diff --git a/404.html b/404.html
index ed1063d..6c0d095 100644
--- a/404.html
+++ b/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="http://www.schlosslab.org/Clustur/index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,6 +36,7 @@
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
 </form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch">
@@ -64,7 +65,7 @@ <h1>Page not found (404)</h1>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/LICENSE-text.html b/LICENSE-text.html
new file mode 100644
index 0000000..104ef7b
--- /dev/null
+++ b/LICENSE-text.html
@@ -0,0 +1,63 @@
+<!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, shrink-to-fit=no"><title>License • clustur</title><script src="lightswitch.js"></script><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top " aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="index.html">clustur</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/clustur.html">clustur</a></li>
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
+  <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="dark"><span class="fa fa-moon"></span> Dark</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="auto"><span class="fa fa-adjust"></span> Auto</button></li>
+  </ul></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-title-body">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>License</h1>
+
+    </div>
+
+<pre>YEAR: 2024
+COPYRIGHT HOLDER: clustur authors
+</pre>
+
+  </main></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/LICENSE.html b/LICENSE.html
new file mode 100644
index 0000000..ed3eb16
--- /dev/null
+++ b/LICENSE.html
@@ -0,0 +1,67 @@
+<!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, shrink-to-fit=no"><title>MIT License • clustur</title><script src="lightswitch.js"></script><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="MIT License"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top " aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="index.html">clustur</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/clustur.html">clustur</a></li>
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
+  <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="dark"><span class="fa fa-moon"></span> Dark</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="auto"><span class="fa fa-adjust"></span> Auto</button></li>
+  </ul></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-title-body">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>MIT License</h1>
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/LICENSE.md" class="external-link"><code>LICENSE.md</code></a></small>
+    </div>
+
+<div id="mit-license" class="section level1">
+
+<p>Copyright (c) 2024 clustur authors</p>
+<p>Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:</p>
+<p>The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.</p>
+<p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
+</div>
+
+  </main></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/articles/clustur.html b/articles/clustur.html
index b23a066..b98aff7 100644
--- a/articles/clustur.html
+++ b/articles/clustur.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,6 +36,7 @@
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
 </form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch">
@@ -60,7 +61,7 @@
       <h1>clustur</h1>
             
       
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/vignettes/clustur.Rmd" class="external-link"><code>vignettes/clustur.Rmd</code></a></small>
       <div class="d-none name"><code>clustur.Rmd</code></div>
     </div>
 
@@ -79,8 +80,8 @@ <h2 id="starting-up">Starting Up<a class="anchor" aria-label="anchor" href="#sta
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># install via github</span></span>
 <span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"SchlossLab/Clustur"</span><span class="op">)</span></span></code></pre></div>
-<p>clustur was developed to be similar to the <a href="https://www.mothur.org" class="external-link">mothur implementation</a> that was written
-in C++, however there are a few differences to note. In order to cluster
+<p>clustur was developed to be similar to the <a href="https://mothur.org" class="external-link">mothur implementation</a> that was written in
+C++, however there are a few differences to note. In order to cluster
 your data, we are requiring users to build out there own sparse matrix
 (we also support phylip files) and count table in R or mothur. Once
 these objects are built out you can call the cluster function. We
@@ -199,7 +200,7 @@ <h3 id="output-data-from-clustering">Output data from clustering<a class="anchor
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/articles/index.html b/articles/index.html
index 910efd4..d50e20b 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +19,7 @@
 <li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -47,7 +48,7 @@ <h3>All vignettes</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/authors.html b/authors.html
index 091463a..130cb98 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +19,7 @@
 <li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -40,24 +41,28 @@ <h1>Authors and Citation</h1>
       <h2>Authors</h2>
 
       <ul class="list-unstyled"><li>
-          <p><strong>Gregory Johnson</strong>. Maintainer.
+          <p><strong>Gregory Johnson</strong>. Author. <a href="https://orcid.org/0009-0008-3890-0297" 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>Patrick Schloss</strong>. Author, maintainer, copyright holder. <a href="https://orcid.org/0000-0002-6935-4275" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
       </ul></div>
 
