, South Africa). We refer to this study as the Konza-Kruger (K-K) Experiment. At both sites, we have been manipulating grazing by removing all large herbivores (\>5 kg) from research plots with permanent exclosures (each with a paired plot that grazers can freely access). These exclosures were established in replicated fire frequency experiments ongoing at each site (treatments range from \>25-50 yrs of annual burning, burning every 3-4 yrs, or complete fire exclusion).}, - langid = {english} -} - -@article{snelltaylor2020, - title = {The Relative Importance of Biotic and Abiotic Determinants of Temporal Occupancy for Avian Species in {{North America}}}, - author = {Snell Taylor, Sara and Umbanhowar, James and Hurlbert, Allen H.}, - editor = {Issac, Nick}, - year = {2020}, - month = apr, - journal = {Global Ecology and Biogeography}, - volume = {29}, - number = {4}, - pages = {736--747}, - issn = {1466-822X, 1466-8238}, - doi = {10.1111/geb.13064}, - abstract = {Aim: We examined the relative importance of competitor abundance and environmental variables in determining the species distributions of 175 bird species across North America. Unlike previous studies, which tend to model distributions in terms of presence and absence, we take advantage of a geographically extensive dataset of community time series to model the temporal occupancy of species at sites throughout their expected range.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/UKB44RG2/Snell Taylor et al. - 2020 - The relative importance of biotic and abiotic dete.pdf} -} - -@article{sofaer2020, - title = {Human-Associated Species Dominate Passerine Communities across the {{United States}}}, - author = {Sofaer, Helen R. and Flather, Curtis H. and Jarnevich, Catherine S. and Davis, Kristin P. and Pejchar, Liba}, - year = {2020}, - journal = {Global Ecology and Biogeography}, - volume = {29}, - number = {5}, - pages = {885--895}, - issn = {1466-8238}, - doi = {10.1111/geb.13071}, - abstract = {Aim Human development and agriculture can have transformative and homogenizing effects on natural systems, shifting the composition of ecological communities towards non-native and native species that tolerate or thrive under human-dominated conditions. These impacts cannot be fully captured by summarizing species presence, as they include dramatic changes to patterns of species abundance. However, how human land use patterns and species invasions intersect to shape patterns of abundance and dominance within ecological communities is poorly understood even in well-known taxa. Location Conterminous United States. Time period 2010\textendash 2012. Major taxa studied Passeriformes. Methods We analyse continental-scale monitoring data to study the proportional abundance of non-native and native synanthropic species within passerine bird communities. Synanthropic species are those that benefit from an association with humans. We estimate how the amount and configuration of human development and agriculture relate to the degree to which human-associated species dominate passerine communities across the continent. Results Human-associated species comprised the majority of detected passerine individuals across two-thirds of bird surveys. Non-native and synanthropic species responded differently to land cover and reached highest relative abundance in different portions of the continent. The proportional abundance of synanthropic birds increased rapidly with development, but was not related to the configuration of land cover. The proportion of non-native individuals was higher when intensively-used land cover was more aggregated. Main conclusions Even low amounts of intensively-used lands were associated with a dramatic reshaping of passerine communities, with consequences for patterns of relative abundance across the continent.}, - langid = {english}, - keywords = {habitat fragmentation,habitat loss,land cover,non-native species,synanthropic species}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.13071}, - file = {/Users/renatadiaz/Zotero/storage/QT26I55S/Sofaer et al. - 2020 - Human-associated species dominate passerine commun.pdf;/Users/renatadiaz/Zotero/storage/5YFI6YUV/geb.html} -} - -@article{sole2021, - title = {Revisiting {{Van Valen}}'s {{Red Queen Hypothesis}}}, - author = {Sole, Ricard}, - year = {2021}, - pages = {6}, - abstract = {Leigh Van Valen was an American evolutionary biologist who made major contributions to evolutionary theory and is particularly remembered by his groundbreaking paper ''A New Evolutionary Law'' (1973) where he provided evidence from fossil record data that this law maintains that the probability of extinction within any group remains essentially constant through time. In order to explain such unexpected result, Van Valen formulated a very influential idea that he dubbed the ''Red Queen hypothesis''. It states that the constant decay must be a consequence of evolutionary interactions among connected species within ecological networks. In Van Valen's picture, species do not merely evolve: they also coevolve with other species. As a consequence, when thinking in adaptation to an external environment, the other species must be considered as part (may be a major part) of such external world. Van Valen's law provided the first complex systems theory of coevolutionary dynamics and inspired a whole range of theoretical and experimental developments and scholars from very diverse fields, from economics to physics. In that respect, Leigh Van Valen's contribution percolated far beyond its original formulation. Red Queen arms races are nowadays considered a widespread feature of complex adaptive systems.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/79VSEPC6/Sole - 2021 - Revisiting Van Valen’s Red Queen Hypothesis.pdf} -} - -@article{sorte2005, - title = {Temporal Turnover of Common Species in Avian Assemblages in {{North America}}}, - author = {Sorte, Frank A. La and Boecklen, William J.}, - year = {2005}, - journal = {Journal of Biogeography}, - volume = {32}, - number = {7}, - pages = {1151--1160}, - issn = {1365-2699}, - doi = {10.1111/j.1365-2699.2005.01271.x}, - abstract = {Aim We examine patterns of temporal turnover of common species in avian assemblages in North America to test the hypothesis that changes in avian diversity structure observed in these assemblages were associated with the colonization of common species. Location The contiguous United States and southern Canada. Methods We measured temporal turnover from 1968 to 2003 for 547 avian species at 1673 North American Breeding Bird Survey (BBS) routes. We used the Euclidian distance between expected and observed presence/absence vectors and randomization tests to place species into two categories, common and not-common, and into three categories for common species: (1) always common, (2) common and colonizing, and (3) common and extirpated. We used these categories to identify species experiencing extreme colonization and extirpation events and to examine changes in species composition at BBS routes. We also determined how these patterns were associated with changes in species richness and changes in similarity in species composition. Results Nine of the 547 species represented outliers, where the number of BBS routes colonized greatly exceeded the number extirpated; no species showed extreme values for extirpation. The nine species colonized BBS routes primarily in the upper Midwest and north-eastern United States. Presence of the nine species at BBS routes was correlated with increasing net gain in common species (difference between common colonized and common extirpated), higher levels of species richness and increasing species richness over time, more similar species compositions and increasing similarity over time, and a greater prevalence of common species over not-common species. The literature indicates that all nine species experienced some form of geographical range expansion during the time of the survey involving four elements: (1) introduction and invasion; (2) the ability to use human-altered environments, including habitats associated with agricultural, suburban, or urban areas; (3) intensive management activities, including habitat improvements and reintroductions and (4) the ability to use habitats formed through forest regeneration. These factors in combination point to anthropogenic activities and related land use histories as the primary drivers of change. One of the nine species colonized regions well outside its historic geographical range and the remaining eight species were native within the regions they colonized. Main conclusions Our results suggest that a combination of anthropogenic activities promoted, within certain regions of North America, the geographical expansion of a limited number of common species that were native to those regions. These colonization events were correlated with changes in diversity structure, implying that large-scale diversity patterns were being influenced by anthropogenic activities. These changes can be characterized primarily by gains in species richness, an increased prevalence of common species, and more similar species compositions. Thus, using simple large-scale measures of diversity could be problematic if recent biogeographical patterns of species diversity are not considered. Specifically, using species richness or an indicator species to assess diversity could bias assessments towards common species whose populations have recently benefited through anthropogenic activities.}, - langid = {english}, - keywords = {Anthropogenic activities,avian assemblages,common species,homogenization,North American Breeding Bird Survey,species turnover,temporal turnover}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2699.2005.01271.x}, - file = {/Users/renatadiaz/Zotero/storage/J27YP5Y5/Sorte and Boecklen - 2005 - Temporal turnover of common species in avian assem.pdf;/Users/renatadiaz/Zotero/storage/RM858V84/j.1365-2699.2005.01271.html} -} - -@article{spooner2018, - title = {Rapid Warming Is Associated with Population Decline among Terrestrial Birds and Mammals Globally}, - author = {Spooner, Fiona E. B. and Pearson, Richard G. and Freeman, Robin}, - year = {2018}, - month = oct, - journal = {Global Change Biology}, - volume = {24}, - number = {10}, - pages = {4521--4531}, - issn = {13541013}, - doi = {10.1111/gcb.14361}, - abstract = {Animal populations have undergone substantial declines in recent decades. These declines have occurred alongside rapid, human-driven environmental change, including climate warming. An association between population declines and environmental change is well established, yet there has been relatively little analysis of the importance of the rates of climate warming and its interaction with conversion to anthropogenic land use in causing population declines. Here we present a global assessment of the impact of rapid climate warming and anthropogenic land use conversion on 987 populations of 481 species of terrestrial birds and mammals since 1950. We collated spatially referenced population trends of at least 5 years' duration from the Living Planet database and used mixed effects models to assess the association of these trends with observed rates of climate warming, rates of conversion to anthropogenic land use, body mass, and protected area coverage. We found that declines in population abundance for both birds and mammals are greater in areas where mean temperature has increased more rapidly, and that this effect is more pronounced for birds. However, we do not find a strong effect of conversion to anthropogenic land use, body mass, or protected area coverage. Our results identify a link between rapid warming and population declines, thus supporting the notion that rapid climate warming is a global threat to biodiversity.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/XAJDIRD4/Spooner et al. - 2018 - Rapid warming is associated with population declin.pdf} -} - -@article{stegen2013, - title = {Stochastic and Deterministic Drivers of Spatial and Temporal Turnover in Breeding Bird Communities: {{Drivers}} of Spatial and Temporal Turnover}, - shorttitle = {Stochastic and Deterministic Drivers of Spatial and Temporal Turnover in Breeding Bird Communities}, - author = {Stegen, James C. and Freestone, Amy L. and Crist, Thomas O. and Anderson, Marti J. and Chase, Jonathan M. and Comita, Liza S. and Cornell, Howard V. and Davies, Kendi F. and Harrison, Susan P. and Hurlbert, Allen H. and Inouye, Brian D. and Kraft, Nathan J. B. and Myers, Jonathan A. and Sanders, Nathan J. and Swenson, Nathan G. and Vellend, Mark}, - editor = {Evans, Karl}, - year = {2013}, - month = feb, - journal = {Global Ecology and Biogeography}, - volume = {22}, - number = {2}, - pages = {202--212}, - issn = {1466822X}, - doi = {10.1111/j.1466-8238.2012.00780.x}, - abstract = {Aim A long-standing challenge in ecology is to identify the suite of factors that lead to turnover in species composition in both space and time. These factors might be stochastic (e.g. sampling and priority effects) or deterministic (e.g. competition and environmental filtering). While numerous studies have examined the relationship between turnover and individual drivers of interest (e.g. primary productivity, habitat heterogeneity, or regional \textendash{} `gamma' \textendash{} diversity), few studies have disentangled the simultaneous influences of multiple stochastic and deterministic processes on both temporal and spatial turnover. If turnover is governed primarily by stochastic sampling processes, removing the sampling effects of gamma diversity should result in non-significant relationships between turnover and environmental variables. Conversely, if deterministic processes govern turnover patterns, removing sampling effects will have little influence on turnover gradients. Here, we test these predictions.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/LZNG4SLG/Stegen et al. - 2013 - Stochastic and deterministic drivers of spatial an.pdf} -} - -@article{stein2011, - title = {Super-Spreaders in Infectious Diseases}, - author = {Stein, Richard A.}, - year = {2011}, - month = aug, - journal = {International Journal of Infectious Diseases}, - volume = {15}, - number = {8}, - pages = {e510-e513}, - issn = {1201-9712}, - doi = {10.1016/j.ijid.2010.06.020}, - abstract = {Early studies that explored host\textendash pathogen interactions assumed that infected individuals within a population have equal chances of transmitting the infection to others. Subsequently, in what became known as the 20/80 rule, a small percentage of individuals within any population was observed to control most transmission events. This empirical rule was shown to govern inter-individual transmission dynamics for many pathogens in several species, and individuals who infect disproportionately more secondary contacts, as compared to most others, became known as super-spreaders. Studies conducted in the wake of the severe acute respiratory syndrome (SARS) pandemic revealed that, in the absence of super-spreading events, most individuals infect few, if any, secondary contacts. The analysis of SARS transmission, and reports from other outbreaks, unveil a complex scenario in which super-spreading events are shaped by multiple factors, including co-infection with another pathogen, immune suppression, changes in airflow dynamics, delayed hospital admission, misdiagnosis, and inter-hospital transfers. Predicting and identifying super-spreaders open significant medical and public health challenges, and represent important facets of infectious disease management and pandemic preparedness plans.}, - langid = {english}, - keywords = {Modeling,SARS,Super-spreaders,Transmission}, - file = {/Users/renatadiaz/Zotero/storage/B7ZJLXCR/Stein - 2011 - Super-spreaders in infectious diseases.pdf;/Users/renatadiaz/Zotero/storage/PL6KLGJ4/S1201971211000245.html} -} - -@article{stuchiner2022, - title = {Intentional Mentoring Should Increase Inclusivity in Ecology}, - author = {Stuchiner, Emily R. and Lin Hunter, Danielle E. and Neuwald, Jennifer L. and Webb, Colleen T. and Balgopal, Meena M.}, - year = {2022}, - journal = {Ecosphere}, - volume = {13}, - number = {1}, - pages = {e3902}, - issn = {2150-8925}, - doi = {10.1002/ecs2.3902}, - abstract = {High-quality mentoring relationships can be pivotal to recruitment, retention, and long-term persistence in ecology majors and careers. The graduate\textendash undergraduate student mentoring relationship can become uniquely important during activities like ecological fieldwork. However, graduate students often have little experience as research mentors, which can lead to negative research experiences for undergraduate mentees. Given the potential for mentoring relationships to impact people's decisions on pursuing ecological studies and/or careers, we created and piloted a mentoring professional development program designed around intentional mentoring. Intentional mentoring requires that mentors preemptively identify what skills and knowledge their mentee should develop as well as the practices to help mentees develop these competencies. Our rationale for using intentional mentoring was that it has the potential to increase mentors' and mentees' awareness of issues around diversity, equity, inclusion, and social justice in research experiences, in addition to developing professional competencies. To evaluate our program, we conducted focus group interviews with graduate and undergraduate student participants following a multi-week mentoring training workshop, the primary aspect of the program. Participants described an increased valuation of intentional mentoring and a desire to be more intentional in their mentoring relationships. Graduate student mentors described an increased desire to be more intentional mentors, whereas undergraduate mentees described an increased desire to seek mentors with whom they could develop intentional relationships. Undergraduates also better recognized the importance of academic mentors. Based on our evaluation, we posit that intentional mentoring can increase the retention and persistence of students with diverse identities in ecology by fostering a sense of belonging. We advocate the implementation of mentoring training workshops as a part of academic ecological programs to increase inclusion in our discipline.}, - langid = {english}, - keywords = {diversity,equity,fieldwork,graduate student,inclusion,mentoring,professional development,undergraduate research}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3902}, - file = {/Users/renatadiaz/Zotero/storage/A8IA48JZ/Stuchiner et al. - 2022 - Intentional mentoring should increase inclusivity .pdf;/Users/renatadiaz/Zotero/storage/35VD26J9/ecs2.html} -} - -@article{supp2012, - title = {An Experimental Test of the Response of Macroecological Patterns to Altered Species Interactions}, - author = {Supp, S. R. and Xiao, X. and Ernest, S. K. M. and White, E. P.}, - year = {2012}, - month = dec, - journal = {Ecology}, - volume = {93}, - number = {12}, - pages = {2505--2511}, - issn = {0012-9658}, - doi = {10.1890/12-0370.1}, - abstract = {Macroecological patterns such as the species\textendash area relationship (SAR), the species-abundance distribution (SAD), and the species\textendash time relationship (STR) exhibit regular behavior across ecosystems and taxa. However, determinants of these patterns remain poorly understood. Emerging theoretical frameworks for macroecology attempt to understand this regularity by ignoring detailed ecological interactions and focusing on the influence of a small number of community-level state variables, such as species richness and total abundance, on these patterns. We present results from a 15-year rodent removal experiment evaluating the response of three different macroecological patterns in two distinct annual plant communities (summer and winter) to two levels of manipulated seed predation. Seed predator manipulations significantly impacted species composition on all treatments in both communities, but did not significantly impact richness, community abundance, or macroecological patterns in most cases. However, winter community abundance and richness responded significantly to the removal of all rodents. Changes in richness and abundance were coupled with significant shifts in macroecological patterns (SADs, SARs, and STRs). Because altering species interactions only impacted macroecological patterns when the state variables of abundance and richness also changed, we suggest that, in this system, local-scale processes primarily act indirectly through these properties to determine macroecological patterns.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/RFIKBURR/Supp et al. - 2012 - An experimental test of the response of macroecolo.pdf} -} - -@misc{supp2014, - title = {Manipulated {{Animal Community Database}}}, - author = {Supp, Sarah}, - year = {2014}, - month = mar, - doi = {10.6084/m9.figshare.969831.v1}, - abstract = {6,698 records indicated the presence and abundance of animal species, including representatives across trophic groups and size classes documented at 254 sites throughout the world, encompassing a variety of habitats. We accessed peer-reviewed articles, government publications, and theses that were freely available with the Utah State University library subscription and were published in English. We extracted data from articles that reported species-level abundance for a control community and at least one manipulated community.~The data here represent a single data point each for the control treatment and the manipulated treatment(s) in each study. Data came from a wide variety of sites including artificial experiments (i.e., caged exclosures, habitat modules, nutrient addition) and human-mediated ``natural'' experiments (e.g., wildfire or controlled burn, logging, grazed plots, pollution). Sites represent all continents except Antarctica, and widely varying terrestrial animal groups (arachnid, insect, herpetofauna [reptiles and amphibians], mammal, and bird).}, - keywords = {biodiversity,community,composition,ecology,experiment,manipulated}, - file = {/Users/renatadiaz/Zotero/storage/6PHB72EE/969831.pdf} -} - -@article{supp2014a, - title = {Species-Level and Community-Level Responses to Disturbance: A Cross-Community Analysis}, - shorttitle = {Species-Level and Community-Level Responses to Disturbance}, - author = {Supp, Sarah R. and Ernest, S. K. Morgan}, - year = {2014}, - month = jul, - journal = {Ecology}, - volume = {95}, - number = {7}, - pages = {1717--1723}, - issn = {0012-9658}, - doi = {10.1890/13-2250.1}, - abstract = {Communities are comprised of individual species that respond to changes in their environment depending in part on their niche requirements. These species comprise the biodiversity of any given community. Common biodiversity metrics such as richness, evenness, and the species abundance distribution are frequently used to describe biodiversity across ecosystems and taxonomic groups. While it is increasingly clear that researchers will need to forecast changes in biodiversity, ecology currently lacks a framework for understanding the natural background variability in biodiversity or how biodiversity patterns will respond to environmental change. We predict that while species populations depend on local ecological mechanisms (e.g., niche processes) and should respond strongly to disturbance, communitylevel properties that emerge from these species should generally be less sensitive to disturbance because they depend on regional mechanisms (e.g., compensatory dynamics). Using published data from terrestrial animal communities, we show that community-level properties were generally resilient under a suite of artificial and natural manipulations. In contrast, species responded readily to manipulation. Our results suggest that community-level measures are poor indicators of change, perhaps because many systems display strong compensatory dynamics maintaining community-level properties. We suggest that ecologists consider using multiple metrics that measure composition and structure in biodiversity response studies.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/7FC5NS6E/Supp and Ernest - 2014 - Species-level and community-level responses to dis.pdf;/Users/renatadiaz/Zotero/storage/AHMBL8TH/Supp and Ernest - 2014 - Species-level and community-level responses to dis.pdf} -} - -@article{supp2015, - title = {Using Life History Trade-Offs to Understand Core-Transient Structuring of a Small Mammal Community}, - author = {Supp, Sarah R. and Koons, David N. and Ernest, S. K. Morgan}, - year = {2015}, - month = oct, - journal = {Ecosphere}, - volume = {6}, - number = {10}, - pages = {art187}, - issn = {2150-8925}, - doi = {10.1890/ES15-00239.1}, - abstract = {An emerging conceptual framework suggests that communities are composed of two main groups of species through time: core species that are temporally persistent, and transient species that are temporally intermittent. Core and transient species have been shown to differ in spatiotemporal turnover, diversity patterns, and importantly, survival strategies targeted at local versus regional habitat use. While the core-transient framework has typically been a site-specific designation for species, we suggest that if core and transient species have local versus regional survival strategies across sites, and consistently differ in population-level spatial structure and gene flow, they may also typically exhibit different life-history strategies. Specifically, core species should display relatively low movement rates, low reproductive effort, high ecological specialization and high survival rates compared to transient species, which may display a wider range of traits given that transience may result from source-sink dynamics or from the ability to emigrate readily in a nomadic fashion. We present results from 21 years of capture-mark-recapture data in a diverse rodent community, evaluating the linkages between temporal persistence, local abundance, and trade-offs among life-history traits. Core species at our site conservatively supported our hypotheses, differing in ecological specialization, survival and movement probabilities, and reproductive effort relative to transient species. Transient species exhibited a wider range of characteristics, which likely stems from the multiple processes generating transience in local communities, such as source-sink dynamics at larger regional scales or nomadic life history strategies. We suggest that trait associations among core-transient species may be similar in other systems and warrants further study.