Merge branch 'master' of github.com:weecology/portalPredictions into …

…adjust_report

PortalHindcasts.R

@@ -15,12 +15,31 @@ forecast_date = Sys.Date()
 #Hindcast will set the time based on these NewMoonNumbers. For each one
 #a hindcast will be made which pretends that sampleing period had just happened. 
 #403 to 490 is Jan,2010 - Jan,2017. 
-initial_time_NewMoons=403:490
+initial_time_newmoons=403:490
 
-for(this_NewMoon in initial_time_NewMoons){
+trappings = read.csv(FullPath('PortalData/Rodents/Portal_rodent_trapping.csv', '~'))
+incomplete_samples = portalr::find_incomplete_censuses(trappings)
+
+for(this_newmoon in initial_time_newmoons){
+
+  moons = get_moon_data()
+
+  this_newmoon_sampling_date = moons %>%
+    filter(newmoonnumber == this_newmoon) %>%
+    pull(censusdate)
+
+  this_newmoon_period = moons %>%
+    filter(newmoonnumber == this_newmoon) %>%
+    pull(period)
+
+  #Don't do hindcasting from newmoons that had incomplete samplings
+  #or were not sampled at all
+  if(this_newmoon_period %in% incomplete_samples$period | is.na(this_newmoon_sampling_date)){
+    next
+  }
 
   moons = get_moon_data() %>%
-    filter(newmoonnumber<=this_NewMoon)
+    filter(newmoonnumber<=this_newmoon)
 
   #Beginning and end of the forecast timeperiod
   most_recent_newmoon = moons$newmoonnumber[which.max(moons$period)]
@@ -33,12 +52,12 @@ for(this_NewMoon in initial_time_NewMoons){
 
   rodent_data = get_rodent_data(moons, forecast_date, filename_suffix)
   rodent_data$all = rodent_data$all %>%
-    filter(newmoonnumber <= this_NewMoon)
+    filter(newmoonnumber <= this_newmoon)
   rodent_data$controls = rodent_data$controls %>%
-    filter(newmoonnumber <= this_NewMoon)
+    filter(newmoonnumber <= this_newmoon)
 
   weather_data = get_weather_data(moons, rodent_data$all, first_forecast_newmoon, last_forecast_newmoon) %>%
-    filter(newmoonnumber <= this_NewMoon)
+    filter(newmoonnumber <= this_newmoon)
 
   #Get only relevent columns now that this is isn't needed to subset weather.
   rodent_data$all = rodent_data$all %>%
@@ -49,7 +68,7 @@ for(this_NewMoon in initial_time_NewMoons){
   zero_abund_forecast = list(pred=rep(0,12), interval=matrix(rep(0,24), ncol=2))
   colnames(zero_abund_forecast$interval) = c('lower','upper')
 
-  allforecasts=forecastall(rodent_data$all,"All",weather_data,weathermeans, forecast_date, forecast_newmoons, forecast_months, forecast_years)
-  controlsforecasts=forecastall(rodent_data$controls,"Controls",weather_data,weathermeans, forecast_date, forecast_newmoons, forecast_months, forecast_years)
+  allforecasts=try(forecastall(rodent_data$all,"All",weather_data,weathermeans, forecast_date, forecast_newmoons, forecast_months, forecast_years))
+  controlsforecasts=try(forecastall(rodent_data$controls,"Controls",weather_data,weathermeans, forecast_date, forecast_newmoons, forecast_months, forecast_years))
 
-}
+}

about.md

@@ -1,10 +1,20 @@
 ---
 title: "About Portal Forecasts"
 ---
+<br>
 
-# Who we are
+# The Portal Project
 
-# What is Portal?
+[The Portal project](http://portal.weecology.org/), located in the Chihuahuan desert of southern Arizona, is a long-term experimental monitoring project in desert ecology. There are over 40 years of data on rodents, plants, ants, and weather at the site. Rodent data are collected approximately monthly, an ideal scenario for short-term forecasts of rodent abundance.
 
-#What is this?
-There is a need for short term iterative forecasts in Ecology. To this end we are forecasting rodent abundances for our monthly sampling
+<br>
+
+# Ecological Forecasting
+
+There is a need for short term iterative forecasts in ecology. We are using our monthly rodent trapping to create a platform for automated and validated forecasting.
+
+<br>
+
+# [Weecology](http://weecology.org/) 
+
+We are a group of ecologists at the University of Florida, interested in collaborative approaches to ecology, open science, and open data.

docs/about.html

@@ -204,15 +204,20 @@ <h1 class="title toc-ignore">About Portal Forecasts</h1>
 </div>
 
 
-<div id="who-we-are" class="section level1">
-<h1>Who we are</h1>
+<p><br></p>
+<div id="the-portal-project" class="section level1">
+<h1>The Portal Project</h1>
+<p><a href="http://portal.weecology.org/">The Portal project</a>, located in the Chihuahuan desert of southern Arizona, is a long-term experimental monitoring project in desert ecology. There are over 40 years of data on rodents, plants, ants, and weather at the site. Rodent data are collected approximately monthly, an ideal scenario for short-term forecasts of rodent abundance.</p>
+<p><br></p>
 </div>
-<div id="what-is-portal" class="section level1">
-<h1>What is Portal?</h1>
+<div id="ecological-forecasting" class="section level1">
+<h1>Ecological Forecasting</h1>
+<p>There is a need for short term iterative forecasts in ecology. We are using our monthly rodent trapping to create a platform for automated and validated forecasting.</p>
+<p><br></p>
 </div>
-<div id="what-is-this" class="section level1">
-<h1>What is this?</h1>
-<p>There is a need for short term iterative forecasts in Ecology. To this end we are forecasting rodent abundances for our monthly sampling</p>
+<div id="weecology" class="section level1">
+<h1><a href="http://weecology.org/">Weecology</a></h1>
+<p>We are a group of ecologists at the University of Florida, interested in collaborative approaches to ecology, open science, and open data.</p>
 </div>