     <div class="section level2">
       <h2 id="citation">Citation</h2>
-      <p></p>
+      <p><small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Johnson G (2024).
-<em>clustur: What the Package Does in One 'Title Case' Line</em>.
-R package version 1.0, <a href="http://www.schlosslab.org/Clustur/">http://www.schlosslab.org/Clustur/</a>.
+      <p>Johnson G, Schloss P (2024).
+<em>clustur: Clustering</em>.
+R package version 0.1, https://github.com/SchlossLab/Clustur, <a href="http://www.schlosslab.org/Clustur/">http://www.schlosslab.org/Clustur/</a>.
 </p>
       <pre>@Manual{,
-  title = {clustur: What the Package Does in One 'Title Case' Line},
-  author = {Gregory Johnson},
+  title = {clustur: Clustering},
+  author = {Gregory Johnson and Patrick Schloss},
   year = {2024},
-  note = {R package version 1.0},
+  note = {R package version 0.1, https://github.com/SchlossLab/Clustur},
   url = {http://www.schlosslab.org/Clustur/},
 }</pre>
     </div>
@@ -67,7 +72,7 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/index.html b/index.html
index bcf8012..7998f05 100644
--- a/index.html
+++ b/index.html
@@ -5,14 +5,14 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<title>What the Package Does in One Title Case Line • clustur</title>
+<title>Clustering • clustur</title>
 <script src="lightswitch.js"></script><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
 <link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
-<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="What the Package Does in One Title Case Line">
-<meta name="description" content="One paragraph description of what the package does as one or more full sentences.">
-<meta property="og:description" content="One paragraph description of what the package does as one or more full sentences.">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Clustering">
+<meta name="description" content="A tool that implements the clustering algorithms from mothur (Schloss PD et al. (2009) &lt;doi:10.1128/AEM.01541-09&gt;). Clustur make use of the cluster and make.shared command from mothur. The cluster command has five different algorithms implemented: opticlust, furthest, nearest, average, and weighted. Opticlust is an optimized OTU clustering algorithm, and you can learn more here, (Westcott SL, Schloss PD (2017) &lt;doi:10.1128/mspheredirect.00073-17&gt;). The make.shared command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.">
+<meta property="og:description" content="A tool that implements the clustering algorithms from mothur (Schloss PD et al. (2009) &lt;doi:10.1128/AEM.01541-09&gt;). Clustur make use of the cluster and make.shared command from mothur. The cluster command has five different algorithms implemented: opticlust, furthest, nearest, average, and weighted. Opticlust is an optimized OTU clustering algorithm, and you can learn more here, (Westcott SL, Schloss PD (2017) &lt;doi:10.1128/mspheredirect.00073-17&gt;). The make.shared command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.">
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,6 +38,7 @@
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
 </form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch">
@@ -53,7 +54,8 @@
   </div>
 </nav><div class="container template-home">
 <div class="row">
-  <main id="main" class="col-md-9"><div class="section level1">
+  <main id="main" class="col-md-9">
+<div class="section level1">
 <div class="page-header"><h1 id="mothur">mothur<a class="anchor" aria-label="anchor" href="#mothur"></a>
 </h1></div>
 <p>mothur is an open-sourced software used for the analysis of ecological data. It has a strong presence in the use of analyzing 16S rRNA gene sequences. mothur itself has a plethora of features, such as, clustering based on genetic similarity, sequence alignment, taxomic assignment, alpha and beta diversity, and phylotype analysis. There have been numerous publications using this software by individuals and intuitions alike. We plan to take advantage of the power of mothur, and isolate the clustering feature. We believe this will allow scientist to work with a familiar tool and give rise for the creation of more pipelines utilizing this package.</p>
@@ -75,7 +77,7 @@ <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
 <div class="section level2">
 <h2 id="getting-started">Getting Started<a class="anchor" aria-label="anchor" href="#getting-started"></a>
 </h2>
-<p>To get started, look at the <a href="">“Getting started”</a> page.</p>
+<p>To get started, look at the <a href="www.schlosslab.org/Clustur/">“Getting started”</a> page.</p>
 </div>
 <div class="section level2">
 <h2 id="contributions">Contributions<a class="anchor" aria-label="anchor" href="#contributions"></a>
@@ -84,10 +86,19 @@ <h2 id="contributions">Contributions<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 
-  </main><aside class="col-md-3"><div class="license">
+  </main><aside class="col-md-3"><div class="links">
+<h2 data-toc-skip>Links</h2>
+<ul class="list-unstyled">
+<li><a href="https://github.com/SchlossLab/Clustur/" class="external-link">Browse source code</a></li>
+<li><a href="https://github.com/SchlossLab/Clustur/issues" class="external-link">Report a bug</a></li>
+</ul>
+</div>
+
+<div class="license">
 <h2 data-toc-skip>License</h2>
 <ul class="list-unstyled">
-<li>GPL (&gt;= 2)</li>
+<li><a href="LICENSE.html">Full license</a></li>
+<li><small><a href="https://opensource.org/licenses/mit-license.php" class="external-link">MIT</a> + file <a href="LICENSE-text.html">LICENSE</a></small></li>
 </ul>
 </div>
 