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/L24NLPXS/Supp et al. - 2015 - Using life history trade-offs to understand core-t.pdf} -} - -@article{swartz2010, - title = {Coexisting Desert Rodents Differ in Selection of Microhabitats for Cache Placement and Pilferage}, - author = {Swartz, Maryke J. and Jenkins, Stephen H. and Dochtermann, Ned A.}, - year = {2010}, - month = oct, - journal = {Journal of Mammalogy}, - volume = {91}, - number = {5}, - pages = {1261--1268}, - publisher = {{Oxford Academic}}, - issn = {0022-2372}, - doi = {10.1644/09-MAMM-A-280.1}, - abstract = {Abstract. Seed caching by desert rodents in the family Heteromyidae is an important behavioral adaptation for animals living in environments with limited and u}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/EE3WUD9I/Swartz et al. - 2010 - Coexisting desert rodents differ in selection of m.pdf;/Users/renatadiaz/Zotero/storage/FHRCCGKT/902950.html} -} - -@article{swenson2011, - title = {Deterministic Tropical Tree Community Turnover: Evidence from Patterns of Functional Beta Diversity along an Elevational Gradient}, - shorttitle = {Deterministic Tropical Tree Community Turnover}, - author = {Swenson, Nathan G. and {Anglada-Cordero}, Pedro and Barone, John A.}, - year = {2011}, - month = mar, - journal = {Proceedings of the Royal Society B: Biological Sciences}, - volume = {278}, - number = {1707}, - pages = {877--884}, - issn = {0962-8452, 1471-2954}, - doi = {10.1098/rspb.2010.1369}, - abstract = {Explaining the mechanisms that produce the enormous diversity within and between tropical tree communities is a pressing challenge for plant community ecologists. Mechanistic hypotheses range from niche-based deterministic to dispersal-based stochastic models. Strong tests of these hypotheses require detailed information regarding the functional strategies of species. A few tropical studies to date have examined trait dispersion within individual forest plots using species trait means in order to ask whether coexisting species tend to be more or less functionally similar than expected given a null model. The present work takes an alternative approach by: (i) explicitly incorporating population-level trait variability; and (ii) quantifying the functional beta diversity in a series of 15 tropical forest plots arrayed along an elevational gradient. The results show a strong pattern of decay in community functional similarity with elevation. These observed patterns of functional beta diversity are shown to be highly non-random and support a deterministic model of tropical tree community assembly and turnover.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/5YTN9G22/Swenson et al. - 2011 - Deterministic tropical tree community turnover ev.pdf} -} - -@article{tajima1989, - title = {Statistical Method for Testing the Neutral Mutation Hypothesis by {{DNA}} Polymorphism.}, - author = {Tajima, F.}, - year = {1989}, - month = nov, - journal = {Genetics}, - volume = {123}, - number = {3}, - pages = {585--595}, - publisher = {{Genetics}}, - issn = {0016-6731, 1943-2631}, - abstract = {The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.}, - chapter = {INVESTIGATIONS}, - copyright = {Copyright \textcopyright{} 1989 by the Genetics Society of America}, - langid = {english}, - pmid = {2513255}, - file = {/Users/renatadiaz/Zotero/storage/TH7MEM6M/Tajima - 1989 - Statistical method for testing the neutral mutatio.pdf;/Users/renatadiaz/Zotero/storage/564A9H6H/585.html} -} - -@article{taylor2018, - title = {The Prevalence and Impact of Transient Species in Ecological Communities}, - author = {Taylor, Sara J. Snell and Evans, Brian S. and White, Ethan P. and Hurlbert, Allen H.}, - year = {2018}, - journal = {Ecology}, - volume = {99}, - number = {8}, - pages = {1825--1835}, - issn = {1939-9170}, - doi = {10.1002/ecy.2398}, - abstract = {Transient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 19,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with increasing spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species\textendash abundance distributions, species\textendash energy relationships, species\textendash area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.}, - langid = {english}, - keywords = {community assembly,occupancy,spatial scale,species abundance distribution,species-energy,species–area,temporal turnover,transient species}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2398}, - file = {/Users/renatadiaz/Zotero/storage/388XP67A/Taylor et al. - 2018 - The prevalence and impact of transient species in .pdf;/Users/renatadiaz/Zotero/storage/4UTKBVBC/Snell Taylor et al. - 2018 - The prevalence and impact of transient species in .pdf;/Users/renatadiaz/Zotero/storage/BQRACULM/Taylor et al. - 2018 - The prevalence and impact of transient species in .pdf;/Users/renatadiaz/Zotero/storage/V7P44H3B/Taylor et al. - 2018 - The prevalence and impact of transient species in .pdf;/Users/renatadiaz/Zotero/storage/WEMYTLZG/Taylor et al. - 2018 - The prevalence and impact of transient species in .pdf;/Users/renatadiaz/Zotero/storage/JBIB76FH/ecy.html;/Users/renatadiaz/Zotero/storage/P3G4NWP7/ecy.html;/Users/renatadiaz/Zotero/storage/RERZQ645/ecy.html} -} - -@article{terry2015, - title = {Energy Flow and Functional Compensation in {{Great Basin}} Small Mammals under Natural and Anthropogenic Environmental Change}, - author = {Terry, Rebecca C. and Rowe, Rebecca J.}, - year = {2015}, - month = aug, - journal = {Proceedings of the National Academy of Sciences}, - volume = {112}, - number = {31}, - pages = {9656--9661}, - publisher = {{National Academy of Sciences}}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.1424315112}, - abstract = {Research on the ecological impacts of environmental change has primarily focused at the species level, leaving the responses of ecosystem-level properties like energy flow poorly understood. This is especially so over millennial timescales inaccessible to direct observation. Here we examine how energy flow within a Great Basin small mammal community responded to climate-driven environmental change during the past 12,800 y, and use this baseline to evaluate responses observed during the past century. Our analyses reveal marked stability in energy flow during rapid climatic warming at the terminal Pleistocene despite dramatic turnover in the distribution of mammalian body sizes and habitat-associated functional groups. Functional group turnover was strongly correlated with climate-driven changes in regional vegetation, with climate and vegetation change preceding energetic shifts in the small mammal community. In contrast, the past century has witnessed a substantial reduction in energy flow caused by an increase in energetic dominance of small-bodied species with an affinity for closed grass habitats. This suggests that modern changes in land cover caused by anthropogenic activities\textemdash particularly the spread of nonnative annual grasslands\textemdash has led to a breakdown in the compensatory dynamics of energy flow. Human activities are thus modifying the small mammal community in ways that differ from climate-driven expectations, resulting in an energetically novel ecosystem. Our study illustrates the need to integrate across ecological and temporal scales to provide robust insights for long-term conservation and management.}, - chapter = {Biological Sciences}, - langid = {english}, - pmid = {26170294}, - keywords = {body size,desert rodents,invasive grass,paleoecology,Quaternary}, - file = {/Users/renatadiaz/Zotero/storage/36459FTM/Terry and Rowe - 2015 - Energy flow and functional compensation in Great B.pdf;/Users/renatadiaz/Zotero/storage/7ITV957V/9656.html} -} - -@article{thibault2008, - title = {Impact of an Extreme Climatic Event on Community Assembly}, - author = {Thibault, Katherine M. and Brown, James H.}, - year = {2008}, - month = mar, - journal = {Proceedings of the National Academy of Sciences of the United States of America}, - volume = {105}, - number = {9}, - pages = {3410--3415}, - publisher = {{Natl Acad Sciences}}, - address = {{Washington}}, - issn = {0027-8424}, - doi = {10.1073/pnas.0712282105}, - abstract = {Extreme climatic events are predicted to increase in frequency and magnitude, but their ecological impacts are poorly understood. Such events are large, infrequent, stochastic perturbations that can change the outcome of entrained ecological processes. Here we show how an extreme flood event affected a desert rodent community that has been monitored for 30 years. The flood (i) caused catastrophic, species-specific mortality; (ii) eliminated the incumbency advantage of previously dominant species; (iii) reset long-term population and community trends; (iv) interacted with competitive and metapopulation dynamics; and (v) resulted in rapid, wholesale reorganization of the community. This and a previous extreme rainfall event were punctuational perturbations - they caused large, rapid population and community-level changes that were superimposed on a background of more gradual trends driven by climate and vegetation change. Captured by chance through long-term monitoring, the impacts of such large, infrequent events provide unique insights into the processes that structure ecological communities.}, - langid = {english}, - keywords = {compensation,competition,desert rodent community,drought,dynamics,food addition,grassland,long-term,species-diversity,terrestrial ecosystems}, - annotation = {WOS:000253846500043}, - file = {/Users/renatadiaz/Zotero/storage/64DRP3NG/Thibault and Brown - 2008 - Impact of an extreme climatic event on community a.pdf} -} - -@article{thibault2010, - title = {Redundant or Complementary? {{Impact}} of a Colonizing Species on Community Structure and Function}, - shorttitle = {Redundant or Complementary?}, - author = {Thibault, Katherine M. and Ernest, S. K. Morgan and Brown, James H.}, - year = {2010}, - journal = {Oikos}, - volume = {119}, - number = {11}, - pages = {1719--1726}, - publisher = {{Wiley}}, - issn = {0030-1299}, - abstract = {Recent studies suggest that species with similar functional traits will have similar effects on ecosystems, but evidence for redundancy of species impacts is limited. Here we use a long-term experiment to gain insight into functional relationships within a desert rodent community. Experimental removal of kangaroo rats, Dipodomys spp., coupled with the recent, serendipitous colonization of a single species of large pocket mouse Chaetodipus baileyi yielded treatments that differed in the diversity of large granivorous rodents present. We evaluated functional overlap of C. baileyi and the other resident large granivores (i.e. the kangaroo rats) by comparing total energy use of granivorous rodents and total abundance and species richness of small granivores across treatments before and after the arrival of C. baileyi. We found that C. baileyi almost completely compensated for the changes in these key ecosystem-level properties caused by kangaroo rat removal, but it differentially impacted the population dynamics of individual small granivorous rodent species. Thus, its effects were largely complementary, rather than redundant, to those of the missing kangaroo rats. Although short-term or single-measure analyses may suggest redundancy, our results support the longstanding dictum that niches of coexisting species are often similar but rarely, if ever, identical.}, - keywords = {biodiversity,colonization,competition,desert rodent community,diversity,ecosystem processes,equivalence,long-term,neutral theory,plant-communities}, - file = {/Users/renatadiaz/Zotero/storage/N3AUGD9H/Thibault et al. - 2010 - Redundant or complementary Impact of a colonizing.pdf;/Users/renatadiaz/Zotero/storage/XLTB2P36/Thibault et al. - 2010 - Redundant or complementary Impact of a colonizing.pdf;/Users/renatadiaz/Zotero/storage/DHDS6WGE/j.1600-0706.2010.18378.html} -} - -@article{thibault2011, - title = {Multimodality in the Individual Size Distributions of Bird Communities}, - author = {Thibault, Katherine M. and White, Ethan P. and Hurlbert, Allen H. and Ernest, S. K. Morgan}, - year = {2011}, - journal = {Global Ecology and Biogeography}, - volume = {20}, - number = {1}, - pages = {145--153}, - issn = {1466-8238}, - doi = {10.1111/j.1466-8238.2010.00576.x}, - abstract = {Aim Body size often plays a significant role in community assembly through its impacts on the life history and ecological attributes of species. Insight into the importance of size in structuring communities can be gained by examining the distribution of sizes of individuals [i.e. the individual size distribution (ISD) or size spectrum] in a community. ISDs have been studied extensively in aquatic and tree communities, but have received little attention in terrestrial animal communities. Here, we conduct the first macroecological analysis of ISDs in terrestrial animal communities to determine whether they show broad-scale consistency in shape. Location North America, north of Mexico. Methods Using likelihood-based methods and Gaussian mixture modelling, coupled with data from the Breeding Bird Survey and Christmas Bird Count, we determine whether the ISDs for thousands of breeding and wintering North American bird communities are: (1) monotonically decreasing, (2) unimodal or (3) multimodal. Results We find that avian ISDs are consistently multimodal, with most characterized by more than five modes in both breeding and wintering communities from local to continental scales. In addition, the positions of these modes along the size axis are remarkably consistent. Main conclusions The striking consistency in the ISD within bird communities, as with tree and aquatic communities, indicates that the ISD is an important and informative characterization of resource utilization within an ecological assemblage. The differences in shape of the ISD among these groups also suggest that differences in body size-related constraints affect interactions within a group and with the environment. Our results confirm that avian assemblages do exhibit structure along the body size axis, and therefore it will be fruitful to explore this pattern in greater detail.}, - langid = {english}, - keywords = {Birds,community assembly,community structure,multimodality,North America,size distributions,size spectra}, - file = {/Users/renatadiaz/Zotero/storage/CFJ4X6E4/Thibault et al. - 2011 - Multimodality in the individual size distributions.pdf;/Users/renatadiaz/Zotero/storage/WH4JUTZ7/Thibault et al. - 2011 - Multimodality in the individual size distributions.pdf;/Users/renatadiaz/Zotero/storage/XSVLNKPE/j.1466-8238.2010.00576.html} -} - -@article{thibault2011a, - title = {Species Composition and Abundance of Mammalian Communities}, - author = {Thibault, Katherine M. and Supp, Sarah R. and Giffin, Mikaelle and White, Ethan P. and Ernest, S. K. Morgan}, - year = {2011}, - journal = {Ecology}, - volume = {92}, - number = {12}, - pages = {2316--2316}, - issn = {1939-9170}, - doi = {10.1890/11-0262.1}, - abstract = {Ecologists have long sought to understand the mechanisms underlying the assembly and structure of communities. Such understanding is relevant to both basic science and conservation-related issues. The macroecological approach to this problem involves asking scientific questions using a large number of communities in order to elucidate generalities in pattern and process. Such analyses are typically conducted using a substantial amount of data from a particular taxonomic group across a diversity of systems. Large community databases are available for a number of taxa, but no publicly available database exists for mammals. Given the logistical challenges of collecting such data de novo, compiling existing information from the literature provides the best avenue for acquiring the necessary data. Here, we provide a data set that includes species lists for 1000 mammal communities, excluding bats, with species-level abundances available for 940 of these communities. All communities found in the literature that included complete, site-specific sampling data, composed of species lists with or without associated abundances, were included in the data set. Most, but not all, sites are limited to species groups that are sampled using a single technique (e.g., small mammals sampled with Sherman traps). The data set consists of 7977 records from 1000 georeferenced sites encompassing a variety of habitats throughout the world, and it includes data on 660 mammal species with sizes ranging from 2 g to {$>$}500 kg. The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at {$\langle$}http://esapubs.org/archive{$\rangle$}. (The accession number for each Data Paper is given directly beneath the title.)}, - copyright = {\textcopyright{} 2011 by the Ecological Society of America}, - langid = {english}, - keywords = {abundance,community,community assembly,community structure,composition,mammals}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/11-0262.1}, - file = {/Users/renatadiaz/Zotero/storage/TJ4NIYWG/Thibault et al. - 2011 - Species composition and abundance of mammalian com.pdf;/Users/renatadiaz/Zotero/storage/EXBSF6SZ/11-0262.html} -} - -@article{thompson2020, - title = {A Process-Based Metacommunity Framework Linking Local and Regional Scale Community Ecology}, - author = {Thompson, Patrick L. and Guzman, Laura Melissa and Meester, Luc De and Horv{\'a}th, Zs{\'o}fia and Ptacnik, Robert and Vanschoenwinkel, Bram and Viana, Duarte S. and Chase, Jonathan M.}, - year = {2020}, - journal = {Ecology Letters}, - volume = {23}, - number = {9}, - pages = {1314--1329}, - issn = {1461-0248}, - doi = {10.1111/ele.13568}, - abstract = {The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: (1) density-independent responses to abiotic conditions, (2) density-dependent biotic interactions and (3) dispersal. Stochasticity is incorporated in the demographic realisation of each of these processes. We formalise this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning and stability within metacommunities.}, - copyright = {\textcopyright{} 2020 The Authors. Ecology Letters published by CNRS and John Wiley \& Sons Ltd}, - langid = {english}, - keywords = {Abiotic niche,coexistence,competition,dispersal,diversity,environmental change,functioning,stability,temporal}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13568}, - file = {/Users/renatadiaz/Zotero/storage/DRRXISPX/Thompson et al. - 2020 - A process-based metacommunity framework linking lo.pdf;/Users/renatadiaz/Zotero/storage/TCW2M487/ele.html} -} - -@article{thomsen2019, - title = {Compensatory Responses Can Alter the Form of the Biodiversity-Function Relation Curve}, - author = {Thomsen, Matthias S. and Godbold, Jasmin A. and Garcia, Clement and Bolam, Stefan G. and Parker, Ruth and Solan, Martin}, - year = {2019}, - month = apr, - journal = {Proceedings of the Royal Society B-Biological Sciences}, - volume = {286}, - number = {1901}, - pages = {20190287}, - publisher = {{Royal Soc}}, - address = {{London}}, - issn = {0962-8452}, - doi = {10.1098/rspb.2019.0287}, - abstract = {There is now strong evidence that ecosystem properties are influenced by alterations in biodiversity. The consensus that has emerged from over two decades of research is that the form of the biodiversity-functioning relationship follows a saturating curve. However, the foundation from which these conclusions are drawn mostly stems from empirical investigations that have not accounted for post-extinction changes in community composition and structure, or how surviving species respond to new circumstances and modify their contribution to functioning. Here, we use marine sediment-dwelling invertebrate communities to experimentally assess whether post-extinction compensatory mechanisms (simulated by increasing species biomass) have the potential to alter biodiversity-ecosystem function relations. Consistent with recent numerical simulations, we find that the form of the biodiversity-function curve is dependent on whether or not compensatory responses are present, the cause and extent of extinction, and species density. When species losses are combined with the compensatory responses of surviving species, both community composition, dominance structure, and the pool and relative expression of functionally important traits change and affect species interactions and behaviour. These observations emphasize the importance of post-extinction community composition in determining the stability of ecosystem functioning following extinction. Our results caution against the use of the generalized biodiversity-function curve when generating probabilistic estimates of post-extinction ecosystem properties for practical application.}, - langid = {english}, - keywords = {behavioral-responses,climate-change,community,diversity,ecosystem function,effect traits,evenness,extinction debt,in-situ,mass extinction,response traits,species response,species richness,stability}, - annotation = {WOS:000465657800015}, - file = {/Users/renatadiaz/Zotero/storage/9EV264B9/Thomsen et al. - 2019 - Compensatory responses can alter the form of the b.pdf} -} - -@article{thornton2019, - title = {Friends and Allies: {{LGBT}}+ Inclusion in Statistics and Data Science}, - shorttitle = {Friends and Allies}, - author = {Thornton, Suzanne and Green, Brittany and Benn, Emma}, - year = {2019}, - journal = {Significance}, - volume = {16}, - number = {3}, - pages = {39--41}, - issn = {1740-9713}, - doi = {10.1111/j.1740-9713.2019.01280.x}, - abstract = {At a conference last year, Suzanne Thornton, Brittany Green and Emma Benn organised a panel session to share advice and recommendations for making the statistics and data science community more inclusive and supportive of gender non-conforming and LGBTQ persons. Here they summarise their discussion in the hope of continuing the conversation}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1740-9713.2019.01280.x}, - file = {/Users/renatadiaz/Zotero/storage/YCCIWP69/Thornton et al. - 2019 - Friends and allies LGBT+ inclusion in statistics .pdf;/Users/renatadiaz/Zotero/storage/LMNRQ92C/j.1740-9713.2019.01280.html} -} - -@article{tiwari2005, - title = {Bayesian {{Model Selection}} for {{Join Point Regression}} with {{Application}} to {{Age-Adjusted Cancer Rates}}}, - author = {Tiwari, Ram C. and Cronin, Kathleen A. and Davis, William and Feuer, Eric J. and Yu, Binbing and Chib, Siddhartha}, - year = {2005}, - journal = {Journal of the Royal Statistical Society. Series C (Applied Statistics)}, - volume = {54}, - number = {5}, - pages = {919--939}, - publisher = {{[Wiley, Royal Statistical Society]}}, - issn = {0035-9254}, - abstract = {The method of Bayesian model selection for join point regression models is developed. Given a set of K + 1 join point models \$M\_0, M\_1, ..., M\_K\$ with 0, 1, ..., K join points respectively, the posterior distributions of the parameters and competing models Mk are computed by Markov chain Monte Carlo simulations. The Bayes information criterion BIC is used to select the model Mk with the smallest value of BIC as the best model. Another approach based on the Bayes factor selects the model Mk with the largest posterior probability as the best model when the prior distribution of Mk is discrete uniform. Both methods are applied to analyse the observed US cancer incidence rates for some selected cancer sites. The graphs of the join point models fitted to the data are produced by using the methods proposed and compared with the method of Kim and co-workers that is based on a series of permutation tests. The analyses show that the Bayes factor is sensitive to the prior specification of the variance {$\sigma$}2, and that the model which is selected by BIC fits the data as well as the model that is selected by the permutation test and has the advantage of producing the posterior distribution for the join points. The Bayesian join point model and model selection method that are presented here will be integrated in the National Cancer Institute's join point software (www.srab.cancer.gov/joinpoint/) and will be available to the public.} -} - -@article{toms2003, - title = {Piecewise {{Regression}}: {{A Tool}} for {{Identifying Ecological Thresholds}}}, - shorttitle = {Piecewise {{Regression}}}, - author = {Toms, Judith D. and Lesperance, Mary L.}, - year = {2003}, - journal = {Ecology}, - volume = {84}, - number = {8}, - pages = {2034--2041}, - issn = {1939-9170}, - doi = {10.1890/02-0472}, - abstract = {We demonstrate the use of piecewise regression as a statistical technique to model ecological thresholds. Recommended procedures for analysis are illustrated with a case study examining the width of edge effects in two understory plant communities. Piece-wise regression models are ``broken-stick'' models, where two or more lines are joined at unknown points, called ``breakpoints.'' Breakpoints can be used as estimates of thresholds and are used here to determine the width of edge effects. We compare a sharp-transition model with three models incorporating smooth transitions: the hyperbolic-tangent, bent-hyperbola, and bent-cable models. We also calculate three types of confidence intervals for the breakpoint estimate: an interval based on the computed standard error of the estimate from the fitting procedure, an empirical bootstrap confidence interval, and a confidence interval derived from an inverted F test. We recommend use of the inverted F test confidence interval when sample sizes are large, and cautious use of bootstrapped confidence intervals when sample sizes are smaller. Our analysis demonstrates the need for a careful study of the likelihood surface when fitting and interpreting the results from piecewise-regression models.}, - langid = {english}, - keywords = {bootstrapping,change-point regression,edge effects,forest understory community (Vancouver Island),piecewise regression,plant community,principal components analysis,segmented regression}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/02-0472}, - file = {/Users/renatadiaz/Zotero/storage/R3ENPL7U/Toms and Lesperance - 2003 - Piecewise Regression A Tool for Identifying Ecolo.pdf;/Users/renatadiaz/Zotero/storage/DRNFPNE3/02-0472.html} -} - -@article{touchon2016, - title = {The Mismatch between Current Statistical Practice and Doctoral Training in Ecology}, - author = {Touchon, Justin C. and McCoy, Michael W.