@@ -102,18 +113,27 @@ <h2 data-toc-skip>Citation</h2>
 <div class="developers">
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
-<li>Gregory Johnson <br><small class="roles"> Maintainer </small>  </li>
+<li>Gregory Johnson <br><small class="roles"> Author </small> <a href="https://orcid.org/0009-0008-3890-0297" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Patrick Schloss <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0002-6935-4275" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 </ul>
 </div>
 
-
+<div class="dev-status">
+<h2 data-toc-skip>Dev status</h2>
+<ul class="list-unstyled">
+<li><a href="https://github.com/SchlossLab/Clustur/actions/workflows/check-full.yml" class="external-link"><img src="https://github.com/SchlossLab/Clustur/actions/workflows/check-full.yml/badge.svg" alt="R-CMD-check"></a></li>
+<li><a href="https://github.com/SchlossLab/Clustur/actions/workflows/test-coverage.yml" class="external-link"><img src="https://github.com/SchlossLab/Clustur/actions/workflows/test-coverage.yml/badge.svg" alt="test-coverage"></a></li>
+<li><a href="https://github.com/SchlossLab/Clustur/actions/workflows/lintr.yml" class="external-link"><img src="https://github.com/SchlossLab/Clustur/actions/workflows/lintr.yml/badge.svg" alt="lint"></a></li>
+<li><a href="https://github.com/SchlossLab/Clustur/actions/workflows/pkgdown.yaml" class="external-link"><img src="https://github.com/SchlossLab/Clustur/actions/workflows/pkgdown.yaml/badge.svg" alt="pkgdown"></a></li>
+</ul>
+</div>
 
   </aside>
 </div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/news/index.html b/news/index.html
new file mode 100644
index 0000000..b872727
--- /dev/null
+++ b/news/index.html
@@ -0,0 +1,63 @@
+<!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, shrink-to-fit=no"><title>Changelog • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top " aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">clustur</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/clustur.html">clustur</a></li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
+  <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="dark"><span class="fa fa-moon"></span> Dark</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="auto"><span class="fa fa-adjust"></span> Auto</button></li>
+  </ul></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-news">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Changelog</h1>
+      <small>Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
+    </div>
+
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.1" id="clustur-01">clustur 0.1<a class="anchor" aria-label="anchor" href="#clustur-01"></a></h2>
+<ul><li>Initial CRAN submission.</li>
+</ul></div>
+  </main></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/pkgdown.yml b/pkgdown.yml
index 2301e8d..68d7949 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   clustur: clustur.html
-last_built: 2024-10-16T20:56Z
+last_built: 2024-10-21T18:42Z
 urls:
   reference: http://www.schlosslab.org/Clustur/reference
   article: http://www.schlosslab.org/Clustur/articles
diff --git a/reference/cluster.html b/reference/cluster.html
index 6f559c1..f805a64 100644
--- a/reference/cluster.html
+++ b/reference/cluster.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +19,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -34,7 +35,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Cluster Description</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/Cluster.R" class="external-link"><code>R/Cluster.R</code></a></small>
       <div class="d-none name"><code>cluster.Rd</code></div>
     </div>
 
@@ -44,7 +45,7 @@ <h1>Cluster Description</h1>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cluster</span><span class="op">(</span><span class="va">distance_object</span>, <span class="va">method</span>, random_seed <span class="op">=</span> <span class="fl">123</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cluster</span><span class="op">(</span><span class="va">distance_object</span>, method <span class="op">=</span> <span class="st">"opti"</span>, random_seed <span class="op">=</span> <span class="fl">123</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -53,7 +54,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 <dl><dt id="arg-distance-object">distance_object<a class="anchor" aria-label="anchor" href="#arg-distance-object"></a></dt>
 <dd><p>The distance object that
-was created using the read_dist function.</p></dd>
+was created using the `read_dist()` function.</p></dd>
 