}, - year = {2016}, - journal = {Ecosphere}, - volume = {7}, - number = {8}, - pages = {e01394}, - issn = {2150-8925}, - doi = {10.1002/ecs2.1394}, - abstract = {Ecologists are studying increasingly complex and important issues such as climate change and ecosystem services. These topics often involve large data sets and the application of complicated quantitative models. We evaluated changes in statistics used by ecologists by searching nearly 20,000 published articles in ecology from 1990 to 2013. We found that there has been a rise in sophisticated and computationally intensive statistical techniques such as mixed effects models and Bayesian statistics and a decline in reliance on approaches such as ANOVA or t tests. Similarly, ecologists have shifted away from software such as SAS and SPSS to the open source program R. We also searched the published curricula and syllabi of 154 doctoral programs in the United States and found that despite obvious changes in the statistical practices of ecologists, more than one-third of doctoral programs showed no record of required or optional statistics classes. Approximately one-quarter of programs did require a statistics course, but most of those did not cover contemporary statistical philosophy or advanced techniques. Only one-third of doctoral programs surveyed even listed an optional course that teaches some aspect of contemporary statistics. We call for graduate programs to lead the charge in improving training of future ecologists with skills needed to address and understand the ecological challenges facing humanity.}, - langid = {english}, - keywords = {ANOVA,Bayesian,generalized linear model,JMP,linear regression,mixed effects model,nonparametric,R,SAS,SPSS,statistics,t test}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.1394}, - file = {/Users/renatadiaz/Zotero/storage/MUGYPAYK/Touchon and McCoy - 2016 - The mismatch between current statistical practice .pdf;/Users/renatadiaz/Zotero/storage/FK64PQJ6/ecs2.html} -} - -@article{touchton2011, - title = {Species Loss, Delayed Numerical Responses, and Functional Compensation in an Antbird Guild}, - author = {Touchton, Janeene M. and Smith, James N. M.}, - year = {2011}, - journal = {Ecology}, - volume = {92}, - number = {5}, - pages = {1126--1136}, - issn = {1939-9170}, - doi = {10.1890/10-1458.1}, - abstract = {When a community loses species through fragmentation, its total food consumption may drop. Compensatory responses of remaining species, whereby survivors assume roles of extinct competitors, may reduce the impact of species loss through numerical or functional responses. We measured compensatory responses in two remaining antbird species on Barro Colorado Island, Panama, four decades after the loss of their dominant competitor, the Ocellated Antbird, Phaenostictus mcleannani. We compared current abundances and behavior of these two species on Barro Colorado to those reported before the island lost Ocellated Antbirds, and to those in a nearby mainland population where all three species still exist as a space-for-time substitution. The smaller, more subordinate Spotted Antbird, Hylophylax naevioides, responded far more strongly than the larger Bicolored Antbird, Gymnopithys leucaspis, which is functionally more like the Ocellated Antbird. Islandwide density of Spotted Antbirds has more than doubled since the loss of Ocellated Antbirds. Moreover, Spotted Antbirds now spend so much more of their time following ant swarms that their metabolic biomass at these swarms has more than tripled since Ocellated Antbirds disappeared. These responses in Spotted Antbirds were apparently delayed by {$>$}20 years. Bicolored Antbirds have not increased substantially in islandwide density or metabolic biomass at ant swarms. We hypothesize that behavioral flexibility, as shown by Spotted Antbirds on Barro Colorado Island, is a major factor governing the extent to which fragmented ecosystems can buffer the impacts of species loss.}, - langid = {english}, - keywords = {ant-following birds,army ants,Barro Colorado Island,behavioral plasticity,competitive release,delayed responses,fragmentation,Gymnopithys leucaspis,Hylophylax naevioides,Panama,Phaenostictus mcleannani,species compensation}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/10-1458.1}, - file = {/Users/renatadiaz/Zotero/storage/A2B2BRMI/Touchton and Smith - 2011 - Species loss, delayed numerical responses, and fun.pdf;/Users/renatadiaz/Zotero/storage/G46UE5J3/10-1458.html} -} - -@article{trebilco2013, - title = {Ecosystem Ecology: Size-Based Constraints on the Pyramids of Life}, - shorttitle = {Ecosystem Ecology}, - author = {Trebilco, Rowan and Baum, Julia K. and Salomon, Anne K. and Dulvy, Nicholas K.}, - year = {2013}, - month = jul, - journal = {Trends in Ecology \& Evolution}, - volume = {28}, - number = {7}, - pages = {423--431}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2013.03.008}, - abstract = {Biomass distribution and energy flow in ecosystems are traditionally described with trophic pyramids, and increasingly with size spectra, particularly in aquatic ecosystems. Here, we show that these methods are equivalent and interchangeable representations of the same information. Although pyramids are visually intuitive, explicitly linking them to size spectra connects pyramids to metabolic and size-based theory, and illuminates size-based constraints on pyramid shape. We show that bottom-heavy pyramids should predominate in the real world, whereas top-heavy pyramids indicate overestimation of predator abundance or energy subsidies. Making the link to ecological pyramids establishes size spectra as a central concept in ecosystem ecology, and provides a powerful framework both for understanding baseline expectations of community structure and for evaluating future scenarios under climate change and exploitation.}, - langid = {english}, - keywords = {biomass pyramid,body-size-distribution,ecological baselines,macroecology,metabolic theory of ecology,omnivory,ontogenetic diet shift,size spectra,trophic pyramid,turnover}, - file = {/Users/renatadiaz/Zotero/storage/S9BSFYGF/S0169534713000888.html} -} - -@article{tseng2020, - title = {Strategies and Support for {{Black}}, {{Indigenous}}, and People of Colour in Ecology and Evolutionary Biology}, - author = {Tseng, Michelle and {El-Sabaawi}, Rana W. and Kantar, Michael B. and Pantel, Jelena H. and Srivastava, Diane S. and Ware, Jessica L.}, - year = {2020}, - month = oct, - journal = {Nature Ecology \& Evolution}, - volume = {4}, - number = {10}, - pages = {1288--1290}, - publisher = {{Nature Publishing Group}}, - issn = {2397-334X}, - doi = {10.1038/s41559-020-1252-0}, - abstract = {We know that it can be tough to be a person of colour working in ecology and evolution. Here is what has worked for us.}, - copyright = {2020 Springer Nature Limited}, - langid = {english}, - keywords = {Careers,Ecology,Evolution,Scientific community}, - annotation = {Bandiera\_abtest: a Cg\_type: Nature Research Journals Primary\_atype: Comments \& Opinion Subject\_term: Careers;Ecology;Evolution;Scientific community Subject\_term\_id: careers;ecology;evolution;scientific-community}, - file = {/Users/renatadiaz/Zotero/storage/F3VQWGY6/Tseng et al. - 2020 - Strategies and support for Black, Indigenous, and .pdf;/Users/renatadiaz/Zotero/storage/P845LEPV/s41559-020-1252-0.html} -} - -@article{turnbull2014, - title = {Weighing in: {{Size}} Spectra as a Standard Tool in Soil Community Analyses}, - shorttitle = {Weighing In}, - author = {Turnbull, Matthew S. and George, Paul B.L. and Lindo, Zo{\"e}}, - year = {2014}, - month = jan, - journal = {Soil Biology and Biochemistry}, - volume = {68}, - pages = {366--372}, - issn = {00380717}, - doi = {10.1016/j.soilbio.2013.10.019}, - abstract = {The variety and abundance of organism sizes in a community allows valuable conclusions to be drawn concerning trophic transfer efficiency, process rate dynamics, and ecological stability. Body size spectrum analyses have been applied to great effect in aquatic systems, but have only relatively recently gained interest for the description of soil communities. This approach should be added to existing sorting protocols and adopted as a standard tool of soil fauna analysis because of its ease of use, universal applicability regardless of taxonomy, and value as a predictor of both soil fauna function and response. This paper reviews the available methods for calculating soil fauna mass, constructing of body size spectra, and relating these spectra to existing fauna analysis frameworks such as the nematode maturity index. We also detail several of the functional conclusions that can be drawn from shifts in body size spectra and how this methodology can be further improved to supplement existing soil ecology methods. \'O 2013 Elsevier Ltd. All rights reserved.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/M62I52H5/Turnbull et al. - 2014 - Weighing in Size spectra as a standard tool in so.pdf;/Users/renatadiaz/Zotero/storage/S7JRA99Y/Turnbull et al. - 2014 - Weighing in Size spectra as a standard tool in so.pdf} -} - -@article{ulrich2004, - title = {Frequent and Occasional Species and the Shape of Relative-Abundance Distributions}, - author = {Ulrich, Werner and Ollik, Marcin}, - year = {2004}, - journal = {Diversity and Distributions}, - volume = {10}, - number = {4}, - pages = {263--269}, - issn = {1472-4642}, - doi = {10.1111/j.1366-9516.2004.00082.x}, - abstract = {Recently, three different models have been proposed to explain the distribution of abundances in natural communities: the self-similarity model; the zero-sum ecological drift model; and the occasional\textendash frequent species model of Magurran and Henderson. Here we study patterns of relative abundance in a large community of forest Hymenoptera and show that it is indeed possible to divide the community into a group of frequent species and a group of occasional species. In accordance with the third model, frequent species followed a lognormal distribution. Relative abundances of the occasional species could be described by the self-similarity model, but did not follow a log-series as proposed by the occasional\textendash frequent model. The zero-sum ecological drift model makes no explicit predictions about frequent and occasional species but the abundance distributions of the hymenopteran species did not show the excess of rare species predicted by this model. Separate fits of this model to the frequent and to the occasional species were worse than the respective fits of the lognormal and the self-similarity model.}, - langid = {english}, - keywords = {Ecological drift,hymenoptera,log-series,lognormal,parasitoids,relative-abundance distribution,self-similarity,zero-sum multinomial}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1366-9516.2004.00082.x}, - file = {/Users/renatadiaz/Zotero/storage/QRDYTY59/Ulrich and Ollik - 2004 - Frequent and occasional species and the shape of r.pdf;/Users/renatadiaz/Zotero/storage/QRV8DIV2/j.1366-9516.2004.00082.html} -} - -@article{ulrich2010, - title = {A Meta-Analysis of Species\textendash Abundance Distributions}, - author = {Ulrich, Werner and Ollik, Marcin and Ugland, Karl Inne}, - year = {2010}, - journal = {Oikos}, - volume = {119}, - number = {7}, - pages = {1149--1155}, - issn = {1600-0706}, - doi = {10.1111/j.1600-0706.2009.18236.x}, - abstract = {The species\textendash abundance distribution (SAD) describes the abundances of all species within a community. Many different models have been proposed to describe observed SADs. Best known are the logseries, the lognormal, and a variety of niche division models. They are most often visualized using either species richness \textendash{} log abundance class (Preston) plots or abundance \textendash{} species rank order (Whittaker) plots. Because many of the models predict very similar shapes, model distinction and testing become problematic. However, the variety of models can be classified into three basic types: one that predicts a double S-shape in Whittaker plots and a unimodal distribution in Preston plots (the lognormal type), a second that lacks the mode in Preston plots (the logseries type), and a third that predicts power functions in both plotting types (the power law type). Despite the interest of ecologists in SADs no formal meta-analysis of models and plotting types has been undertaken so far. Here we use a compilation of 558 species\textendash abundance distributions from 306 published papers to infer the frequency of the three SAD shapes in dependence of environmental variables and type of plotting. Our results highlight the importance of distinguishing between fully censused and incompletely sampled communities in the study of SADs. We show that completely censused terrestrial or freshwater animal communities tend to follow lognormal type SADs more often than logseries or power law types irrespective of species richness, spatial scale, and geographic position. However, marine communities tend to follow the logseries type, while plant communities tend to follow the power law. In incomplete sets the power law fitted best in Whittaker plots, and the logseries in Preston plots. Finally our study favors the use of Whittaker over Preston plots.}, - copyright = {\textcopyright{} 2009 The Authors}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0706.2009.18236.x}, - file = {/Users/renatadiaz/Zotero/storage/CNUYQRUJ/Ulrich et al. - 2010 - A meta-analysis of species–abundance distributions.pdf;/Users/renatadiaz/Zotero/storage/HKBAAJC3/Ulrich et al. - 2010 - A meta-analysis of species–abundance distributions.pdf;/Users/renatadiaz/Zotero/storage/3ZFPUAR5/j.1600-0706.2009.18236.html;/Users/renatadiaz/Zotero/storage/BEBEVZJS/j.1600-0706.2009.18236.html} -} - -@article{ulrich2017, - title = {The Tangled Link between {$\beta$}- and {$\gamma$}-Diversity: A {{Narcissus}} Effect Weakens Statistical Inferences in Null Model Analyses of Diversity Patterns}, - shorttitle = {The Tangled Link between {$\beta$}- and {$\gamma$}-Diversity}, - author = {Ulrich, Werner and Baselga, Andres and Kusumoto, Buntarou and Shiono, Takayuki and Tuomisto, Hanna and Kubota, Yasuhiro}, - year = {2017}, - journal = {Global Ecology and Biogeography}, - volume = {26}, - number = {1}, - pages = {1--5}, - issn = {1466-8238}, - doi = {10.1111/geb.12527}, - abstract = {Understanding the structure of and spatial variability in the species composition of ecological communities is at the heart of biogeography. In particular, there has been recent controversy about possible latitudinal trends in compositional heterogeneity across localities ({$\beta$}-diversity). A gradient in the size of the regional species pool alone can be expected to impose a parallel gradient on {$\beta$}-diversity, but whether {$\beta$}-diversity also varies independently of the size of the species pool remains unclear. A recently suggested methodological approach to correct latitudinal {$\beta$}-diversity gradients for the species pool effect is based on randomization null models that remove the effects of gradients in {$\alpha$}- and {$\gamma$}-diversity on {$\beta$}-diversity. However, the randomization process imposes constraints on the variability of {$\alpha$}-diversity, which in turn force {$\gamma$}- and {$\beta$}-diversity to become interdependent, such that any change in one is mirrored in the other. We argue that simple null model approaches are inadequate to discern whether correlations between {$\alpha$}-, {$\beta$}- and {$\gamma$}-diversity reflect processes of ecological interest or merely differences in the size of the species pool among localities. We demonstrate that this kind of Narcissus effect may also apply to other metrics of spatial or phylogenetic species distribution. We highlight that Narcissus effects may lead to artificially high rejection rates for the focal pattern (Type II errors) and caution that these errors have not received sufficient attention in the ecological literature.}, - langid = {english}, - keywords = {Diversity,diversity partitioning,latitudinal gradient,null model,species pool,statistical inference}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12527}, - file = {/Users/renatadiaz/Zotero/storage/L94YTCWC/Ulrich et al. - 2017 - The tangled link between β- and γ-diversity a Nar.pdf;/Users/renatadiaz/Zotero/storage/NV6UTHGY/geb.html} -} - -@article{valle2014, - title = {Decomposing Biodiversity Data Using the {{Latent Dirichlet Allocation}} Model, a Probabilistic Multivariate Statistical Method}, - author = {Valle, Denis and Baiser, Benjamin and Woodall, Christopher W. and Chazdon, Robin}, - editor = {Chave, Jerome}, - year = {2014}, - month = dec, - journal = {Ecology Letters}, - volume = {17}, - number = {12}, - pages = {1591--1601}, - issn = {1461023X}, - doi = {10.1111/ele.12380}, - abstract = {We propose a novel multivariate method to analyse biodiversity data based on the Latent Dirichlet Allocation (LDA) model. LDA, a probabilistic model, reduces assemblages to sets of distinct component communities. It produces easily interpretable results, can represent abrupt and gradual changes in composition, accommodates missing data and allows for coherent estimates of uncertainty. We illustrate our method using tree data for the eastern United States and from a tropical successional chronosequence. The model is able to detect pervasive declines in the oak community in Minnesota and Indiana, potentially due to fire suppression, increased growing season precipitation and herbivory. The chronosequence analysis is able to delineate clear successional trends in species composition, while also revealing that site-specific factors significantly impact these successional trajectories. The proposed method provides a means to decompose and track the dynamics of species assemblages along temporal and spatial gradients, including effects of global change and forest disturbances.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/XI5TDPMQ/Valle et al. - 2014 - Decomposing biodiversity data using the Latent Dir.pdf} -} - -@article{valone1994, - title = {Interactions between {{Rodents}} and {{Ants}} in the {{Chihuahuan Desert}}: {{An Update}}}, - shorttitle = {Interactions between {{Rodents}} and {{Ants}} in the {{Chihuahuan Desert}}}, - author = {Valone, Thomas J. and Brown, James H. and Heske, Edward J.}, - year = {1994}, - month = jan, - journal = {Ecology}, - volume = {75}, - number = {1}, - pages = {252--255}, - issn = {00129658}, - doi = {10.2307/1939400}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/KHTQB6RN/Valone et al. - 1994 - Interactions between Rodents and Ants in the Chihu.pdf} -} - -@article{valone1995, - title = {Catastrophic {{Decline}} of a {{Desert Rodent}}, {{Dipodomys}} Spectabilis: {{Insights}} from a {{Long-Term Study}}}, - shorttitle = {Catastrophic {{Decline}} of a {{Desert Rodent}}, {{Dipodomys}} Spectabilis}, - author = {Valone, T. J. and Brown, J. H. and Jacobi, C. L.}, - year = {1995}, - month = may, - journal = {Journal of Mammalogy}, - volume = {76}, - number = {2}, - pages = {428--436}, - issn = {1545-1542, 0022-2372}, - doi = {10.2307/1382353}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/S8JADRQL/Valone et al. - 1995 - Catastrophic Decline of a Desert Rodent, Dipodomys.pdf;/Users/renatadiaz/Zotero/storage/TIZYAYJA/Valone et al. - 1995 - Catastrophic Decline of a Desert Rodent, Dipodomys.pdf} -} - -@misc{valsamis2019, - type = {Research {{Article}}}, - title = {Segmented {{Linear Regression Modelling}} of {{Time-Series}} of {{Binary Variables}} in {{Healthcare}}}, - author = {Valsamis, Epaminondas Markos and Husband, Henry and Chan, Gareth Ka-Wai}, - year = {2019}, - month = dec, - journal = {Computational and Mathematical Methods in Medicine}, - volume = {2019}, - pages = {e3478598}, - publisher = {{Hindawi}}, - issn = {1748-670X}, - doi = {10.1155/2019/3478598}, - abstract = {Introduction. In healthcare, change is usually detected by statistical techniques comparing outcomes before and after an intervention. A common problem faced by researchers is distinguishing change due to secular trends from change due to an intervention. Interrupted time-series analysis has been shown to be effective in describing trends in retrospective time-series and in detecting change, but methods are often biased towards the point of the intervention. Binary outcomes are typically modelled by logistic regression where the log-odds of the binary event is expressed as a function of covariates such as time, making model parameters difficult to interpret. The aim of this study was to present a technique that directly models the probability of binary events to describe change patterns using linear sections. Methods. We describe a modelling method that fits progressively more complex linear sections to the time-series of binary variables. Model fitting uses maximum likelihood optimisation and models are compared for goodness of fit using Akaike's Information Criterion. The best model describes the most likely change scenario. We applied this modelling technique to evaluate hip fracture patient mortality rate for a total of 2777 patients over a 6-year period, before and after the introduction of a dedicated hip fracture unit (HFU) at a Level 1, Major Trauma Centre. Results. The proposed modelling technique revealed time-dependent trends that explained how the implementation of the HFU influenced mortality rate in patients sustaining proximal femoral fragility fractures. The technique allowed modelling of the entire time-series without bias to the point of intervention. Modelling the binary variable of interest directly, as opposed to a transformed variable, improved the interpretability of the results. Conclusion. The proposed segmented linear regression modelling technique using maximum likelihood estimation can be employed to effectively detect trends in time-series of binary variables in retrospective studies.}, - howpublished = {https://www.hindawi.com/journals/cmmm/2019/3478598/}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2T6EIC88/Valsamis et al. - 2019 - Segmented Linear Regression Modelling of Time-Seri.pdf;/Users/renatadiaz/Zotero/storage/C2A9DFHK/3478598.html} -} - -@article{vanbuskirk2010, - title = {Declining Body Sizes in {{North American}} Birds Associated with Climate Change}, - author = {Van Buskirk, Josh and Mulvihill, Robert S. and Leberman, Robert C.}, - year = {2010}, - month = mar, - journal = {Oikos}, - volume = {119}, - number = {6}, - pages = {1047--1055}, - issn = {00301299, 16000706}, - doi = {10.1111/j.1600-0706.2009.18349.x}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VQTBC2W2/Van Buskirk et al. - 2010 - Declining body sizes in North American birds assoc.pdf} -} - -@article{vanbuskirk2010a, - title = {Declining Body Sizes in {{North American}} Birds Associated with Climate Change}, - author = {Van Buskirk, Josh and Mulvihill, Robert S. and Leberman, Robert C.}, - year = {2010}, - journal = {Oikos}, - volume = {119}, - number = {6}, - pages = {1047--1055}, - issn = {1600-0706}, - doi = {10.1111/j.1600-0706.2009.18349.x}, - abstract = {Recent climate change has caused comparatively rapid shifts in the phenology and geographic distributions of many plants and animals. However, there is debate over the degree to which populations can meet the challenges of climate change with evolutionary or phenotypic responses in life history and morphology. We report that migrating birds captured at a banding station in western Pennsylvania, USA, have exhibited steadily decreasing fat-free mass and wing chord since 1961, consistent with a response to a warmer climate. This confirms that phenotypic responses to climate change are currently underway in entire avian assemblages. Declines in body size were not explained by an index of habitat condition within the breeding or wintering distributions. Instead, size was negatively correlated with temperature in the previous year, and long-term trends were associated with the direction of natural selection acting on size over the winter: species undergoing the strongest selection favoring small wing chord showed the most rapid long-term declines in wing. Phenotypic changes are therefore in line with the prevailing selection regime.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0706.2009.18349.x}, - file = {/Users/renatadiaz/Zotero/storage/VP56997B/j.1600-0706.2009.18349.html} -} - -@inproceedings{vandoninck2021, - title = {Explaining {{Patterns}} of {{Biodiversity Across Neon Sites Using Landsat-Based Disturbance Metrics}}}, - booktitle = {2021 {{IEEE International Geoscience}} and {{Remote Sensing Symposium IGARSS}}}, - author = {Van Doninck, Jasper and Smith, Annie C. and Knott, Jon and Record, Sydne and Zarnetske, Phoebe L.}, - year = {2021}, - month = jul, - pages = {6252--6255}, - issn = {2153-7003}, - doi = {10.1109/IGARSS47720.2021.9554859}, - abstract = {Disturbance regimes can strongly influence geographic patterns of biodiversity. The types of disturbances and their frequencies can have varying impacts on different dimensions of biodiversity and taxonomic groups, and their influence can also vary with spatial scale. Yet disturbance layers are lacking at sufficiently high spatial resolution and extent to uncover these relationships with biodiversity. We detected disturbances for the conterminous United States from Landsat time series using the established LandTrendr temporal segmentation with a novel secondary classification that incorporates spatial context. We then included these disturbance layers, aggregated to metrics at different temporal and spatial scales, into model of species richness at National Ecological Observatory Network sites.}, - keywords = {Artificial satellites,biodiversity,Biological system modeling,disturbance detection,Earth,Landsat,Measurement,Neon,NEON,Predictive models,time series analysis,Time series analysis}, - file = {/Users/renatadiaz/Zotero/storage/Z438KN2Z/Van Doninck et al. - 2021 - Explaining Patterns of Biodiversity Across Neon Si.pdf;/Users/renatadiaz/Zotero/storage/DVMP3BJB/9554859.html} -} - -@article{vanklink2022, - title = {Emerging Technologies Revolutionise Insect Ecology and Monitoring}, - author = {{van Klink}, Roel and August, Tom and Bas, Yves and Bodesheim, Paul and Bonn, Aletta and Foss{\o}y, Frode and H{\o}ye, Toke T. and Jongejans, Eelke and Menz, Myles H.M. and Miraldo, Andreia and Roslin, Tomas and Roy, Helen E. and Ruczy{\'n}ski, Ireneusz and Schigel, Dmitry and Sch{\"a}ffler, Livia and Sheard, Julie K. and Svenningsen, Cecilie and Tschan, Georg F. and W{\"a}ldchen, Jana and Zizka, Vera M.A. and {\AA}str{\"o}m, Jens and Bowler, Diana E.}, - year = {2022}, - month = oct, - journal = {Trends in Ecology \& Evolution}, - volume = {37}, - number = {10}, - pages = {872--885}, - issn = {01695347}, - doi = {10.1016/j.tree.2022.06.001}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/9C2TN5CI/van Klink et al. - 2022 - Emerging technologies revolutionise insect ecology.pdf} -} - -@article{vannouhuys2005, - title = {Metacommunities of Butterflies, Their Host Plants and Their Parasitoids}, - author = {Van Nouhuys, S and Hanski, I}, - year = {2005}, - journal = {Metacommunities : spatial dynamics and ecological communities}, - pages = {99--121}, - file = {/Users/renatadiaz/Zotero/storage/JV6UY8ZJ/10030515351.html} -} - -@article{vanvalen1973, - title = {A New Evolutionary Law}, - author = {Van Valen, Leigh}, - year = {1973}, - journal = {Evolutionary Theory}, - volume = {1}, - number = {1}, - pages = {1--30}, - file = {/Users/renatadiaz/Zotero/storage/LV9SPHEU/vol-1-no-1-pages-1-30-l-van-valen-a-new-evolutionary-law.pdf} -} - -@article{vasseur2007, - title = {{{SPECTRAL ANALYSIS UNMASKS SYNCHRONOUS AND COMPENSATORY DYNAMICS IN PLANKTON COMMUNITIES}}}, - author = {Vasseur, David A. and Gaedke, Ursula}, - year = {2007}, - month = aug, - journal = {Ecology}, - volume = {88}, - number = {8}, - pages = {2058--2071}, - issn = {0012-9658}, - doi = {10.1890/06-1899.1}, - abstract = {Community biomass is often less variable than the biomasses of populations within the community, yet attempts to implicate compensatory dynamics between populations as a cause of this relationship often fail. In part, this may be due to the lack of appropriate metrics for variability, but there is also great potential for large-scale processes such as seasonality or longer-term environmental change to obscure important dynamics at other temporal scales. In this study, we apply a scale-resolving method to long-term plankton data, to identify the specific temporal scales at which community-level variability is influenced by synchrony or compensatory dynamics at the population level. We show that variability at both the population and community level is influenced strongly by a few distinct temporal scales: in phytoplankton, ciliate, rotifer, and crustacean communities, synchronous dynamics are predominant at most temporal scales. However, in phytoplankton and crustacean communities, compensatory dynamics occur at a sub-annual scale (and at the annual scale in crustaceans) leading to substantial reductions in community-level variability. Aggregate measures of population and community variability do not detect compensatory dynamics in these communities; thus, resolving their scale dependence unmasks dynamics that are important for community stability in this system. The methods and results presented herein will ultimately lead to a better understanding of how stability is achieved in communities.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/YSRR7EYZ/Vasseur and Gaedke - 2007 - SPECTRAL ANALYSIS UNMASKS SYNCHRONOUS AND COMPENSA.pdf} -} - -@article{vellend2004, - title = {Parallel {{Effects}} of {{Land-Use History}} on {{Species Diversity}} and {{Genetic Diversity}} of {{Forest Herbs}}}, - author = {Vellend, Mark}, - year = {2004}, - journal = {Ecology}, - volume = {85}, - number = {11}, - pages = {3043--3055}, - issn = {1939-9170}, - doi = {10.1890/04-0435}, - abstract = {The two most fundamental levels of biodiversity, species diversity and genetic diversity, are seldom studied simultaneously despite a strikingly similar set of processes that underlie patterns at the two levels. Agricultural land use drastically reduces populations of forest herbs in the north-temperate zone, so that bottlenecks or founder events in forests on abandoned agricultural land (i.e., secondary forests) may have a long-term impact on both species diversity and genetic diversity. Using forest-herb community surveys and molecular-genetic analysis of populations of Trillium grandiflorum, a representative species of forest herb, I investigated the influence of land-use history, landscape context, and environmental conditions on diversity and divergence at the population and community levels. Secondary forests (70\textendash 100 years old) had reduced diversity of both genes and species relative to primary forests (i.e., stands never cleared for agriculture). The community in secondary forests had an overrepresentation of the most common species in the landscape, though divergence in species' relative abundances within stands suggested an influence of community drift via local bottlenecks. Secondary-forest populations of T. grandiflorum were more genetically divergent than those in primary forests, again indicating drift in small populations. Land-use history and the size of populations and communities drove correlations between species diversity and genetic diversity (and community divergence \texttimes{} genetic divergence), though the strength of correlations was relatively weak. These results extend the generality of positive species\textendash genetic diversity correlations previously observed for islands, and they demonstrate a long-term legacy of land-use history at multiple levels of biodiversity.}, - langid = {english}, - keywords = {biodiversity,forest herbs,forest stands,genetic diversity,land-use history,New York (USA),species diversity,Tompkins County,Trillium grandiflorum}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/04-0435}, - file = {/Users/renatadiaz/Zotero/storage/KSD96RTE/Vellend - 2004 - Parallel Effects of Land-Use History on Species Di.pdf;/Users/renatadiaz/Zotero/storage/BLHJ7FTK/04-0435.html} -} - -@article{vellend2005, - title = {Species {{Diversity}} and {{Genetic Diversity}}: {{Parallel Processes}} and {{Correlated Patterns}}.}, - shorttitle = {Species {{Diversity}} and {{Genetic Diversity}}}, - author = {Vellend, Mark}, - year = {2005}, - month = aug, - journal = {The American Naturalist}, - volume = {166}, - number = {2}, - pages = {199--215}, - publisher = {{The University of Chicago Press}}, - issn = {0003-0147}, - doi = {10.1086/431318}, - abstract = {Species diversity and genetic diversity may be correlated as a result of processes acting in parallel at the two levels. However, no theories predict the conditions under which different relationships between species diversity and genetic diversity might arise and therefore when one level of diversity may be predicted using the other. I used simulation models to investigate the parallel influence of locality area, immigration rate, and environmental heterogeneity on species diversity and genetic diversity. The most common pattern was moderate to strong positive species-genetic diversity correlations (SGDCs). Such correlations may be driven by any one of the three locality characteristics examined, but important exceptions and patterns emerged. Genetic diversity and species diversity were more weakly correlated when genetic diversity was measured for rare versus common species. Environmental heterogeneity not only imposes spatially varying selection on populations and communities but also causes changes in species' population sizes and therefore genetic diversity; these interacting processes can create positive, negative, or unimodal relationships of genetic diversity with species diversity. When species are considered as part of multispecies communities, predictions from single-species models of genetic diversity apply in some instances (effects of area and immigration) but often not in others (effects of environmental heterogeneity).}, - keywords = {area,environmental heterogeneity,immigration,neutral theory,selection}, - file = {/Users/renatadiaz/Zotero/storage/R5WDRGLZ/Vellend - 2005 - Species Diversity and Genetic Diversity Parallel .pdf;/Users/renatadiaz/Zotero/storage/ZGLWJDQP/Vellend - 2005 - Species Diversity and Genetic Diversity Parallel .pdf} -} - -@article{vellend2005a, - title = {Connections between Species Diversity and Genetic Diversity}, - author = {Vellend, Mark and Geber, Monica A.}, - year = {2005}, - journal = {Ecology Letters}, - volume = {8}, - number = {7}, - pages = {767--781}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2005.00775.x}, - abstract = {Species diversity and genetic diversity remain the nearly exclusive domains of community ecology and population genetics, respectively, despite repeated recognition in the literature over the past 30 years of close parallels between these two levels of diversity. Species diversity within communities and genetic diversity within populations are hypothesized to co-vary in space or time because of locality characteristics that influence the two levels of diversity via parallel processes, or because of direct effects of one level of diversity on the other via several different mechanisms. Here, we draw on a wide range of studies in ecology and evolution to examine the theoretical underpinnings of these hypotheses, review relevant empirical literature, and outline an agenda for future research. The plausibility of species diversity\textendash genetic diversity relationships is supported by a variety of theoretical and empirical studies, and several recent studies provide direct, though preliminary support. Focusing on potential connections between species diversity and genetic diversity complements other approaches to synthesis at the ecology\textendash evolution interface, and should contribute to conceptual unification of biodiversity research at the levels of genes and species.}, - langid = {english}, - keywords = {Biodiversity,coexistence,community ecology,drift,genetic diversity,migration,neutral model,population genetics,selection,species diversity}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2005.00775.x}, - file = {/Users/renatadiaz/Zotero/storage/NFN4CFE5/Vellend and Geber - 2005 - Connections between species diversity and genetic .pdf;/Users/renatadiaz/Zotero/storage/M69H38W8/j.1461-0248.2005.00775.html} -} - -@article{vellend2010, - title = {Conceptual {{Synthesis}} in {{Community Ecology}}}, - author = {Vellend, Mark}, - year = {2010}, - month = jun, - journal = {The Quarterly Review of Biology}, - volume = {85}, - number = {2}, - pages = {183--206}, - publisher = {{The University of Chicago Press}}, - issn = {0033-5770}, - doi = {10.1086/652373}, - abstract = {Community ecology is often perceived as a mess, given the seemingly vast number of processes that can underlie the many patterns of interest, and the apparent uniqueness of each study system. However, at the most general level, patterns in the composition and diversity of speciesthe subject matter of community ecologyare influenced by only four classes of process: selection, drift, speciation, and dispersal. Selection represents deterministic fitness differences among species, drift represents stochastic changes in species abundance, speciation creates new species, and dispersal is the movement of organisms across space. All theoretical and conceptual models in community ecology can be understood with respect to their emphasis on these four processes. Empirical evidence exists for all of these processes and many of their interactions, with a predominance of studies on selection. Organizing the material of community ecology according to this framework can clarify the essential similarities and differences among the many conceptual and theoretical approaches to the discipline, and it can also allow for the articulation of a very general theory of community dynamics: species are added to communities via speciation and dispersal, and the relative abundances of these species are then shaped by drift and selection, as well as ongoing dispersal, to drive community dynamics.}, - keywords = {community ecology,dispersal,drift,population genetics,selection,speciation}, - file = {/Users/renatadiaz/Zotero/storage/SHMH28AT/Vellend - 2010 - Conceptual Synthesis in Community Ecology.pdf} -} - -@article{verhoeven2005, - title = {Implementing False Discovery Rate Control: Increasing Your Power}, - shorttitle = {Implementing False Discovery Rate Control}, - author = {Verhoeven, Koen J. F. and Simonsen, Katy L. and McIntyre, Lauren M.}, - year = {2005}, - journal = {Oikos}, - volume = {108}, - number = {3}, - pages = {643--647}, - issn = {1600-0706}, - doi = {10.1111/j.0030-1299.2005.13727.x}, - abstract = {Popular procedures to control the chance of making type I errors when multiple statistical tests are performed come at a high cost: a reduction in power. As the number of tests increases, power for an individual test may become unacceptably low. This is a consequence of minimizing the chance of making even a single type I error, which is the aim of, for instance, the Bonferroni and sequential Bonferroni procedures. An alternative approach, control of the false discovery rate (FDR), has recently been advocated for ecological studies. This approach aims at controlling the proportion of significant results that are in fact type I errors. Keeping the proportion of type I errors low among all significant results is a sensible, powerful, and easy-to-interpret way of addressing the multiple testing issue. To encourage practical use of the approach, in this note we illustrate how the proposed procedure works, we compare it to more traditional methods that control the familywise error rate, and we discuss some recent useful developments in FDR control.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2KLAV764/Verhoeven et al. - 2005 - Implementing false discovery rate control increas.pdf;/Users/renatadiaz/Zotero/storage/SIA24X9F/j.0030-1299.2005.13727.html} -} - -@article{vermote2016, - title = {Preliminary Analysis of the Performance of the {{Landsat}} 8/{{OLI}} Land Surface Reflectance Product}, - author = {Vermote, Eric and Justice, Chris and Claverie, Martin and Franch, Belen}, - year = {2016}, - month = apr, - journal = {Remote Sensing of Environment}, - volume = {Volume 185}, - number = {Iss 2}, - pages = {46--56}, - issn = {0034-4257}, - doi = {10.1016/j.rse.2016.04.008}, - abstract = {The surface reflectance, i.e., satellite derived top of atmosphere (TOA) reflectance corrected for the temporally, spatially and spectrally varying scattering and absorbing effects of atmospheric gases and aerosols, is needed to monitor the land surface reliably. For this reason, the surface reflectance, and not TOA reflectance, is used to generate the greater majority of global land products, for example, from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) sensors. Even if atmospheric effects are minimized by sensor design, atmospheric effects are still challenging to correct. In particular, the strong impact of aerosols in the Visible and Near Infrared spectral range can be difficult to correct, because they can be highly discrete in space and time (e.g., smoke plumes) and because of the complex scattering and absorbing properties of aerosols that vary spectrally and with aerosol size, shape, chemistry and density. This paper presents the Landsat 8 Operational Land Imager (OLI) atmospheric correction algorithm that has been developed using the Second Simulation of the Satellite Signal in the Solar Spectrum Vectorial (6SV) model, refined to take advantage of the narrow OLI spectral bands (compared to Thematic Mapper/Enhanced Thematic Mapper (TM/ETM+)), improved radiometric resolution and signal-to-noise. In addition, the algorithm uses the new OLI Coastal aerosol band (0.433-0.450{$\mu$}m), which is particularly helpful for retrieving aerosol properties, as it covers shorter wavelengths than the conventional Landsat, TM and ETM+ blue bands. A cloud and cloud shadow mask has also been developed using the "cirrus" band (1.360-1.390 {$\mu$}m) available on OLI, and the thermal infrared bands from the Thermal Infrared Sensor (TIRS) instrument. The performance of the surface reflectance product from OLI is analyzed over the Aerosol Robotic Network (AERONET) sites using accurate atmospheric correction (based on in situ measurements of the atmospheric properties), by comparison with the MODIS Bidirectional Reflectance Distribution Function (BRDF) adjusted surface reflectance product and by comparison of OLI derived broadband albedo from United States Surface Radiation Budget Network (US SURFRAD) measurements.}, - langid = {english}, - pmcid = {PMC6999666}, - pmid = {32020955}, - file = {/Users/renatadiaz/Zotero/storage/HMBI5LW2/Vermote et al. - 2016 - Preliminary analysis of the performance of the Lan.pdf} -} - -@article{via2020, - title = {{$<$}p{$>$}{{Course}} Design: {{Considerations}} for Trainers \textendash{} a {{Professional Guide}}{$<$}/P{$>$}}, - shorttitle = {{$<$}p{$>$}{{Course}} Design}, - author = {Via, Allegra and Palagi, Patricia M. and Lindvall, Jessica M. and Tractenberg, Rochelle E. and Attwood, Teresa K. and Foundation, The GOBLET}, - year = {2020}, - month = nov, - journal = {F1000Research}, - volume = {9}, - number = {1377}, - pages = {1377}, - publisher = {{F1000 Research Limited}}, - doi = {10.7490/f1000research.1118395.1}, - abstract = {This Professional\ Guide in the Resources for Training Trainers series introduces a structured approach to course design, highlighting the importance of articulating learning outcomes commensurate with the cognitive complexity of the target learning, prior to devising learning experiences and course content. The specific focus here is on face-to-face activities, but the guidance is also relevant for those designing online courses.\ {$<$}br /{$>$} {$<$}br /{$>$} Specifically, this Guide outlines a series of steps that can help trainers to devise and deploy effective courses. On reading this Guide, and engaging with the reflective exercises, you will be able to: {$<$}ul{$>$} {$<$}li{$>$}\emph{list\ }five key phases of curriculum \& course development;{$<$}/li{$>$} {$<$}li{$>$}\emph{expl}\emph{ain\ }the primary role of learning outcomes;{$<$}/li{$>$} {$<$}li{$>$}\emph{write\ }learning outcomes for a course; \emph{\ \ }{$<$}/li{$>$} {$<$}li{$>$}\emph{identify\ }the Bloom's-level accomplishments that different types of learning experience are likely to support;{$<$}/li{$>$} {$<$}li{$>$}\emph{describe\ }the role of learning outcomes in selecting relevant content;{$<$}/li{$>$} {$<$}li{$>$}\emph{distinguish\ }different types of assessment \& their role in supporting learner progression towards learning outcomes; and{$<$}/li{$>$} {$<$}li{$>$}\emph{summarise }the benefits of course evaluation.{$<$}/li{$>$} {$<$}/ul{$>$}}, - copyright = {http://creativecommons.org/licenses/by/4.0/}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/NEJGFUAR/Via et al. - 2020 - Course design Considerations for trainers – a .pdf;/Users/renatadiaz/Zotero/storage/9U3HKCKR/9-1377.html} -} - -@article{virkkala2016, - title = {Long-Term Decline of Southern Boreal Forest Birds: Consequence of Habitat Alteration or Climate Change?}, - shorttitle = {Long-Term Decline of Southern Boreal Forest Birds}, - author = {Virkkala, Raimo}, - year = {2016}, - month = jan, - journal = {Biodiversity and Conservation}, - volume = {25}, - number = {1}, - pages = {151--167}, - issn = {1572-9710}, - doi = {10.1007/s10531-015-1043-0}, - abstract = {Climate change and habitat degradation due to land use are the key factors threatening biodiversity. It is important to study both the separate and joined effects of climate warming and land use on biodiversity. In this work long-term population changes of southern boreal forest birds were studied in relation to climate change and direct habitat alteration due to forestry. The study was based on annually repeated bird censuses in 23 consecutive years (1993\textendash 2015) in a managed forest landscape. Results were compared with population changes in protected areas where logging is not allowed. During the study period, total bird density declined by 18~\% with a change in the bird community composition. Out of the 12 most abundant species seven showed a significant negative trend and only one species a positive trend. Population declines could be connected with the direct alteration of habitat as a consequence of forestry or with the effect of climate change in the case of those species which declined also in protected areas. The increased species are abundant across Europe in human-modified habitats. Due to habitat alteration and climate warming, specific characteristics of southern boreal forest bird communities are changing with communities representing a pattern towards global homogenization. Thus, habitat alteration strengthens the negative effects of climate change.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/CU7PZHSS/Virkkala - 2016 - Long-term decline of southern boreal forest birds.pdf} -} - -@article{walker1992, - title = {Biodiversity and {{Ecological Redundancy}}}, - author = {Walker, Brian H.}, - year = {1992}, - journal = {Conservation Biology}, - volume = {6}, - number = {1}, - pages = {18--23}, - issn = {1523-1739}, - doi = {10.1046/j.1523-1739.1992.610018.x}, - abstract = {Abstract: This paper addresses the problem of which biota to choose to best satisfy the conservation goals for a particular region in the face of inadequate resources, Biodiversity is taken to be the integration of biological variability across all scales, from the genetic, through species and ecosystems, to landscapes. Conserving biodiversity is a daunting task, and the paper asserts that focusing on species is not the best approach. The best way to minimize species loss is to maintain the integrity of ecosystem function. The important questions therefore concern the kinds of biodiversity that are significant to ecosystem functioning. To best focus our efforts we need to establish how much (or how little) redundancy there is in the biological composition of ecosystems. An approach is suggested, based on the use of functional groups of organisms defined according to ecosystem processes. Functional groups with little or no redundancy warrant priority conservation effort. Complementary species-based approaches for maximizing the inclusion of biodiversity within a set of conservation areas are compared to the functional-group approach.}, - langid = {english}, - annotation = {\_eprint: https://conbio.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1523-1739.1992.610018.x}, - file = {/Users/renatadiaz/Zotero/storage/SXZ2LCBK/j.1523-1739.1992.610018.html} -} - -@article{walker1995, - title = {Conserving {{Biological Diversity}} through {{Ecosystem Resilience}}}, - author = {Walker, Brian}, - year = {1995}, - journal = {Conservation Biology}, - volume = {9}, - number = {4}, - pages = {747--752}, - issn = {1523-1739}, - doi = {10.1046/j.1523-1739.1995.09040747.x}, - abstract = {Confusion over the term ecological redundancy (Walker 1992) requires that the concept be clarified in order to advance the developing theory that maintaining ecosystem function conserves biological diversity. The species approach to conserving biological diversity assumes that the species in trouble are already identified. The ecosystem approach attempts to deal with the problem of conserving all the species in an ecosystem, including those not yet known. This is best achieved by ensuring that the ecosystem continues to function approximately as it has by maintaining its essential structure. Ecosystem stability (the probability of all species persisting) is enhanced if each important functional group of organisms (important for maintaining function and structure) comprises several ecologically equivalent species, each with different responses to environmental factors. In this sense ecological redundancy is good because it enhances ecosystem resilience, but functionally important groups (guilds, functional types) that have only one or very few species deserve priority conservation attention because their functions could be quickly lost with species extinctions.}, - langid = {english}, - annotation = {\_eprint: https://conbio.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1523-1739.1995.09040747.x}, - file = {/Users/renatadiaz/Zotero/storage/ETPKEILW/j.1523-1739.1995.09040747.html} -} - -@article{warrenii, - title = {Seeing Shapes in Clouds: The Fallacy of Deriving Ecological Hypotheses from Statistical Distributions}, - shorttitle = {Seeing Shapes in Clouds}, - author = {Warren II, Robert J. and Costa, James T. and Bradford, Mark A.}, - journal = {Oikos}, - volume = {n/a}, - number = {n/a}, - pages = {e09315}, - issn = {1600-0706}, - doi = {10.1111/oik.09315}, - abstract = {The explanations behind observations of global patterning in species diversity pre-date the field of ecology itself. The generation of new species\textendash area theories, in particular, far outpaces their falsification, resulting in a centuries-old accumulation in species diversity theories. We use historical assessment and new data analysis to argue that one of the earliest recognized and most consistent patterns in species diversity is not strictly an ecological phenomenon and, when ecological mechanism is invoked, the range of potential mechanisms is too numerous for tractable hypothesis falsification. We provide a historical parallel in that the normal distribution once was treated as a pattern assuming a biological mechanism rather than a statistical distribution that can be generated by biological and non-biological forces. Similarly, power law distributions are ubiquitous in aggregated data, such as the species\textendash area relationship. That nearly identical broad-scale aggregation patterns are observed for both ecological and non-ecological data as a function of area suggest that these broad-scale patterns reflect a statistical distribution that, in itself, cannot be used to discern between or among ecological and non-ecological mechanisms. We argue that by seeking processes in such a ubiquitous pattern, ecologists may read ecological mechanism into statistical patterns, and we suggest that falsifying broad-scale diversity distribution hypotheses should be a greater priority than generating or parameterizing new ones.}, - langid = {english}, - keywords = {correlation versus causation,hypothesis falsification,logical inference fallacies,power law,scale,species–area relationship}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/oik.09315}, - file = {/Users/renatadiaz/Zotero/storage/GWA76R7C/oik.html} -} - -@article{warwick1994, - title = {Relearning the {{ABC}}: Taxonomic Changes and Abundance/Biomass Relationships in Disturbed Benthic Communities}, - shorttitle = {Relearning the {{ABC}}}, - author = {Warwick, R. M. and Clarke, K. R.}, - year = {1994}, - month = mar, - journal = {Marine Biology}, - volume = {118}, - number = {4}, - pages = {739--744}, - issn = {1432-1793}, - doi = {10.1007/BF00347523}, - abstract = {For marine macrobenthic communities, a shift from higher biomass dominance with increasing levels of disturbance can be determined by the abundance/biomass comparison (ABC) method. This response results from (i) a shift in the proportions of different phyla present in communities, some phyla having larger-bodied species than others, and (ii) a shift in the relative distributions of abundance and biomass among species within the Annelida (specifically Polychaeta) but not within any of the other major phyla (Mollusca, Crustacea, Echinodermata). The shift within polychaetes reflects the substitution of largerbodied by smaller-bodied species, and not a change in the average size of individuals within a species. In most instances the phyletic changes reinforce the trend in species substitutions within the polychaetes, to produce the overall ABC response, but in some cases they may work against each other. Indications of pollution or disturbance detected by this method should be viewed with caution if the species responsible for the polluted configurations are not polychaetes. These observations provide an aid to interpretation of the ABC plots, especially in some situations where they have been deemed to give a false impression of the disturbance status of a community.}, - langid = {english} -} - -@article{webb2012, - title = {Marine and Terrestrial Ecology: Unifying Concepts, Revealing Differences}, - shorttitle = {Marine and Terrestrial Ecology}, - author = {Webb, Thomas J.}, - year = {2012}, - month = oct, - journal = {Trends in Ecology \& Evolution}, - volume = {27}, - number = {10}, - pages = {535--541}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2012.06.002}, - abstract = {The extent to which similar ecological processes operate on land and in the sea has been much debated, with apparently `fundamental' differences often disappearing when appropriate comparisons are made. However, marine and terrestrial ecology have developed as largely separate intellectual endeavours, which has hampered the search for general patterns and mechanisms. Here, I argue that marine\textendash terrestrial comparative studies can be extremely useful at uncovering mechanisms when they explicitly consider those facets of the environment that are important to a particular hypothesis. Furthermore, the binary `marine\textendash terrestrial' division misses many opportunities for more interesting comparisons, several of which I highlight here. Increasing the flow of concepts, hypotheses, and data between marine and terrestrial ecologists is essential to reveal those differences that really are important.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/5AMNELRB/Webb - 2012 - Marine and terrestrial ecology unifying concepts,.pdf;/Users/renatadiaz/Zotero/storage/6H49GLFH/S0169534712001437.html} -} - -@article{weeks2020, - title = {Shared Morphological Consequences of Global Warming in {{North American}} Migratory Birds}, - author = {Weeks, Brian C. and Willard, David E. and Zimova, Marketa and Ellis, Aspen A. and Witynski, Max L. and Hennen, Mary and Winger, Benjamin M.}, - year = {2020}, - journal = {Ecology Letters}, - volume = {23}, - number = {2}, - pages = {316--325}, - issn = {1461-0248}, - doi = {10.1111/ele.13434}, - abstract = {Increasing temperatures associated with climate change are predicted to cause reductions in body size, a key determinant of animal physiology and ecology. Using a four-decade specimen series of 70 716 individuals of 52 North American migratory bird species, we demonstrate that increasing annual summer temperature over the 40-year period predicts consistent reductions in body size across these diverse taxa. Concurrently, wing length \textendash{} an index of body shape that impacts numerous aspects of avian ecology and behaviour \textendash{} has consistently increased across species. Our findings suggest that warming-induced body size reduction is a general response to climate change, and reveal a similarly consistent and unexpected shift in body shape. We hypothesise that increasing wing length represents a compensatory adaptation to maintain migration as reductions in body size have increased the metabolic cost of flight. An improved understanding of warming-induced morphological changes is important for predicting biotic responses to global change.}, - langid = {english}, - keywords = {Allometry,body size,climate change,migration,morphology}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13434}, - file = {/Users/renatadiaz/Zotero/storage/5Y2PIIVD/Weeks et al. - 2020 - Shared morphological consequences of global warmin.pdf;/Users/renatadiaz/Zotero/storage/SIWLZ8BR/ele.html} -} - -@article{welch2014, - title = {Bioinformatics {{Curriculum Guidelines}}: {{Toward}} a {{Definition}} of {{Core Competencies}}}, - shorttitle = {Bioinformatics {{Curriculum Guidelines}}}, - author = {Welch, Lonnie and Lewitter, Fran and Schwartz, Russell and Brooksbank, Cath and Radivojac, Predrag and Gaeta, Bruno and Schneider, Maria Victoria}, - year = {2014}, - month = mar, - journal = {PLOS Computational Biology}, - volume = {10}, - number = {3}, - pages = {e1003496}, - publisher = {{Public Library of Science}}, - issn = {1553-7358}, - doi = {10.1371/journal.pcbi.1003496}, - langid = {english}, - keywords = {Bioinformatics,Biological data management,Careers,Computational biology,Computer software,Data mining,Genome analysis,Statistical data}, - file = {/Users/renatadiaz/Zotero/storage/9XNE9WP3/Welch et al. - 2014 - Bioinformatics Curriculum Guidelines Toward a Def.pdf;/Users/renatadiaz/Zotero/storage/R368UQ4C/article.html} -} - -@article{wen2018, - title = {Abundance\textendash Occupancy and Abundance\textendash Body Mass Relationships of Small Mammals in a Mountainous Landscape}, - author = {Wen, Zhixin and Cheng, Jilong and Ge, Deyan and Xia, Lin and Lv, Xue and Yang, Qisen}, - year = {2018}, - month = oct, - journal = {Landscape Ecology}, - volume = {33}, - number = {10}, - pages = {1711--1724}, - issn = {0921-2973, 1572-9761}, - doi = {10.1007/s10980-018-0695-z}, - abstract = {Context Mountainous landscapes are characterized by strong spatial heterogeneity, leading to increasing geographical isolation and decreasing area with elevation. Consequently, the colonization rate decreases from the low to high elevation zone, while the extinction rate shows the opposite.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/HEUF4RS3/Wen et al. - 2018 - Abundance–occupancy and abundance–body mass relati.pdf} -} - -@article{white, - title = {Tradeoffs in {{Community Properties Through Time}} in a {{Desert Rodent Community}}}, - author = {White, Ethan P and Ernest, S K Morgan and Thibault, K M}, - pages = {24}, - abstract = {Resource limitation represents an important constraint on ecological communities, which restricts the total abundance, biomass, and community energy flux a given community can support. However, the exact relationship among these three measures of biological activity remains unclear. Here we use a simple framework that links abundance and biomass with an energetic constraint. Under constant energetic availability, it is expected that changes in abundance and biomass can result from shifts in the distribution of individual masses. We test these predictions using long-term data from a desert rodent community. Total energy use for the community has not changed directionally for 25 years, but species composition has. As a result, the average body size has decreased by almost 50\% and average abundance has doubled. These results lend support to the idea of resource limitation on desert rodent communities and demonstrate that systems are able to maintain community energy flux in the face of environmental change, through changes in composition and structure.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/AF3M9JP7/White et al. - Tradeoffs in Community Properties Through Time in .pdf} -} - -@article{white2004, - title = {Trade-offs in {{Community Properties}} through {{Time}} in a {{Desert Rodent Community}}.}, - author = {White, Ethan~P. and Ernest, S.~K.~Morgan and Thibault, Katherine~M.}, - year = {2004}, - month = nov, - journal = {The American Naturalist}, - volume = {164}, - number = {5}, - pages = {670--676}, - issn = {0003-0147}, - doi = {10.1086/424766}, - abstract = {Resource limitation represents an important constraint on ecological communities, which restricts the total abundance, biomass, and community energy flux a given community can support. However, the exact relationship among these three measures of biological activity remains unclear. Here we use a simple framework that links abundance and biomass with an energetic constraint. Under constant energetic availability, it is expected that changes in abundance and biomass can result from shifts in the distribution of individual masses. We test these predictions using long-term data from a desert rodent community. Total energy use for the community has not changed directionally for 25 years, but species composition has. As a result, the average body size has decreased by almost 50\%, and average abundance has doubled. These results lend support to the idea of resource limitation on desert rodent communities and demonstrate that systems are able to maintain community energy flux in the face of environmental change, through changes in composition and structure.}, - file = {/Users/renatadiaz/Zotero/storage/JCGS2HRE/White et al. - 2004 - Trade‐offs in Community Properties through Time in.pdf;/Users/renatadiaz/Zotero/storage/LTQJHHNY/424766.html} -} - -@article{white2004a, - title = {Two-Phase Species\textendash Time Relationships in {{North American}} Land Birds}, - author = {White, Ethan P.}, - year = {2004}, - journal = {Ecology Letters}, - volume = {7}, - number = {4}, - pages = {329--336}, - issn = {1461-0248}, - doi = {10.1111/j.1461-0248.2004.00581.x}, - abstract = {The species\textendash time relationship (STR) is a macroecological pattern describing the increase in the observed species richness with the length of time censused. Understanding STRs is important for understanding the ecological processes underlying temporal turnover and species richness. However, accurate characterization of the STR has been hampered by the influence of sampling. I analysed STRs for 521 breeding bird survey communities. I used a model of sampling effects to demonstrate that the increase in richness was not due exclusively to sampling. I estimated the time scale at which ecological processes became dominant over sampling effects using a two-phase model combining a sampling phase and either a power function or logarithmic ecological phase. These two-phase models performed significantly better than sampling alone and better than simple power and logarithmic functions. Most community dynamics were dominated by ecological processes over scales {$<$}5 years. This technique provides an example of a rigorous, quantitative approach to separating sampling from ecological processes.}, - langid = {english}, - keywords = {Breeding Bird Survey,macroecology,sampling,species richness,species–area relationship,species–time relationship,temporal scaling,temporal turnover}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2004.00581.x}, - file = {/Users/renatadiaz/Zotero/storage/LZEVGEJL/White - 2004 - Two-phase species–time relationships in North Amer.pdf;/Users/renatadiaz/Zotero/storage/YJW8U2U9/j.1461-0248.2004.00581.html} -} - -@article{white2007, - title = {Relationships between Body Size and Abundance in Ecology}, - author = {White, Ethan P. and Ernest, S. K. Morgan and Kerkhoff, Andrew J. and Enquist, Brian J.}, - year = {2007}, - month = jun, - journal = {Trends in Ecology \& Evolution}, - volume = {22}, - number = {6}, - pages = {323--330}, - issn = {0169-5347}, - doi = {10.1016/j.tree.2007.03.007}, - abstract = {Body size is perhaps the most fundamental property of an organism and is related to many biological traits, including abundance. The relationship between abundance and body size has been extensively studied in an attempt to quantify the form of the relationship and to understand the processes that generate it. However, progress has been impeded by the underappreciated fact that there are four distinct, but interrelated, relationships between size and abundance that are often confused in the literature. Here, we review and distinguish between these four patterns, and discuss the linkages between them. We argue that a synthetic understanding of size\textendash abundance relationships will result from more detailed analyses of individual patterns and from careful consideration of how and why the patterns are related.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/7MFJIETQ/White et al. - 2007 - Relationships between body size and abundance in e.pdf} -} - -@article{white2007a, - title = {Relationships between Body Size and Abundance in Ecology}, - author = {White, Ethan P. and Ernest, S.K. Morgan and Kerkhoff, Andrew J. and Enquist, Brian J.}, - year = {2007}, - month = jun, - journal = {Trends in Ecology \& Evolution}, - volume = {22}, - number = {6}, - pages = {323--330}, - issn = {01695347}, - doi = {10.1016/j.tree.2007.03.007}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/D5C7YWML/White et al. - 2007 - Relationships between body size and abundance in e.pdf} -} - -@article{white2008, - title = {On {{Estimating}} the {{Exponent}} of {{Power-Law Frequency Distributions}}}, - author = {White, Ethan P. and Enquist, Brian J. and Green, Jessica L.}, - year = {2008}, - journal = {Ecology}, - volume = {89}, - number = {4}, - pages = {905--912}, - issn = {1939-9170}, - doi = {10.1890/07-1288.1}, - abstract = {Power-law frequency distributions characterize a wide array of natural phenomena. In ecology, biology, and many physical and social sciences, the exponents of these power laws are estimated to draw inference about the processes underlying the phenomenon, to test theoretical models, and to scale up from local observations to global patterns. Therefore, it is essential that these exponents be estimated accurately. Unfortunately, the binning-based methods traditionally used in ecology and other disciplines perform quite poorly. Here we discuss more sophisticated methods for fitting these exponents based on cumulative distribution functions and maximum likelihood estimation. We illustrate their superior performance at estimating known exponents and provide details on how and when ecologists should use them. Our results confirm that maximum likelihood estimation outperforms other methods in both accuracy and precision. Because of the use of biased statistical methods for estimating the exponent, the conclusions of several recently published papers should be revisited.}, - langid = {english}, - keywords = {binning,distribution,exponent,maximum likelihood estimation,power laws}, - file = {/Users/renatadiaz/Zotero/storage/KL9YTPV7/White et al. - 2008 - On Estimating the Exponent of Power-Law Frequency .pdf;/Users/renatadiaz/Zotero/storage/XQLP7NR2/07-1288.html} -} - -@article{white2008a, - title = {On {{Estimating}} the {{Exponent}} of {{Power-Law Frequency Distributions}}}, - author = {White, Ethan P. and Enquist, Brian J. and Green, Jessica L.}, - year = {2008}, - journal = {Ecology}, - volume = {89}, - number = {4}, - pages = {905--912}, - issn = {1939-9170}, - doi = {10.1890/07-1288.1}, - abstract = {Power-law frequency distributions characterize a wide array of natural phenomena. In ecology, biology, and many physical and social sciences, the exponents of these power laws are estimated to draw inference about the processes underlying the phenomenon, to test theoretical models, and to scale up from local observations to global patterns. Therefore, it is essential that these exponents be estimated accurately. Unfortunately, the binning-based methods traditionally used in ecology and other disciplines perform quite poorly. Here we discuss more sophisticated methods for fitting these exponents based on cumulative distribution functions and maximum likelihood estimation. We illustrate their superior performance at estimating known exponents and provide details on how and when ecologists should use them. Our results confirm that maximum likelihood estimation outperforms other methods in both accuracy and precision. Because of the use of biased statistical methods for estimating the exponent, the conclusions of several recently published papers should be revisited.}, - langid = {english}, - keywords = {binning,distribution,exponent,maximum likelihood estimation,power laws}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/07-1288.1}, - file = {/Users/renatadiaz/Zotero/storage/VFXNHHYD/White et al. - 2008 - On Estimating the Exponent of Power-Law Frequency .pdf;/Users/renatadiaz/Zotero/storage/2F95VD2L/07-1288.html} -} - -@article{white2010, - title = {The {{Combined Influence}} of the {{Local Environment}} and {{Regional Enrichment}} on {{Bird Species Richness}}}, - author = {White, Ethan~P. and Hurlbert, Allen~H.}, - year = {2010}, - month = feb, - journal = {The American Naturalist}, - volume = {175}, - number = {2}, - pages = {E35-E43}, - issn = {0003-0147, 1537-5323}, - doi = {10.1086/649578}, - abstract = {It is generally accepted that local species richness at a site reflects the combined influence of local and regional processes. However, most empirical studies evaluate the influence of either local environmental variables or regional enrichment but not both simultaneously. Here we demonstrate the importance of combining these processes to understand continental-scale richness patterns in breeding birds. We show that neither regional enrichment nor the local environment in isolation is sufficient to characterize observed patterns of species richness. Combining both sets of variables into a single model results in improved model fit and the removal of residual spatial autocorrelation. At short timescales, local processes are most important for determining local richness, but as the timescale of analysis increases, regional enrichment becomes increasingly important. These results emphasize the need for increased integration of multiple scales of processes into models of species richness.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/2QGNUFA4/White and Hurlbert - 2010 - The Combined Influence of the Local Environment an.pdf} -} - -@article{white2012, - title = {Characterizing Species Abundance Distributions across Taxa and Ecosystems Using a Simple Maximum Entropy Model}, - author = {White, Ethan P. and Thibault, Katherine M. and Xiao, Xiao}, - year = {2012}, - journal = {Ecology}, - volume = {93}, - number = {8}, - pages = {1772--1778}, - issn = {1939-9170}, - doi = {10.1890/11-2177.1}, - abstract = {The species abundance distribution (SAD) is one of the most studied patterns in ecology due to its potential insights into commonness and rarity, community assembly, and patterns of biodiversity. It is well established that communities are composed of a few common and many rare species, and numerous theoretical models have been proposed to explain this pattern. However, no attempt has been made to determine how well these theoretical characterizations capture observed taxonomic and global-scale spatial variation in the general form of the distribution. Here, using data of a scope unprecedented in community ecology, we show that a simple maximum entropy model produces a truncated log-series distribution that can predict between 83\% and 93\% of the observed variation in the rank abundance of species across 15 848 globally distributed communities including birds, mammals, plants, and butterflies. This model requires knowledge of only the species richness and total abundance of the community to predict the full abundance distribution, which suggests that these factors are sufficient to understand the distribution for most purposes. Since geographic patterns in richness and abundance can often be successfully modeled, this approach should allow the distribution of commonness and rarity to be characterized, even in locations where empirical data are unavailable.}, - langid = {english}, - keywords = {birds,butterflies,citizen science,commonness,community structure,informatics,mammals,maximum entropy,rarity,species abundance distribution,trees}, - file = {/Users/renatadiaz/Zotero/storage/H36FF8IS/White et al. - 2012 - Characterizing species abundance distributions acr.pdf;/Users/renatadiaz/Zotero/storage/PDB9A4SR/White et al. - 2012 - Characterizing species abundance distributions acr.pdf;/Users/renatadiaz/Zotero/storage/MIWREN9B/11-2177.html;/Users/renatadiaz/Zotero/storage/NV7AC6MB/11-2177.html} -} - -@article{whitea, - title = {Effects of Population-Level Aggregation, Autocorrelation, and Interspecific Association on the Species\textendash Time Relationship in Two Desert Communities}, - author = {White, Ethan P and Gilchrist, Michael A}, - pages = {20}, - abstract = {Question: Can population-level patterns be used to model the species\textendash time relationship? Which non-random patterns in population time-series are necessary for modelling the species\textendash time relationship? Statistical modelling methods: The presence of aggregation, autocorrelation, and interspecific association was determined using Morisita's IM, Moran's I, and Ive's C respectively. Models for the species\textendash time relationship were constructed from these sub-patterns using a combination of analytical models and randomization methods.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/XRPIKAGW/White and Gilchrist - Effects of population-level aggregation, autocorre.pdf} -} - -@misc{whitney2022, - title = {Open Access Journals Lack Image Accessibility Considerations in Author Guidelines}, - author = {Whitney, Kaitlin Stack and Perrone, Julia and Bahlai, Christie A.}, - year = {2022}, - month = dec, - publisher = {{MetaArXiv}}, - doi = {10.31222/osf.io/zsjqw}, - abstract = {In recent decades, there has been a move to "open" research, that is, to increase the reach of research products to broader audiences. One component of open access is accessibility. Accessibility generally refers to data and other products being free and open to use by others, but accessibility also refers to considering and meeting the needs of people with disabilities for participation and inclusion. Ensuring that visual content is understandable is a major component of ensuring open access publications are accessible, and alt text is a common way to make inaccessible images and non-text content more accessible. Using image accessibility and alt text as a lens, our objective was to evaluate how open access journals incorporate disability accessibility as part of open access publishing. Using a random sample of 300 English language open access journals, we assessed author guidelines to understand image requirements for submissions and open access statements to understand how journals conceive of openness and accessibility. We found that most open access journals do not include disability accessibility elements in their guidelines to authors when submitting images as part of their scholarship. While over half the journals had required parameters for image submission, none of them required alt text. And while the majority of journals included the word 'access' or 'accessibility' in their open access statements, almost none included disability or inclusion related terms. Our results highlight the importance of guidelines. Our findings speak to the limits of some of the current frameworks of open access. Incorporating disability accessibility into open access has the potential to bridge existing information inequalities for people with disabilities - and to make sure that mandates for open research do not exacerbate those inequalities.}, - langid = {american}, - keywords = {access,accessibility,alt text,image description,Library and Information Science,Medicine and Health Sciences,open access,open science,Physical Sciences and Mathematics,Scholarly Communication,Scholarly Publishing,Social and Behavioral Sciences,UDL,universal design,UX}, - file = {/Users/renatadiaz/Zotero/storage/U4QNC9JX/Whitney et al. - 2022 - Open access journals lack image accessibility cons.pdf} -} - -@article{williams2007, - title = {Novel Climates, No-Analog Communities, and Ecological Surprises}, - author = {Williams, John W. and Jackson, Stephen T.}, - year = {2007}, - journal = {Frontiers in Ecology and the Environment}, - volume = {5}, - number = {9}, - pages = {475--482}, - issn = {1540-9309}, - doi = {10.1890/070037}, - abstract = {No-analog communities (communities that are compositionally unlike any found today) occurred frequently in the past and will develop in the greenhouse world of the future. The well documented no-analog plant communities of late-glacial North America are closely linked to ``novel'' climates also lacking modern analogs, characterized by high seasonality of temperature. In climate simulations for the Intergovernmental Panel on Climate Change A2 and B1 emission scenarios, novel climates arise by 2100 AD, primarily in tropical and subtropical regions. These future novel climates are warmer than any present climates globally, with spatially variable shifts in precipitation, and increase the risk of species reshuffling into future no-analog communities and other ecological surprises. Most ecological models are at least partially parameterized from modern observations and so may fail to accurately predict ecological responses to these novel climates. There is an urgent need to test the robustness of ecological models to climate conditions outside modern experience.}, - langid = {english}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/070037}, - file = {/Users/renatadiaz/Zotero/storage/V7X8XB5W/Williams and Jackson - 2007 - Novel climates, no-analog communities, and ecologi.pdf;/Users/renatadiaz/Zotero/storage/87V7SEY8/070037.html} -} - -@book{wilson2020, - title = {Teaching {{Tech Together}}: {{How}} to {{Make Your Lessons Work}} and {{Build}} a {{Teaching Community}} around {{Them}}}, - shorttitle = {Teaching {{Tech Together}}}, - author = {Wilson, Greg}, - year = {2020}, - publisher = {{CRC Press}}, - address = {{Boca Raton}}, - abstract = {Hundreds of grassroots groups have sprung up around the world to teach programming, web design, robotics, and other skills outside traditional classrooms. These groups exist so that people don't have to learn these things on their own, but ironically, their founders and instructors are often teaching themselves how to teach. There's a better way. This book presents evidence-based practices that will help you create and deliver lessons that work and build a teaching community around them. Topics}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/FJWIFWJ8/9780367352974.html} -} - -@article{woelmer2021, - title = {Ten Simple Rules for Training Yourself in an Emerging Field}, - author = {Woelmer, Whitney M. and Bradley, L. M. and Haber, Lisa T. and Klinges, David H. and Lewis, Abigail S. L. and Mohr, Elizabeth J. and Torrens, Christa L. and Wheeler, Kathryn I. and Willson, Alyssa M.}, - year = {2021}, - month = oct, - journal = {PLOS Computational Biology}, - volume = {17}, - number = {10}, - pages = {e1009440}, - publisher = {{Public Library of Science}}, - issn = {1553-7358}, - doi = {10.1371/journal.pcbi.1009440}, - abstract = {The opportunity to participate in and contribute to emerging fields is increasingly prevalent in science. However, simply thinking about stepping outside of your academic silo can leave many students reeling from the uncertainty. Here, we describe 10 simple rules to successfully train yourself in an emerging field, based on our experience as students in the emerging field of ecological forecasting. Our advice begins with setting and revisiting specific goals to achieve your academic and career objectives and includes several useful rules for engaging with and contributing to an emerging field.}, - langid = {english}, - keywords = {Careers,Community ecology,Forecasting,Human learning,Scientists,Textbooks,Theoretical ecology,Workshops}, - file = {/Users/renatadiaz/Zotero/storage/68K4VS95/Woelmer et al. - 2021 - Ten simple rules for training yourself in an emerg.pdf} -} - -@article{wold1957, - title = {A {{Model Explaining}} the {{Pareto Distribution}} of {{Wealth}}}, - author = {Wold, H. O. A. and Whittle, P.}, - year = {1957}, - month = oct, - journal = {Econometrica}, - volume = {25}, - number = {4}, - pages = {591}, - issn = {00129682}, - doi = {10.2307/1905385}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/3CRCNDG6/Wold and Whittle - 1957 - A Model Explaining the Pareto Distribution of Weal.pdf;/Users/renatadiaz/Zotero/storage/6HIFCMAP/Wold and Whittle - 1957 - A Model Explaining the Pareto Distribution of Weal.pdf;/Users/renatadiaz/Zotero/storage/EJDEQTRN/Wold and Whittle - 1957 - A Model Explaining the Pareto Distribution of Weal.pdf;/Users/renatadiaz/Zotero/storage/X4VIM299/Wold and Whittle - 1957 - A Model Explaining the Pareto Distribution of Weal.pdf} -} - -@article{woolhouse1997, - title = {Heterogeneities in the Transmission of Infectious Agents: {{Implications}} for the Design of Control Programs}, - shorttitle = {Heterogeneities in the Transmission of Infectious Agents}, - author = {Woolhouse, M. E. J. and Dye, C. and Etard, J.-F. and Smith, T. and Charlwood, J. D. and Garnett, G. P. and Hagan, P. and Hii, J. L. K. and Ndhlovu, P. D. and Quinnell, R. J. and Watts, C. H. and Chandiwana, S. K. and Anderson, R. M.}, - year = {1997}, - month = jan, - journal = {Proceedings of the National Academy of Sciences}, - volume = {94}, - number = {1}, - pages = {338--342}, - publisher = {{National Academy of Sciences}}, - issn = {0027-8424, 1091-6490}, - doi = {10.1073/pnas.94.1.338}, - abstract = {{$<$}p{$>$}From an analysis of the distributions of measures of transmission rates among hosts, we identify an empirical relationship suggesting that, typically, 20\% of the host population contributes at least 80\% of the net transmission potential, as measured by the basic reproduction number, \emph{R}\textsubscript{0}. This is an example of a statistical pattern known as the 20/80 rule. The rule applies to a variety of disease systems, including vector-borne parasites and sexually transmitted pathogens. The rule implies that control programs targeted at the ``core'' 20\% group are potentially highly effective and, conversely, that programs that fail to reach all of this group will be much less effective than expected in reducing levels of infection in the population as a whole.{$<$}/p{$>$}}, - chapter = {Biological Sciences}, - copyright = {Copyright \textcopyright{} 1997, The National Academy of Sciences of the USA}, - langid = {english}, - pmid = {8990210}, - keywords = {basic reproduction number,HIV/AIDS,leishmaniasis,malaria,schistosomiasis}, - file = {/Users/renatadiaz/Zotero/storage/BNA78MVH/Woolhouse et al. - 1997 - Heterogeneities in the transmission of infectious .pdf;/Users/renatadiaz/Zotero/storage/IRUL3UQ5/338.html} -} - -@article{woudenberg2010, - title = {The {{Forest Inventory}} and {{Analysis Database}}: {{Database}} Description and Users Manual Version 4.0 for {{Phase}} 2}, - shorttitle = {The {{Forest Inventory}} and {{Analysis Database}}}, - author = {Woudenberg, Sharon W. and Conkling, Barbara L. and O'Connell, Barbara M. and LaPoint, Elizabeth B. and Turner, Jeffery A. and Waddell, Karen L.}, - year = {2010}, - journal = {Gen. Tech. Rep. RMRS-GTR-245. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 336 p.}, - volume = {245}, - doi = {10.2737/RMRS-GTR-245}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/GEEG7SNJ/Woudenberg et al. - 2010 - The Forest Inventory and Analysis Database Databa.pdf;/Users/renatadiaz/Zotero/storage/3VYMCPW5/37446.html} -} - -@article{xiao2015, - title = {A {{Strong Test}} of the {{Maximum Entropy Theory}} of {{Ecology}}.}, - author = {Xiao, Xiao and McGlinn, Daniel J. and White, Ethan P.}, - year = {2015}, - month = mar, - journal = {The American Naturalist}, - volume = {185}, - number = {3}, - pages = {E70-E80}, - issn = {0003-0147}, - doi = {10.1086/679576}, - abstract = {The maximum entropy theory of ecology (METE) is a unified theory of biodiversity that predicts a large number of macroecological patterns using information on only species richness, total abundance, and total metabolic rate of the community. We evaluated four major predictions of METE simultaneously at an unprecedented scale using data from 60 globally distributed forest communities including more than 300,000 individuals and nearly 2,000 species. METE successfully captured 96\% and 89\% of the variation in the rank distribution of species abundance and individual size but performed poorly when characterizing the size-density relationship and intraspecific distribution of individual size. Specifically, METE predicted a negative correlation between size and species abundance, which is weak in natural communities. By evaluating multiple predictions with large quantities of data, our study not only identifies a mismatch between abundance and body size in METE but also demonstrates the importance of conducting strong tests of ecological theories.}, - file = {/Users/renatadiaz/Zotero/storage/T8N9S8AX/Xiao et al. - 2015 - A Strong Test of the Maximum Entropy Theory of Eco.pdf;/Users/renatadiaz/Zotero/storage/UC9J88XE/679576.html} -} - -@article{xiao2016, - title = {Comparing Process-Based and Constraint-Based Approaches for Modeling Macroecological Patterns}, - author = {Xiao, Xiao and O'Dwyer, James P. and White, Ethan P.}, - year = {2016}, - journal = {Ecology}, - volume = {97}, - number = {5}, - pages = {1228--1238}, - issn = {1939-9170}, - doi = {10.1890/15-0962.1}, - abstract = {Ecological patterns arise from the interplay of many different processes, and yet the emergence of consistent phenomena across a diverse range of ecological systems suggests that many patterns may in part be determined by statistical or numerical constraints. Differentiating the extent to which patterns in a given system are determined statistically, and where it requires explicit ecological processes, has been difficult. We tackled this challenge by directly comparing models from a constraint-based theory, the Maximum Entropy Theory of Ecology (METE) and models from a process-based theory, the size-structured neutral theory (SSNT). Models from both theories were capable of characterizing the distribution of individuals among species and the distribution of body size among individuals across 76 forest communities. However, the SSNT models consistently yielded higher overall likelihood, as well as more realistic characterizations of the relationship between species abundance and average body size of conspecific individuals. This suggests that the details of the biological processes contain additional information for understanding community structure that are not fully captured by the METE constraints in these systems. Our approach provides a first step towards differentiating between process- and constraint-based models of ecological systems and a general methodology for comparing ecological models that make predictions for multiple patterns.}, - copyright = {\textcopyright{} 2016 The Authors. Ecology, published by Wiley Periodicals, Inc., on behalf of the Ecological Society of America.}, - langid = {english}, - keywords = {constraints,maximum entropy theory of ecology,mechanisms,model comparison,neutral theory,processes}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/15-0962.1}, - file = {/Users/renatadiaz/Zotero/storage/EZBPGPQQ/Xiao et al. - 2016 - Comparing process-based and constraint-based appro.pdf;/Users/renatadiaz/Zotero/storage/3F77BGNU/15-0962.html} -} - -@article{xiao2016a, - title = {Characterizing Species Abundance Distributions across Taxa and Ecosystems Using a Simple Maximum Entropy Model}, - author = {Xiao, Xiao}, - year = {2016}, - month = aug, - publisher = {{Wiley}}, - doi = {10.6084/m9.figshare.c.3304845.v1}, - abstract = {The species abundance distribution (SAD) is one of the most studied patterns in ecology due to its potential insights into commonness and rarity, community assembly, and patterns of biodiversity. It is well established that communities are composed of a few common and many rare species, and numerous theoretical models have been proposed to explain this pattern. However, no attempt has been made to determine how well these theoretical characterizations capture observed taxonomic and global-scale spatial variation in the general form of the distribution. Here, using data of a scope unprecedented in community ecology, we show that a simple maximum entropy model produces a truncated log-series distribution that can predict between 83\% and 93\% of the observed variation in the rank abundance of species across 15\,848 globally distributed communities including birds, mammals, plants, and butterflies. This model requires knowledge of only the species richness and total abundance of the community to predict the full abundance distribution, which suggests that these factors are sufficient to understand the distribution for most purposes. Since geographic patterns in richness and abundance can often be successfully modeled, this approach should allow the distribution of commonness and rarity to be characterized, even in locations where empirical data are unavailable.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/TT72AWTM/1.html} -} - -@misc{ye2020, - title = {Macroecological {{Analyses}} of {{Time Series Structure}}}, - author = {Ye, Hao and Bledsoe, Ellen K. and Diaz, Renata and Ernest, S. K. Morgan and Simonis, Juniper L. and White, Ethan P. and Yenni, Glenda M.}, - year = {2020}, - month = may, - doi = {10.5281/zenodo.3823768}, - abstract = {Support for macroecological analyses of time series. The intent of the package is to enable end users to run analyses on a collection of population and community time series data. Functions are provided to download and import datasets, produce reproducible workflows using the `drake` package, and for generating research compendia with code and reports.}, - howpublished = {Zenodo}, - keywords = {ecology,long-term,time-series}, - file = {/Users/renatadiaz/Zotero/storage/G7Q3XCU6/3823768.html} -} - -@article{yeakel2020, - title = {Caching in or {{Falling Back}} at the {{Sevilleta}}: {{The Effects}} of {{Body Size}} and {{Seasonal Uncertainty}} on {{Desert Rodent Foraging}}}, - shorttitle = {Caching in or {{Falling Back}} at the {{Sevilleta}}}, - author = {Yeakel, Justin D. and Bhat, Uttam and Newsome, Seth D.}, - year = {2020}, - month = aug, - journal = {American Naturalist}, - volume = {196}, - number = {2}, - pages = {241--256}, - publisher = {{Univ Chicago Press}}, - address = {{Chicago}}, - issn = {0003-0147}, - doi = {10.1086/709019}, - abstract = {Foraging in uncertain environments requires balancing the risks associated with finding alternative resources against potential gains. In arid-land environments characterized by extreme variation in the amount and seasonal timing of primary production, consumers must weigh the risks associated with foraging for preferred seeds that can be cached against fallback foods of low nutritional quality (e.g., leaves) that must be consumed immediately. Here, we explore the influence of resource scarcity, body size, and seasonal uncertainty on the expected foraging behaviors of caching rodents in the northern Chihuahaun Desert by integrating these elements with a stochastic dynamic program to determine fitness-maximizing foraging strategies. We demonstrate that resource-limited environments promote dependence on fallback foods, reducing the likelihood of starvation while increasing future risk exposure. Our results point to a qualitative difference in the use of fallback foods and the fitness benefits of caching at the threshold body size of 50 g. Above this 50-g body size threshold, we observe large fitness gains associated with the maintenance of even a modest-sized cache, whereas similar gains for smaller consumers require maintenance of unrealistically large caches. This suggests that larger-bodied consumers that cache may be less sensitive to the future uncertainties in monsoonal onset predicted by global climate scenarios, whereas smaller consumers, regardless of caching behavior, may be at greater risk.}, - langid = {english}, - keywords = {caching,competition,energy,evolution,fallback foods,fasting endurance,foraging,long-term,mortality,primate ecology,Sevilleta,stable-isotopes,stochastic dynamic programing,underground-storage organs}, - annotation = {WOS:000548984500011} -} - -@article{yen2017, - title = {Balancing Generality and Specificity in Ecological Gradient Analysis with Species Abundance Distributions and Individual Size Distributions: {{Community}} Distributions along Environmental Gradients}, - shorttitle = {Balancing Generality and Specificity in Ecological Gradient Analysis with Species Abundance Distributions and Individual Size Distributions}, - author = {Yen, Jian D. L. and Thomson, James R. and Keith, Jonathan M. and Paganin, David M. and Fleishman, Erica and Dobkin, David S. and Bennett, Joanne M. and Mac Nally, Ralph}, - year = {2017}, - month = mar, - journal = {Global Ecology and Biogeography}, - volume = {26}, - number = {3}, - pages = {318--332}, - issn = {1466822X}, - doi = {10.1111/geb.12537}, - abstract = {Aim Data on ecological communities are often condensed into single-valued diversity indices, which support comparisons among ecosystems but may discard important information. At the other extreme, some studies retain full data on the identities of all species present, which retains maximum information on community structure but occludes comparisons among ecosystems. We sought to determine whether the analysis of species abundance distributions and individual size distributions could support more detailed inferences than diversity indices while remaining sufficiently general to identify fundamental ecological responses in multiple ecosystems.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/NYNFISAK/Yen et al. - 2017 - Balancing generality and specificity in ecological.pdf} -} - -@article{yen2017a, - title = {How Do Different Aspects of Biodiversity Change through Time? {{A}} Case Study on an {{Australian}} Bird Community}, - shorttitle = {How Do Different Aspects of Biodiversity Change through Time?}, - author = {Yen, Jian D. L. and Thomson, James R. and Keith, Jonathan M. and Paganin, David M. and Nally, Ralph Mac}, - year = {2017}, - journal = {Ecography}, - volume = {40}, - number = {5}, - pages = {642--650}, - issn = {1600-0587}, - doi = {10.1111/ecog.02306}, - abstract = {The study of ecological communities through time can reveal fundamental ecological processes and is key to understanding how natural and human pressures will affect biodiversity. Most studies of ecological communities through time consider only one or a few summary measures (e.g. species richness, total abundance), which might neglect important aspects of community structure or function. We studied temporal variation in several measures of species diversity, size diversity, and species composition in an intensively sampled bird community to determine whether different biodiversity measures change synchronously. We used a novel function regression model, which supports the study of diversity measures that are distributions (e.g. species abundance distributions) alongside measures that are scalar values (e.g. species richness). Most diversity measures changed predictably within years, but inter-annual changes in size diversity and species composition were not reflected in species diversity. Within and among years, there was considerable variation in distributional measures that was not captured in scalar measures. Predictable variation within years probably was related to seasonal variation in weather patterns or food availability, but variation in size diversity among years probably resulted from stochastic changes in species composition. These results suggest that species and size diversity may be decoupled, and that inferences on scalar diversity measures might not reflect fundamental changes to community structure or function. Our method supports the inclusion of size-based measures and distributional measures in ecological analyses, and broader uptake of our approach is likely to provide new insight into the processes structuring ecological communities, and inform the links between structure and function in ecological communities.}, - langid = {english}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.02306}, - file = {/Users/renatadiaz/Zotero/storage/MRM8UJHW/Yen et al. - 2017 - How do different aspects of biodiversity change th.pdf;/Users/renatadiaz/Zotero/storage/FJWLGTPJ/ecog.html} -} - -@article{yenni2012, - title = {Strong Self-Limitation Promotes the Persistence of Rare Species}, - author = {Yenni, Glenda and Adler, Peter B. and Ernest, S. K. Morgan}, - year = {2012}, - journal = {Ecology}, - volume = {93}, - number = {3}, - pages = {456--461}, - issn = {1939-9170}, - doi = {10.1890/11-1087.1}, - abstract = {Theory has recognized a combination of niche and neutral processes each contributing, with varying importance, to species coexistence. However, long-term persistence of rare species has been difficult to produce in trait-based models of coexistence that incorporate stochastic dynamics, raising questions about how rare species persist despite such variability. Following recent evidence that rare species may experience significantly different population dynamics than dominant species, we use a plant community model to simulate the effect of disproportionately strong negative frequency dependence on the long-term persistence of the rare species in a simulated community. This strong self-limitation produces long persistence times for the rare competitors, which otherwise succumb quickly to stochastic extinction. The results suggest that the mechanism causing species to be rare in this case is the same mechanism allowing those species to persist.}, - langid = {english}, - keywords = {coexistence,frequency dependence,niche theory,rare species,self-limitation,species diversity}, - annotation = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/11-1087.1}, - file = {/Users/renatadiaz/Zotero/storage/PL5VVHV8/Yenni et al. - 2012 - Strong self-limitation promotes the persistence of.pdf;/Users/renatadiaz/Zotero/storage/QCYBZ3MS/11-1087.html} -} - -@article{yenni2019, - title = {Developing a Modern Data Workflow for Regularly Updated Data}, - author = {Yenni, Glenda M. and Christensen, Erica M. and Bledsoe, Ellen K. and Supp, Sarah R. and Diaz, Renata M. and White, Ethan P. and Ernest, S. K. Morgan}, - year = {2019}, - month = jan, - journal = {PLOS Biology}, - volume = {17}, - number = {1}, - pages = {e3000125}, - publisher = {{Public Library of Science}}, - issn = {1545-7885}, - doi = {10.1371/journal.pbio.3000125}, - abstract = {Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.}, - langid = {english}, - keywords = {Archives,Biological data management,Data management,Databases,Programming languages,Quality control,Reproducibility,Scientists}, - file = {/Users/renatadiaz/Zotero/storage/YY9JM2BZ/Yenni et al. - 2019 - Developing a modern data workflow for regularly up.pdf;/Users/renatadiaz/Zotero/storage/U3EKL635/article.html} -} - -@article{yenni2019a, - title = {Developing a Modern Data Workflow for Regularly Updated Data}, - author = {Yenni, Glenda M. and Christensen, Erica M. and Bledsoe, Ellen K. and Supp, Sarah R. and Diaz, Renata M. and White, Ethan P. and Ernest, S. K. Morgan}, - year = {2019}, - month = jan, - journal = {PLOS Biology}, - volume = {17}, - number = {1}, - pages = {e3000125}, - publisher = {{Public Library of Science}}, - issn = {1545-7885}, - doi = {10.1371/journal.pbio.3000125}, - abstract = {Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.}, - langid = {english}, - keywords = {Archives,Biological data management,Data management,Databases,Programming languages,Quality control,Reproducibility,Scientists}, - file = {/Users/renatadiaz/Zotero/storage/9LMLRXTS/Yenni et al. - 2019 - Developing a modern data workflow for regularly up.pdf;/Users/renatadiaz/Zotero/storage/VZAXEXDB/article.html} -} - -@article{yom-tov2011, - title = {Recent Spatial and Temporal Changes in Body Size of Terrestrial Vertebrates: Probable Causes and Pitfalls}, - shorttitle = {Recent Spatial and Temporal Changes in Body Size of Terrestrial Vertebrates}, - author = {{Yom-Tov}, Yoram and Geffen, Eli}, - year = {2011}, - journal = {Biological Reviews}, - volume = {86}, - number = {2}, - pages = {531--541}, - issn = {1469-185X}, - doi = {10.1111/j.1469-185X.2010.00168.x}, - abstract = {Geographical and temporal variations in body size are common phenomena among organisms and may evolve within a few years. We argue that body size acts much like a barometer, fluctuating in parallel with changes in the relevant key predictor(s), and that geographical and temporal changes in body size are actually manifestations of the same drivers. Frequently, the principal predictors of body size are food availability during the period of growth and ambient temperature, which often affects food availability. Food availability depends on net primary productivity that, in turn, is determined by climate and weather (mainly temperature and precipitation), and these depend mainly on solar radiation and other solar activities. When the above predictors are related to latitude the changes have often been interpreted as conforming to Bergmann's rule, but in many cases such interpretations should be viewed with caution due to the interrelationships among various environmental predictors. Recent temporal changes in body size have often been related to global warming. However, in many cases the above key predictors are not related to either latitude and/or year, and it is the task of the researcher to determine which particular environmental predictor is the one that determines food availability and, in turn, body size. The chance of discerning a significant change in body size depends to a large extent on sample size (specimens/year). The most recent changes in body size are probably phenotypic, but there are some cases in which they are partly genetic.}, - langid = {english}, - keywords = {Bergmann's rule,birds,body size,climate change,food availability,global warming,mammals}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.2010.00168.x}, - file = {/Users/renatadiaz/Zotero/storage/ABQ7ELJF/j.1469-185X.2010.00168.html} -} - -@article{young2016, - title = {Patterns, {{Causes}}, and {{Consequences}} of {{Anthropocene Defaunation}}}, - author = {Young, Hillary S. and McCauley, Douglas J. and Galetti, Mauro and Dirzo, Rodolfo}, - year = {2016}, - journal = {Annual Review of Ecology, Evolution, and Systematics}, - volume = {47}, - number = {1}, - pages = {333--358}, - doi = {10.1146/annurev-ecolsys-112414-054142}, - abstract = {Anthropocene defaunation, the global extinction of faunal species and populations and the decline in abundance of individuals within populations, has been predominantly documented in terrestrial ecosystems, but indicators suggest defaunation has been more severe in freshwater ecosystems. Marine defaunation is in a more incipient stage, yet pronounced effects are already apparent and its rapid acceleration seems likely. Defaunation now impacts the planet's wildlife with profound cascading consequences, ranging from local to global coextinctions of interacting species to the loss of ecological services critical for humanity. Slowing defaunation will require aggressively reducing animal overexploitation and habitat destruction; mitigating climate disruption; and stabilizing the impacts of human population growth and uneven resource consumption. Given its omnipresence, defaunation should receive status of major global environmental change and should be addressed with the same urgency as deforestation, pollution, and climatic change. Global action is needed to prevent defaunation's current trajectory from catalyzing the planet's sixth major extinction.}, - keywords = {animal conservation,animal overexploitation,defaunation cascades,freshwater fauna,marine fauna,terrestrial fauna}, - annotation = {\_eprint: https://doi.org/10.1146/annurev-ecolsys-112414-054142} -} - -@misc{youngflesh2022, - title = {Abiotic Conditions Shape Spatial and Temporal Morphological Variation in {{North American}} Birds}, - author = {Youngflesh, Casey and Saracco, James F. and Siegel, Rodney B. and Tingley, Morgan W.}, - year = {2022}, - month = feb, - pages = {2022.02.17.480905}, - publisher = {{bioRxiv}}, - doi = {10.1101/2022.02.17.480905}, - abstract = {Abiotic environmental conditions play a key role in driving the size and shape of organisms. Quantifying environment-morphology relationships is important not only for understanding the fundamental processes driving phenotypic diversity within and among species (1), but also for predicting how species will respond to ongoing global change (2). Despite a clear set of expectations motivated by ecological theory (3), broad evidence in support of generalizable effects of abiotic conditions, such as temperature (4), on spatial and temporal intraspecific morphological variation has been limited. Using standardized data from over 250,000 captures of 105 landbird species, we assessed intraspecific shifts in bird morphology since 1989 while simultaneously measuring spatial morphological gradients across the North American continent. Across bird species, we found strong spatial and temporal trends in body size, with warmer temperatures associated with smaller body sizes both at more equatorial latitudes and in more recent years. The magnitude of these thermal effects varied both across and within species, with results suggesting it is the warmest, rather than the coldest, temperatures driving both spatial and temporal trends. Across elevation, we found that body size declines as relative wing length increases, likely due to the benefits that longer wings confer for flight in thin air environments. Our results provide support for both existing and new large-scale ecomorphological gradients and highlight how the response of functional tradeoffs to abiotic variation drives morphological change. Significance Statement Characterizing how the size and shape of organisms varies over space and time is key to understanding the processes that create ecological communities and for predicting how species will respond to climate change. Across more than 100 species of North American birds, we show that within species the size and shape of individuals varies substantially across space and time. Warmer temperatures are associated with smaller body sizes, likely due to the importance of body size for thermoregulation. As the climate continues to warm, these species will likely continue to shrink. We also provide the first large-scale evidence of an increase in wing length with elevation, a pattern that could be attributed to thinner air in high elevation environments.}, - chapter = {New Results}, - copyright = {\textcopyright{} 2022, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/3G3ZI5P5/Youngflesh et al. - 2022 - Abiotic conditions shape spatial and temporal morp.pdf;/Users/renatadiaz/Zotero/storage/R2AMSN9T/2022.02.17.480905v1.html} -} - -@techreport{youngflesh2022a, - type = {Preprint}, - title = {Abiotic Conditions Shape Spatial and Temporal Morphological Variation in {{North American}} Birds}, - author = {Youngflesh, Casey and Saracco, James F. and Siegel, Rodney B. and Tingley, Morgan W.}, - year = {2022}, - month = feb, - institution = {{Ecology}}, - doi = {10.1101/2022.02.17.480905}, - abstract = {Abstract Abiotic environmental conditions play a key role in driving the size and shape of organisms. Quantifying environment-morphology relationships is important not only for understanding the fundamental processes driving phenotypic diversity within and among species ( 1 ), but also for predicting how species will respond to ongoing global change ( 2 ). Despite a clear set of expectations motivated by ecological theory ( 3 ), broad evidence in support of generalizable effects of abiotic conditions, such as temperature ( 4 ), on spatial and temporal intraspecific morphological variation has been limited. Using standardized data from over 250,000 captures of 105 landbird species, we assessed intraspecific shifts in bird morphology since 1989 while simultaneously measuring spatial morphological gradients across the North American continent. Across bird species, we found strong spatial and temporal trends in body size, with warmer temperatures associated with smaller body sizes both at more equatorial latitudes and in more recent years. The magnitude of these thermal effects varied both across and within species, with results suggesting it is the warmest, rather than the coldest, temperatures driving both spatial and temporal trends. Across elevation, we found that body size declines as relative wing length increases, likely due to the benefits that longer wings confer for flight in thin air environments. Our results provide support for both existing and new large-scale ecomorphological gradients and highlight how the response of functional tradeoffs to abiotic variation drives morphological change. Significance Statement Characterizing how the size and shape of organisms varies over space and time is key to understanding the processes that create ecological communities and for predicting how species will respond to climate change. Across more than 100 species of North American birds, we show that within species the size and shape of individuals varies substantially across space and time. Warmer temperatures are associated with smaller body sizes, likely due to the importance of body size for thermoregulation. As the climate continues to warm, these species will likely continue to shrink. We also provide the first large-scale evidence of an increase in wing length with elevation, a pattern that could be attributed to thinner air in high elevation environments.}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/VE5Z8UET/Youngflesh et al. - 2022 - Abiotic conditions shape spatial and temporal morp.pdf} -} - -@article{youngflesh2022b, - title = {Abiotic Conditions Shape Spatial and Temporal Morphological Variation in {{North American}} Birds}, - author = {Youngflesh, Casey and Saracco, James F. and Siegel, Rodney B. and Tingley, Morgan W.}, - year = {2022}, - month = oct, - journal = {Nature Ecology \& Evolution}, - pages = {1--11}, - publisher = {{Nature Publishing Group}}, - issn = {2397-334X}, - doi = {10.1038/s41559-022-01893-x}, - abstract = {Quantifying environment\textendash morphology relationships is important not only for understanding the fundamental processes driving phenotypic diversity within and among species but also for predicting how species will respond to ongoing global change. Despite a clear set of expectations motivated by ecological theory, broad evidence in support of generalizable effects of abiotic conditions on spatial and temporal intraspecific morphological variation has been limited. Using standardized data from {$>$}250,000 captures of 105 landbird species, we assessed intraspecific shifts in the morphology of adult male birds since 1989 while simultaneously measuring spatial morphological gradients across the North American continent. We found strong spatial and temporal trends in average body size, with warmer temperatures associated with smaller body sizes both at more equatorial latitudes and in more recent years. The magnitude of these thermal effects varied both across and within species, with results suggesting it is the warmest, rather than the coldest, temperatures that drive both spatial and temporal trends. Stronger responses to spatial\textemdash rather than temporal\textemdash variation in temperature suggest that morphological change may not be keeping up with the pace of climate change. Additionally, as elevation increases, we found that body size declines as relative wing length increases, probably due to the benefits that longer wings confer for flight in thin air environments. Our results provide support for both existing and new large-scale ecomorphological `rules' and highlight how the response of functional trade-offs to abiotic variation drives morphological change.}, - copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited}, - langid = {english}, - keywords = {Biodiversity,Biogeography,Macroecology}, - file = {/Users/renatadiaz/Zotero/storage/G6ZYULFC/Youngflesh et al. - 2022 - Abiotic conditions shape spatial and temporal morp.pdf;/Users/renatadiaz/Zotero/storage/JJPGJWD4/s41559-022-01893-x.html} -} - -@article{yvon-durocher2011, - title = {Warming Alters the Size Spectrum and Shifts the Distribution of Biomass in Freshwater Ecosystems}, - author = {Yvon-Durocher, Gabriel and Montoya, Jos{\'e} M. and Trimmer, Mark and Woodward, Guy}, - year = {2011}, - journal = {Global Change Biology}, - volume = {17}, - number = {4}, - pages = {1681--1694}, - issn = {1365-2486}, - doi = {10.1111/j.1365-2486.2010.02321.x}, - abstract = {Organism size is one of the key determinants of community structure, and its relationship with abundance can describe how biomass is partitioned among the biota within an ecosystem. An outdoor freshwater mesocosm experiment was used to determine how warming of{$\sim$}4 \textdegree C would affect the size, biomass and taxonomic structure of planktonic communities. Warming increased the steepness of the community size spectrum by increasing the prevalence of small organisms, primarily within the phytoplankton assemblage and it also reduced the mean and maximum size of phytoplankton by approximately one order of magnitude. The observed shifts in phytoplankton size structure were reflected in changes in phytoplankton community composition, though zooplankton taxonomic composition was unaffected by warming. Furthermore, warming reduced community biomass and total phytoplankton biomass, although zooplankton biomass was unaffected. This resulted in an increase in the zooplankton to phytoplankton biomass ratio in the warmed mesocosms, which could be explained by faster turnover within the phytoplankton assemblages. Overall, warming shifted the distribution of phytoplankton size towards smaller individuals with rapid turnover and low standing biomass, resulting in a reorganization of the biomass structure of the food webs. These results indicate future environmental warming may have profound effects on the structure and functioning of aquatic communities and ecosystems.}, - copyright = {\textcopyright{} 2010 Blackwell Publishing Ltd}, - langid = {english}, - keywords = {biomass,body size,food webs,global warming,mass-abundance relationships,phytoplankton,size spectra,zooplankton}, - annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2486.2010.02321.x}, - file = {/Users/renatadiaz/Zotero/storage/RVZNRMV7/Yvon‐Durocher et al. - 2011 - Warming alters the size spectrum and shifts the di.pdf;/Users/renatadiaz/Zotero/storage/FFJJVV7E/j.1365-2486.2010.02321.html;/Users/renatadiaz/Zotero/storage/IHAL8F42/j.1365-2486.2010.02321.html} -} - -@article{zahl1977, - title = {Jackknifing {{An Index}} of {{Diversity}}}, - author = {Zahl, Samuel}, - year = {1977}, - journal = {Ecology}, - volume = {58}, - number = {4}, - pages = {907--913}, - publisher = {{Ecological Society of America}}, - issn = {0012-9658}, - doi = {10.2307/1936227}, - abstract = {The method of jackknifing is introduced for estimating an index of diversity and is illustrated with tree data. The method yields approximately normally distributed jackknife estimates and also gives estimated standard deviations, making possible tests of hypotheses and confidence interval estimates. These results apparently can be obtained under the usual conditions of field sampling, where associations within and between species or between quadrats or segments of a traverse may be found. Because of these associations there is no guarantee that the method works; hence an eyball and a statistical test for the approximate normality of the estimates are given and illustrated with the tree data. The tree data come from 24 quadrats arranged in two blocks of contiguous quadrats. The estimated tree-species diversity, using both indices considered, showed a smooth monotonic decrease over a 19-yr interval providing striking confirmation of the reality of this ecological parameter. The normality tests on this data showed that the normal approximations to the distributions of the jackknife estimates were justified, except in three instances, only one of which seemed to be seriously in error. A conclusion is that it seems reasonable to suppose that in many, if not most, cases, only moderate sample sizes will be needed in practice for the jackknife estimate, at least for forest data.} -} - -@article{zamora2015, - title = {Long-{{Term Changes}} in {{Mountain Passerine Bird Communities}} in the {{Sierra Nevada}} ({{Southern Spain}}): {{A}} 30-{{Year Case Study}}}, - shorttitle = {Long-{{Term Changes}} in {{Mountain Passerine Bird Communities}} in the {{Sierra Nevada}} ({{Southern Spain}})}, - author = {Zamora, Regino and {Barea-Azc{\'o}n}, Jos{\'e} Miguel}, - year = {2015}, - month = jun, - journal = {Ardeola}, - volume = {62}, - number = {1}, - pages = {3--18}, - publisher = {{Spanish Society of Ornithology}}, - issn = {0570-7358, 2341-0825}, - doi = {10.13157/arla.62.1.2015.3}, - abstract = {Shifts in composition and abundance of bird communities were studied along an elevational gradient in the Sierra Nevada (S. Spain), comparing censuses made at the same locations in the 1980s and during 2008\textendash 2012. Censuses were made in three representative ecosystems: 1) Pyrenean oak woodland, 2) high-mountain juniper scrubland, 3) high-mountain summits. In a global change context, avian-community dynamics are related mainly to changes in two of the following drivers: climate change and land-use change occurring over the past 30 years. Our results show a continuous turnover of the bird community, with an overall 27\% change in species composition, in an ecological setting that has changed little, especially in the high-mountain scrubland and summit areas. We detected an increase in species diversity relative to the 1980s, mostly in the Pyrenean oak woodland. Moreover, our results also show a sharp decrease in bird density during the 30-year study period, chiefly affecting the dominant species of the 1980s in the Pyrenean oak forest and in the high-mountain scrubland. In the high-summit ecosystems, the decline of alpine species has paralleled the uphill expansion of some mediterranean ones. The outcome of these processes is a community in continuous flux, both in composition and abundance, where interannual variability is similar to interdecadal variability. We conclude that the bird communities of Sierra Nevada are showing strong spatial and temporal dynamics that are now accelerating, perhaps because of global warming.}, - file = {/Users/renatadiaz/Zotero/storage/RDBNIY9I/Zamora and Barea-Azcón - 2015 - Long-Term Changes in Mountain Passerine Bird Commu.pdf;/Users/renatadiaz/Zotero/storage/XTKNNGC9/arla.62.1.2015.3.html} -} - -@book{zar1999, - title = {Biostatistical {{Analysis}} ({{Fourth Edition}})}, - author = {Zar, Jerrold H.}, - year = {1999}, - edition = {4th edition}, - publisher = {{Pearson Education}}, - address = {{New Delhi}}, - annotation = {Quantity Available: 500} -} - -@misc{zotero-122, - title = {Maximum {{Entropy}} and {{Ecology}} - {{Paperback}} - {{John Harte}} - {{Oxford University Press}}}, - howpublished = {https://global.oup.com/academic/product/maximum-entropy-and-ecology-9780199593422?cc=ca\&lang=en\&}, - file = {/Users/renatadiaz/Zotero/storage/RJY9SHDZ/maximum-entropy-and-ecology-9780199593422.html} -} - -@misc{zotero-1245, - title = {Working with the {{CARE}} Principles: Operationalising {{Indigenous}} Data Governance}, - shorttitle = {Working with the {{CARE}} Principles}, - abstract = {Shifting the focus of data governance from consultation to values-based relationships to promote equitable Indigenous participation in data processes.}, - howpublished = {https://www.adalovelaceinstitute.org/blog/care-principles-operationalising-indigenous-data-governance/}, - langid = {british}, - file = {/Users/renatadiaz/Zotero/storage/W64MCE7S/care-principles-operationalising-indigenous-data-governance.html} -} - -@misc{zotero-125, - title = {{{KNB}}}, - howpublished = {https://knb.ecoinformatics.org/view/esa.86.4}, - file = {/Users/renatadiaz/Zotero/storage/LNBZQ4KX/esa.86.html} -} - -@misc{zotero-1254, - title = {Squareone/{{README}}.Md at Main {$\cdot$} Diazrenata/Squareone}, - journal = {GitHub}, - abstract = {Took a long time to get back here. Energetic compensation post-2010. - squareone/README.md at main {$\cdot$} diazrenata/squareone}, - howpublished = {https://github.com/diazrenata/squareone}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/KGTL7ZJD/squareone.html} -} - -@misc{zotero-126, - title = {Ecological {{Archives E090-118}}}, - howpublished = {http://esapubs.org/archive/ecol/E090/118/}, - file = {/Users/renatadiaz/Zotero/storage/VZ5LAGHU/118.html} -} - -@misc{zotero-1285, - title = {State of the {{Birds}} 2022}, - journal = {State of the Birds 2022}, - abstract = {We Can Bend the Curve to Bring Birds Back The United States and Canada have lost 3 billion breeding birds since 1970\textemdash a loss of 1 in 4 birds, according to research published in Science in 2019. This steep decline in abundance can be reversed with new scales of conservation actions that benefit not}, - howpublished = {https://www.stateofthebirds.org/2022}, - langid = {american}, - file = {/Users/renatadiaz/Zotero/storage/FG2FHI34/2022.html} -} - -@misc{zotero-1377, - title = {Intentionally {{Addressing Equity}} in the {{Classroom}} | {{NSTA}}}, - abstract = {Equity, as we define it, means striving to serve the needs of others and enhancing belonging by focusing on ``whole humans'' in emotional, sociocultural, and personal contexts. Integrating equitable practices in STEM classrooms has advantages ranging from helping students grasp concepts to better fostering student transitions into STEM culture. Through class observations, teacher interviews, and open-ended student surveys, we explore differences in perceptions of equity between major and nonmajor biology and geology courses.}, - howpublished = {https://www.nsta.org/journal-college-science-teaching/journal-college-science-teaching-novemberdecember-2022-1}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/832U3W4R/journal-college-science-teaching-novemberdecember-2022-1.html} -} - -@misc{zotero-1379, - title = {Welcome to {{Data}} Retriever's Documentation! \textemdash{} {{Data Retriever}} v3.1.1-Dev Documentation}, - howpublished = {https://retriever.readthedocs.io/en/latest/index.html} -} - -@misc{zotero-230, - title = {Walker: {{Biodiversity}} and Ecological Redundancy - {{Google Scholar}}}, - howpublished = {https://scholar.google.com/scholar\_lookup?hl=en\&volume=6\&publication\_year=1992\&pages=18-23\&journal=Conserv.+Biol.\&author=B.+H.+Walker\&title=Biodiversity+and+ecological+redundancy} -} - -@misc{zotero-345, - title = {Cross-{{Scale Morphology}}, {{Geometry}}, and {{Dynamics}} of ...: {{Find}} It @ {{UF Results}}}, - howpublished = {http://resolver.ebscohost.com.lp.hscl.ufl.edu/openurl?sid=google\&auinit=CS\&aulast=Holling\&atitle=Cross\%e2\%80\%90scale+morphology\%2c+geometry\%2c+and+dynamics+of+ecosystems\&id=doi\%3a10.2307\%2f2937313\&title=Ecological+Monographs\&volume=62\&issue=4\&date=1992\&spage=447\&issn=1557-7015\&site=ftf-live}, - file = {/Users/renatadiaz/Zotero/storage/QW6V5AQI/openurl.html} -} - -@misc{zotero-353, - title = {{{PRISM}} 30yr {{Normal}} 1981-2010 - {{ScienceBase-Catalog}}}, - howpublished = {https://www.sciencebase.gov/catalog/item/57b3296be4b03bcb0103955d}, - file = {/Users/renatadiaz/Zotero/storage/MIREQ7UU/57b3296be4b03bcb0103955d.html} -} - -@misc{zotero-44, - title = {Change Password | {{United Airlines}}}, - howpublished = {https://www.united.com/ual/en/us/account/security/changepasswordfromemail?sg=p7ukcp3cO7E4tdJvTIIRYcCZOn00CXsxktOhnaYV7LaoXtBV0Ky9M0RiKaLJ7DfpCHkZgtuG9J\%2FE\%2BYSXX1yZIQ\%3D\%3D\&mp=IF2xtq5gnfkNsqPhgnhLAeqn1UVloTkOOf90lwpSwmc\%3D\&ds=jd3t3HpCkgS\%2FDlXz46jLEaoUGKx\%2BPGiZr3Xl1ufgD1Y\%3D}, - file = {/Users/renatadiaz/Zotero/storage/UJIGWGZW/changepasswordfromemail.html} -} - -@misc{zotero-48, - title = {{{SecureCartCheckout}} | ==== {{PARK AVE CDs}}: {{Orlando}}'s {{Finest Music Emporium}}! ====}, - shorttitle = {{{SecureCartCheckout}} | ==== {{PARK AVE CDs}}}, - howpublished = {https://parkavecds.com/SecureCartCheckout}, - langid = {english}, - file = {/Users/renatadiaz/Zotero/storage/AE6JZL78/SecureCartCheckout.html} -} - -@misc{zotero-71, - title = {The {{Carpentries Code}} of {{Conduct}} \textemdash{} {{The Carpentries Handbook}} Documentation}, - howpublished = {https://docs.carpentries.org/topic\_folders/policies/code-of-conduct.html}, - file = {/Users/renatadiaz/Zotero/storage/XY8IG34I/code-of-conduct.html} -} diff --git a/review_edits.md b/review_edits.md deleted file mode 100644 index 3b1a0b1..0000000 --- a/review_edits.md +++ /dev/null @@ -1,356 +0,0 @@ ---- -editor_options: - markdown: - wrap: 72 ---- - -# R1 - -Review Comments (annotations mine :)) - -> This is a useful, well-documented package with a clear and well -> defined scope. The documentation and vignettes have plenty of examples -> that I think most users should easily be able to follow. In addition -> to suggestions I've made in an earlier comment, I have a few -> suggestions that I think would improve the package documentation and -> align the source code better with best practices. - -> Working through the five vignettes, I did wonder if the vignette -> ordering and organization should be re-worked. For me, I found the -> population vignette to be the most useful for understanding what the -> package is actually doing under the hood. After working through this -> vignette, the community vignette made more sense to me. The species -> vignette covers an intermediate-level topic, so probably belongs next, -> followed by scaling since it's a more advanced topic that many users -> won't require knowledge of. Both the README and the "Getting Started" -> vignette contain essentially no code. This feels like missed -> opportunity to shown some of the most basic functionality, e.g. -> simulate a population of a single species and plot a histogram and/or -> simulate a community. Finally, there is fair amount of duplication in -> the vignettes, which makes me wonder if some of them could be combined -> together into one? All this may just be personal preference though, -> and other users may find the current organization better, but -> something to think about. - -Thanks for the feedback! The vignettes have been re-organized. Most of the content from the "population" and "community" vignettes have been consolidated into the "Getting Started" vignette, with smaller examples shown in the README. The "species", "scaling", and "BBS Data" vignettes have remained as separate articles, because those are more in-depth dives into specific subtopics that may be of interest to subpopulations of users. - -> This package relies heavily on BBS data in all examples and package -> functionality. Given its prominence, I think there could more -> description of what the BBS is and the structure of the dataset. I -> initially assumed the bbs-data vignette would cover this, but it -> mostly duplicates what's already found in the community vignette -> without providing additional explanation of the BBS. I think at the -> very least a brief description of the route/stop structure, sampling -> design, and spatial/temporal coverage of the BBS is warranted. Also, I -> see the fields of demo_route_raw are described in the help for that -> dataset, but I think you should point users to that help file or -> directly include a description of the fields in the bbs-data vignette. -> I don't think you need to get into extensive detail since all of this -> is explained in other places, which you've referenced, but you should -> provide at least some explanation. - - -This is really helpful outside perspective! In this revision: - -- There is additional context on the Breeding Bird Survey, including methods and its connection to this project, in the README. -- There is a direct link from the BBS Data vignette to the help page for `demo_route_raw`, which includes (brief) explanations of the column names, and a link to the main BBS data page for further information. - -> Defining species in function arguments could be clarified. In the -> arguments to pop_generate() and species_define(), species can be -> identified either by AOU code or scientific name. Given that both -> genus and species are required, it feels more intuitive to me to use a -> single argument (e.g. scientific_name). The documentation also doesn't -> make it clear that species is the species' epithet and not the -> scientific or common name. As it stands, it feels like you should be -> able to call pop_generate(100, species = "Selasphorus calliope") or -> even pop_generate(100, species = "Calliope Hummingbird"). - -In this version, the `genus` + `species` designation has been replaced by a single argument, `scientific_name`. - -In this revision, I did _not_ try to implement name matching based on the common name. My reasoning here was that the common name would be more prone to variations in spelling, etc, and so matching common names would be another layer of computational infrastructure. This does seem like a good feature to add in later iterations, or one that I could put more thought into if it seems like it would be very widely used! - -> I wonder if the \_summarize() functions are necessary since they're -> essentially just calling group_by() %\>% summarize(). Personally I'd -> prefer to do this directly myself with dplyr so I know exactly what's -> going on and the vignettes could demonstrate exactly how users should -> do it. However, I can imagine that some users aren't as comfortable -> with dplyr so these convenience functions could be useful. - -I agree. In this version, the `*summarize` functions are removed. I added a short demo of computing summary values using `dplyr` in the Getting Started vignette. (This also made it easier to remove tidyverse dependencies, see later comments!) - -> The internal function ind_draw() seems dangerous to me since it has a -> while loop to get rid of negative sizes with potential to run for a -> very long time. This is especially true because there appears to be no -> checks to ensure the mean size is positive. For example the following -> will run indefinitely: - -> pop_generate(1000, mean_size = -1000, sd_size = 0.001) - -> At the very least, please add a check to ensure mean_size and sd_size -> are positive and some method to ensure the while loop won't run -> forever, e.g. after a certain number of iterations maybe it should -> stop and raise an error. Even better would be re-writing this function -> to use a less brute force method to ensure the sizes generated aren't -> negative. It's not immediately clear what that would look like, since -> simple solutions like take the absolute value, won't preserve the -> desired normal distribution. - -Wow, thank you for recognizing this! This completely did not occur to me, but is of course a significant potential bug! - -In this version, I've taken the suggestion to use `truncnorm::rtruncnorm` to draw from a normal distribution truncated with a lower bound of 1 (i.e. 1 gram of bird). Additionally, `pop_generate` now issues a message if the combined mean and standard deviations provided are likely to produce negative values. - -> Some additional, specific comments about the code: - -> ``` -> I believe the standard for documenting package datasets is to document them all in R/data.R rather than individual R files. Not a huge issue, but I think this would help anyone interested find the source for the documentation more easily. See https://r-pkgs.org/data.html#sec-documenting-data. -> ``` - -Ah, ok! The dataset documentation is now all in R/data.R. - -> ``` -> Related to the previous point, you might consider renaming or re-grouping some of the other source files. For example, the only exported function in R/simulate_populations.R is pop_generate(), so why not call that file R/pop_generate.R so it's more obvious what's in the file? -> ``` - -I've rearranged the functions and tried to create a closer match between the functions in a file and the file name. I've kept some single-function scripts (ind_draw.R, pop_generate.R) and grouped others thematically. I hope this is easier to navigate? - -> dplyr has deprecated or superseded a lot of the "scoped" verbs, e.g. -> group_by_at(). Please replace these as appropriate to future proof -> your package. See <https://dplyr.tidyverse.org/reference/scoped.html> - -Yikes, and this is good to keep in mind. I've removed all `dplyr` verbs except for those in the vignette. - -> I see some inconsistency in code styling. For example, in some places -> you use if() and in other places if (). I recommend picking one method -> of formatting your code and sticking with it. See -> <https://style.tidyverse.org/>. - -I've reformatted the code using `styler`. - -> In a few places I see you're using as.numeric(NA) or is.character(NA) -> (e.g. -> <https://github.com/diazrenata/birdsize/blob/main/R/species_define.R#L56>). -> Note that there are NAs specifically for different data types, i.e. -> NA_real\_ and NA_character\_. It seems cleaner to use these rather -> than casting NA to different data types. - -I've replaced nonspecific NAs with data-type-specific NAs. - -> There are a handful of unnecessarily nested if statements (e.g. -> <https://github.com/diazrenata/birdsize/blob/main/R/species_define.R#L54>). -> Anywhere you have if (A) {if (B) {...}} I think it's cleaner to use if -> (A && B) {...}, but that may just be personal preference. - -I've kept these mostly as written, perhaps because it's just much easier for me to parse. -I'm happy to revisit this! - -# R2 - -> I think the purpose of the package is well-defined. It does a few -> well-defined and related tasks, and does them well. It also has -> demonstrated use cases, which is nice. The vignettes were -> well-organized and do a good job of providing examples of all the -> functions. I've divided my comments into three categories: code style, -> documentation, and "science stuff." - -> Code style review - -> The DESCRIPTION file states that the package depends on R \>=2.10 but -> the tidyverse dependencies require R \>= 3.3. - -With the removal of tidyverse dependencies, I _believe_ R >= 2.10 will be sufficient. - -> I agree with Matt that the documentation of the package datasets -> should be in one data.R file which is a little easier to navigate -> (though this is not too relevant to users as they won't ever see that, -> but it would be helpful for contributors) - -Absolutely! The dataset documentation is now consolidated in data.R. - -> This is a tough one, but I generally try to shy away from having -> tidyverse dependencies in packages. For example the lines with -> dplyr::mutate() could be rewritten from - -> community \<- community %\>% dplyr::mutate( richnessSpecies = -> .data\$aou, species_designator = "aou" ) -> -> to -> -> community[['richnessSpecies']] \<- community[['aou']] -> community[['species_designator']] \<- "aou" - -> I understand this would be a lot of work to implement because -> tidyverse is used in most of your functions. If you do not want to -> fully remove the tidyverse dependencies, the most urgent one to -> address would be to replace dplyr::group_by_at() with -> dplyr::group_by(dplyr::across()). group_by_at() has been deprecated -> and will likely be removed from future versions of dplyr. (I'm in -> agreement with Matt's advice on that point). - -> ``` -> Also, having tidyverse dependencies greatly increases the number of downstream dependencies for the package which might not be desirable. -> ``` - -These comments (and conversations outside this) encourage me to move -away from tidyverse dependencies. In this revision, the tidyverse packages are removed, except for examples shown in the vignettes. - -> I also agree with Matt that it would be good to at least rewrite the -> code not to use the magrittr pipes %\>% for the reasons he cited. - -This revision has removed the magrittr pipe. The examples use the new base R pipe (`|>`). - -> ``` -> In filter_bbs_survey(), package data are loaded with unidentified_species <- unidentified_species. I am not sure that is the recommended way to internally use package data. I noticed Matt also brought this up so I would follow his advice there. -> ``` - -I've removed these calls loading internal data. This has introduced the NOTES of "no visible binding for global variable". [RMD - Check that this is still the case when next connected to wifi] - -> In simulate_populations(), the error checking routines that cause -> failure if things like mean and standard deviation aren't provided is -> one level down in the ind_draw() function. To me it would make more -> sense if the input is checked for errors right away instead of further -> down. - -This version has the error checking occurring at both levels. This makes it slightly easier to trace if a user is running `pop_generate` (new name for `simulate_populations`), and keeps the guardrails on within `ind_draw` as well. - -> Line 33 of species_data_functions.R: the argument data to lm() should -> be named. - -Done! (Now at line 24). - -> Documentation review - -> ``` -> I thought the vignettes were well-organized and do a good job of providing examples of all the functions. One suggestion is that the vignettes could have more informative titles. Just the word community does not make it clear exactly what can be learned from going through the vignette. -> ``` - -I hope this is addressed by re-organizing the vignettes so most of the general-purpose information is in "Getting Started", and the remaining vignettes have clear, specific content (BBS data, scaling relationship, species definitions). - -> I also liked the Taylor Swift example but shouldn't the species be -> Taylor and the genus Swift? :-D - -Noted, and updated. :D - -> A user copying and pasting code from the vignettes will not be able to -> run the code containing tidyverse functions including select() and -> pmap_df() because those packages are not explicitly loaded in the -> vignette. - -The package calls have been made visible in the vignettes. - -> The term "AOU" should be defined somewhere - it is known to North -> Americans but not otherwise. I understand this package is most -> intended for use with BBS so users will be familiar but it can't hurt -> to define so that other people can understand what it is (maybe not -> necessarily the user but someone looking over the code). A related -> minor point: in some of the functions where AOU is an argument, it is -> in lowercase aou but I think it would be more consistent to make it -> capitalized AOU. - -I've expanded references to the AOU in the vignettes and code documentation to the "AOU numeric code" and added links to the BBS page. I've also capitalized user-facing instances of "AOU". - -Interestingly, in doing this I found that the BBS AOUs appear to differ from the (more recent) codes put out by the American Ornithological Union. It looks to me like the AOU itself has switched to four-letter alpha character codes, but the BBS has kept with the (original, I believe) numeric codes. So the only lookup table for the AOU numbers to species is the BBS list, which I have linked to. - -> The bar plot with total biomass by AOU in the community vignette, as -> Matt mentioned, would be more informative with species names instead -> of AOU codes. Also, because the fill color legend is redundant with -> the axis labels, it would be cleaner to just label the x axis with the -> species names and suppress the legend of fill colors. - -This plot has been removed with the vignette rearrangement, but I've updated the other plot legends to use scientific names instead of AOUs. - -> Comments on science stuff - -> I would feel better about it if you explicitly incorporated -> uncertainty in the scaling relationships. The parameters for the -> relationship between body mass mean and standard deviation are average -> expectations, so you would end up underestimating the variation in -> body mass if you only use that mean expectation to impute missing -> standard deviations. Is there any way of incorporating uncertainty in -> those scaling parameters? - -This is a tough question. Generally when _I_ work with this method, -I take the estimated mass and sd as the limit of the precision of this -approach. The uncertainty is also variable among species - for some we -have estimates and some measurements; for some species many measurements -and some just one; and from different locations and times and -investigators. For these reasons, I handle these estimates as -"best-guesses suitable for broad-scale questions, but with some -significant limitations as things get precise". I've added language to this effect in the vignettes and README. - -> It would be nice to allow filter_bbs_survey() to take arguments so -> that the user could customize removing specific species groups. For -> instance it would be interesting if the user could remove only -> waterbirds and keep nocturnal birds, if they were so inclined. - -This is an interesting suggestion. To implement it I would need to expand the database of masses included in the package, which would mean going back to Dunning (2008) - which invites expanding the data further than (necessarily) just the Breeding Bird Survey species. I think this becomes a wider conversation about the scope of data reproduction in the package vs. shifting that onto a user. I haven't implemented it in this revision, but if it seems like a necessary value-add it would be possible. - -> The real heart of the body mass distribution simulation is in the file -> simulate_populations.R in ind_draw() at line 34: - -> population \<- rnorm(n = species_abundance, mean = species_mean, sd = -> species_sd) -> -> while (any(population \< 0)) { population[which(population \< 0)] \<- -> rnorm(n = sum(population \< 0), mean = species_mean, sd = species_sd) -> } - -> This looks like you are doing rejection sampling to generate samples -> from a truncated normal distribution with lower truncation bound of 0. -> I think that is fine, but it should be made clear in the documentation -> that you are doing this. I might even recommend allowing the user to -> input a lower truncation bound instead of hard-coding it at 0 (the -> default could be 0 but you could allow the user to modify this). For -> example the user might want to ensure that all masses are greater than -> 2 grams (that is roughly the lowest value I got when I generated the -> body masses for a_hundred_hummingbirds). Not too many birds weigh less -> than the Calliope Hummingbird! :-) Actually, in general I don't think -> it is clear in your documentation that samples are drawn from a normal -> distribution. Yes, it is implied by the fact that the parameters are -> mean and standard deviation but I think it would be good to be -> explicit about it. I also wanted to address Matt's point that the -> while loop in the rejection sampling may run infinitely or nearly so -> if invalid input is provided such as negative body mass. It would be -> good for you to expand the error checking code to cause failure on -> body mass means that are not positive, avoiding the potential of an -> infinite (or almost infinite loop). - -> ``` -> To further address the point about the rejection sampling method, Matt mentioned in his review that it would be good to use a "less brute force" method to ensure the values are >0. Actually, the method of rejection sampling that you are currently using is a well-accepted method. It is used by the R package truncnorm. For almost any realistic values of body mass mean and sd, you will get very few negative values on the initial sample, so the while loop would hardly ever even be necessary. However, if you are interested in a more direct method of sampling from a truncated normal without the while loop, I would check out [this Stackoverflow thread](https://stats.stackexchange.com/questions/56747/simulate-constrained-normal-on-lower-or-upper-bound-in-r) especially [this answer](https://stats.stackexchange.com/a/510821/54923). There are also the existing functions msm::tnorm() and truncnorm::truncnorm() but you may not want to add a dependency to your package. -> ``` - -This is a really good and important observation (see the earlier response to Matt's comment)! I went ahead and switched over to `truncnorm::rtruncnorm` to avoid the negative-values problem. - -I've also added sections right at the beginning of both the README and Getting Started vignette clarifying the assumption of the normal distribution. - -# Others - -- Regarding @ maelle's comment regarding test files and source file names: I have renamed the test files to correspond more closely to the file names. -- tests fail due to an issue with unzip on windows. 👀 -- I've reached out to Dr. Dunning and he agreed to be listed as a Data Contributor. I've added him with this revision. -- I reviewed the Small Fixes PR from @ mstrimas. Because of the scope of revisions, I ended up not merging that pull request and instead implementing the same changes on the revised codebase. Specifically, I tidied up the DESCRIPTION using desc::desc_normalize(), removed `remotes::install_github` from the README, switched T/F to TRUE/FALSE, and switched 1:nrow() to seq_len(nrow()). = was changed to <- via the lintr cleanup, and use of .data$ was removed with the removal of tidyverse functions. - -# From editor: - -* I'd recommend running desc::desc_normalize(): it will order DESCRIPTION fields in a standard way and order dependencies alphabetically. - * *Response*: Done! -* You can remove the {remotes} installation instructions and keep the {devtools} ones only as {devtools} calls {remotes} (might call {pak} in the future?) and is the interface for users. - * *Response*: Done! -* It'd be nice to add grouping to the reference index https://pkgdown.r-lib.org/reference/build_reference.html#reference-index Given your package's naming scheme, you might want to use the starts_with() helper. - * *Response*: I haven't done this because there are so few functions, it seems to me like it verges on redundant. I'm happy to revisit this! -* In the test filenames, why use numbers? If the R files and test files have the same basename, it's easier to navigate between the two in RStudio IDE. https://r-pkgs.org/testing-basics.html#test-organisation - * *Response*: Ah, I learned to use the numbers so that tests fail informatively in order. The tests also don't - all - correspond directly to RScripts. Is this a major barrier? If so, I'm happy to revisit! -* In your test files and scripts I see a lot of vertical space, more than one empty lines between some elements. I'd recommend using one empty line only as it increases the amount of code one can see at a time on the screen. It's still nice to organize the code in paragraphs, I am not suggesting to remove all empty lines. 😁 - * *Response*: I think this has been largely addressed via the re-styling I've done, but please let me know if the issue persists! -* In the README instead of "Package summary" as a header you could use the same text as this issue "birdsize: Estimate avian body size distributions" which is more informative. - * *Response*: Done! -* Regarding data yes it might make sense to contact the author of the included dataset? - * *Response:* Done! I've reached out and Dr. Dunning agreed to be listed as a contributor. I've sent a more recent-follow up with the revisions and giving him the opportunity to confirm. I'm still waiting to hear back there, and will let you know. -* For comments such as https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/R/simulate_community.R#L51 if you add 4 hyphens afterwards ----, the comment will appear in the script outline on the right in RStudio IDE (if you use that IDE), helping code navigation. https://blog.r-hub.io/2023/01/26/code-comments-self-explaining-code/#use-comments-for-the-scripts-outline - * *Response*: I've added these to the long community_generate script. -* why have this "trivial" test file? https://github.com/diazrenata/birdsize/blob/main/tests/testthat/test-01_trivial.R - * *Response*: I use this to test that CI is working, but it's not needed now the package is built. Deleted! -* in test code you don't need to write birdsize::: as testthat loads your package code. Example https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/tests/testthat/test-02_included_data.R#L13 - * *Response*: These are removed! -* why are some expectations commented out? https://github.com/diazrenata/birdsize/blob/7469df457989a9016ecc3761b0dd125497a3be51/tests/testthat/test-07_simulate_community.R#L34 - * *Response*: These were vestigial, removed! - diff --git a/review_template.md b/review_template.md deleted file mode 100644 index de1f4c0..0000000 --- a/review_template.md +++ /dev/null @@ -1,151 +0,0 @@ -<!--- -Below, please enter values for (1) submitting author GitHub handle (replacing "@github_handle@); and (2) Repository URL (replacing "https://repourl"). Values for additional package authors may also be specified, replacing "@github_handle1", "@github_handle2" - delete these if not needed. DO NOT DELETE HTML SYMBOLS (everything between "<!" and ">"). Replace only "@github_handle" and "https://repourl". This comment may be deleted once it has been read and understood. ----> - -Submitting Author Name: Renata Diaz -Submitting Author Github Handle: <!--author1-->@diazrenata<!--end-author1--> -Repository: <!--repourl-->https://github.com/diazrenata/birdsize<!--end-repourl--> -Version submitted:0.0.0.9000 -Submission type: <!--submission-type-->Standard<!--end-submission-type--> -Editor: <!--editor--> TBD <!--end-editor--> -Reviewers: <!--reviewers-list--> TBD <!--end-reviewers-list--> -<!--due-dates-list--><!--end-due-dates-list--> -Archive: TBD -Version accepted: TBD -Language: <!--language-->en<!--end-language--> ---- - - - -- Paste the full DESCRIPTION file inside a code block below: - -``` -Package: birdsize -Title: Estimate Avian Body Size Distributions -Version: 0.0.0.9000 -Authors@R: - person("Renata", "Diaz", , "renata.diaz@weecology.org", role = c("aut", "cre"), - comment = c(ORCID = "0000-0003-0803-4734")) -Description: Generate estimated body size distributions for populations or communities of birds, given either species ID or species' mean body size. Designed to work naturally with the North American Breeding Bird Survey, or with any dataset of bird species, abundance, and/or mean size data. -License: MIT + file LICENSE -URL: https://github.com/diazrenata/birdsize -BugReports: https://github.com/diazrenata/birdsize/issues -Encoding: UTF-8 -LazyData: true -Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.1 -Suggests: - covr, - ggplot2, - knitr, - rmarkdown, - testthat (>= 3.0.0) -Config/testthat/edition: 3 -Depends: - R (>= 2.10) -Imports: - rlang, - dplyr, - magrittr, - purrr, - stats -VignetteBuilder: knitr - -``` - - -## Scope - -- Please indicate which category or categories from our [package fit policies](https://ropensci.github.io/dev_guide/policies.html#package-categories) this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.): - - - [ ] data retrieval - - [ ] data extraction - - [ ] data munging - - [ ] data deposition - - [ ] data validation and testing - - [ ] workflow automation - - [ ] version control - - [ ] citation management and bibliometrics - - [ ] scientific software wrappers - - [x] field and lab reproducibility tools - - [ ] database software bindings - - [ ] geospatial data - - [ ] text analysis - -- Explain how and why the package falls under these categories (briefly, 1-2 sentences): - - -This package automates a workflow (seen in the wild e.g. [here](https://doi.org/10.1111/j.1466-8238.2010.00576.x) and [here](https://doi.org/10.1101/2022.11.08.515659)) of generating estimates of body size and basal metabolic rate, from the individual to ecosystem level, for birds. In my presubmission inquiry (#561, https://github.com/ropensci/software-review/issues/561), the editors determined this was best described as "field and lab reproducibility tools" because it's automating a workflow used by empirical ecologists to work with field data. - -- Who is the target audience and what are scientific applications of this package? - -The target audience is ecologists/biodiversity scientists interested in studying the structure, function, and dynamics of bird populations and communities - specifically linking between abundances/population size and other dimensions of community function, like total biomass. Studying size-based and abundance-based properties of bird communities is key to understanding biodiversity and global change, but it is challenging for most ecologists because most survey methods do not collect size-related data. This package standardizes a computationally-intensive workaround for this challenge and makes it accessible to ecologists with relatively little computational training. - -- Are there other R packages that accomplish the same thing? If so, how does yours differ or meet [our criteria for best-in-category](https://ropensci.github.io/dev_guide/policies.html#overlap)? - -I have not encountered another package that accomplishes this. - -- (If applicable) Does your package comply with our [guidance around _Ethics, Data Privacy and Human Subjects Research_](https://devguide.ropensci.org/policies.html#ethics-data-privacy-and-human-subjects-research)? - -N/A - -- If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted. - -https://github.com/ropensci/software-review/issues/561 - -The editor who responded to me was @annakrystalli. - -As part of that conversation, the question was raised of adding the authors of some of the datasets that this package draws on as "data contributors". I want to make sure that this is done in the way that best describes the way the data are used. - -This package uses two sources of "external" data: - -- First, the `sd_table` dataset included in the package includes (cleaned and selected) data values hand-entered from the CRC Handbook of Avian Body Masses (Dunning 2008; https://doi.org/10.1201/9781420064452). Neither Dunning, nor the authors of the studies cited in the CRC Handbook, were involved in this project. In the current iteration, I've followed the approach I would use for a paper - that is, the package and package documentation cite Dunning liberally, but I have not listed any additional authors as "data contributors" because I generally wouldn't list folks as co-authors without their knowledge and consent. In this context, would you encourage listing Dunning as a contributor, and/or reaching out to open that conversation? - -- Second, this package is designed to _interface_ with the North American Breeding Bird Survey data (https://www.sciencebase.gov/catalog/item/5d65256ae4b09b198a26c1d7, doi:10.5066/P9HE8XYJ), but I have taken care not to redistribute any actual data from the Breeding Bird Survey in the package itself. The `demo_route_raw` and `demo_route_clean` data tables in `birdsize` are synthetic datasets that mimic data from the Breeding Bird Survey. That is, they have the same column names as BBS data, and valid AOU (species identifying codes) values, but the actual data values are simulated. The `bbs-data` vignette directs users to instructions for accessing the BBS data, and demonstrates using the functions in `birdsize` on BBS-*like* data using the demo routes. Again, the package cites the Breeding Bird Survey liberally, but stops short of redistributing data so as to encourage users to access and cite the creators directly. - -For both of these, again, I'm happy to explore whatever approaches to citing/crediting the original data creators seems most appropriate! I'd appreciate any thoughts or guidance in this area. - - -- Explain reasons for any [`pkgcheck` items](https://docs.ropensci.org/pkgcheck/) which your package is unable to pass. - -N/A - -## Technical checks - -Confirm each of the following by checking the box. - -- [x] I have read the [rOpenSci packaging guide](https://devguide.ropensci.org/building.html). -- [x] I have read the [author guide](https://devdevguide.netlify.app/authors-guide.html) and I expect to maintain this package for at least 2 years or to find a replacement. - -This package: - -- [x] does not violate the Terms of Service of any service it interacts with. -- [x] has a CRAN and OSI accepted license. -- [x] contains a [README with instructions for installing the development version](https://ropensci.github.io/dev_guide/building.html#readme). -- [x] includes [documentation with examples for all functions, created with roxygen2](https://ropensci.github.io/dev_guide/building.html#documentation). -- [x] contains a vignette with examples of its essential functions and uses. -- [x] has a [test suite](https://ropensci.github.io/dev_guide/building.html#testing). -- [x] has [continuous integration](https://ropensci.github.io/dev_guide/ci.html), including reporting of test coverage. - -## Publication options - -- [ ] Do you intend for this package to go on CRAN? *tbd* -- [ ] Do you intend for this package to go on Bioconductor? - -- [X] Do you wish to submit an Applications Article about your package to [Methods in Ecology and Evolution](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/)? If so: - -<details> -<summary>MEE Options</summary> - -- [x] The package is novel and will be of interest to the broad readership of the journal. -- [x] The manuscript describing the package is no longer than 3000 words. -- [x] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) -- (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) -- (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) -- (*Please do not submit your package separately to Methods in Ecology and Evolution*) - -</details> - -## Code of conduct - -- [x] I agree to abide by [rOpenSci's Code of Conduct](https://ropensci.org/code-of-conduct/) during the review process and in maintaining my package should it be accepted. diff --git a/tests/testthat/test-06_community_generate.R b/tests/testthat/test-community_generate.R similarity index 100% rename from tests/testthat/test-06_community_generate.R rename to tests/testthat/test-community_generate.R diff --git a/tests/testthat/test-08_direct_bbs_data.R b/tests/testthat/test-direct_bbs_data.R similarity index 100% rename from tests/testthat/test-08_direct_bbs_data.R rename to tests/testthat/test-direct_bbs_data.R diff --git a/tests/testthat/test-05_filter_bbs_data.R b/tests/testthat/test-filter_bbs_survey.R similarity index 100% rename from tests/testthat/test-05_filter_bbs_data.R rename to tests/testthat/test-filter_bbs_survey.R diff --git a/tests/testthat/test-01_included_data.R b/tests/testthat/test-included_data.R similarity index 100% rename from tests/testthat/test-01_included_data.R rename to tests/testthat/test-included_data.R diff --git a/tests/testthat/test-03_ind_draw.R b/tests/testthat/test-ind_draw.R similarity index 100% rename from tests/testthat/test-03_ind_draw.R rename to tests/testthat/test-ind_draw.R diff --git a/tests/testthat/test-07_metabolic_rate.R b/tests/testthat/test-metabolic_rate.R similarity index 100% rename from tests/testthat/test-07_metabolic_rate.R rename to tests/testthat/test-metabolic_rate.R diff --git a/tests/testthat/test-04_pop_generate.R b/tests/testthat/test-pop_generate.R similarity index 100% rename from tests/testthat/test-04_pop_generate.R rename to tests/testthat/test-pop_generate.R diff --git a/tests/testthat/test-02_species_define.R b/tests/testthat/test-species_define.R similarity index 100% rename from tests/testthat/test-02_species_define.R rename to tests/testthat/test-species_define.R