 
 <dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
@@ -67,28 +68,23 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A list of dataframes that contain abundance, and clustering results.</p>
+    <p>A list of `data.frames` that contain abundance, and clustering results.
+If you used "opti", it will also return clustering metrics.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="co"># Convert Phylip of column file to a sparse matrix</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
 <span class="r-in"><span> <span class="va">cutoff</span> <span class="op">&lt;-</span> <span class="fl">0.2</span></span></span>
 <span class="r-in"><span> <span class="va">count_table</span> <span class="op">&lt;-</span> <span class="fu"><a href="read_count.html">read_count</a></span><span class="op">(</span><span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon.count_table"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">distance_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="read_dist.html">read_dist</a></span><span class="op">(</span><span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon_column.dist"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>                            <span class="va">count_table</span>, <span class="va">cutoff</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> This is a column file. Processing now...</span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span> <span class="co"># The clustur using one of the 5 methods</span></span></span>
-<span class="r-in"><span> <span class="co"># opti</span></span></span>
 <span class="r-in"><span> <span class="va">cluster_results</span> <span class="op">&lt;-</span> <span class="fu">cluster</span><span class="op">(</span><span class="va">distance_data</span>, method <span class="op">=</span> <span class="st">"opti"</span><span class="op">)</span></span></span>
-<span class="r-in"><span> <span class="co"># furthest</span></span></span>
 <span class="r-in"><span> <span class="va">cluster_results</span> <span class="op">&lt;-</span> <span class="fu">cluster</span><span class="op">(</span><span class="va">distance_data</span>, method <span class="op">=</span> <span class="st">"furthest"</span><span class="op">)</span></span></span>
-<span class="r-in"><span> <span class="co"># nearest</span></span></span>
 <span class="r-in"><span> <span class="va">cluster_results</span> <span class="op">&lt;-</span> <span class="fu">cluster</span><span class="op">(</span><span class="va">distance_data</span>, method <span class="op">=</span> <span class="st">"nearest"</span><span class="op">)</span></span></span>
-<span class="r-in"><span> <span class="co"># average</span></span></span>
 <span class="r-in"><span> <span class="va">cluster_results</span> <span class="op">&lt;-</span> <span class="fu">cluster</span><span class="op">(</span><span class="va">distance_data</span>, method <span class="op">=</span> <span class="st">"average"</span><span class="op">)</span></span></span>
-<span class="r-in"><span> <span class="co"># weighted</span></span></span>
 <span class="r-in"><span> <span class="va">cluster_results</span> <span class="op">&lt;-</span> <span class="fu">cluster</span><span class="op">(</span><span class="va">distance_data</span>, method <span class="op">=</span> <span class="st">"weighted"</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
@@ -99,7 +95,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/clustur-package.html b/reference/clustur-package.html
index 37a6735..a4a3c69 100644
--- a/reference/clustur-package.html
+++ b/reference/clustur-package.html
@@ -1,5 +1,9 @@
 <!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, shrink-to-fit=no"><title>clustur: What the Package Does in One 'Title Case' Line — clustur-package • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="clustur: What the Package Does in One 'Title Case' Line — clustur-package"><meta name="description" content="One paragraph description of what the package does as one or more full sentences."><meta property="og:description" content="One paragraph description of what the package does as one or more full sentences."></head><body>
+<!-- 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, shrink-to-fit=no"><title>clustur: Clustering — clustur-package • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="clustur: Clustering — clustur-package"><meta name="description" content="A tool that implements the clustering algorithms from mothur (Schloss PD et al. (2009) doi:10.1128/AEM.01541-09
+). Clustur make use of the 'cluster' and 'make.shared' command from mothur. The cluster command has five different algorithms implemented: 'opticlust', 'furthest', 'nearest', 'average', and 'weighted'. Opticlust is an optimized OTU clustering algorithm, and you can learn more here, (Westcott SL, Schloss PD (2017) doi:10.1128/mspheredirect.00073-17
+). The 'make.shared' command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently."><meta property="og:description" content="A tool that implements the clustering algorithms from mothur (Schloss PD et al. (2009) doi:10.1128/AEM.01541-09
+). Clustur make use of the 'cluster' and 'make.shared' command from mothur. The cluster command has five different algorithms implemented: 'opticlust', 'furthest', 'nearest', 'average', and 'weighted'. Opticlust is an optimized OTU clustering algorithm, and you can learn more here, (Westcott SL, Schloss PD (2017) doi:10.1128/mspheredirect.00073-17
+). The 'make.shared' command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +23,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -33,27 +38,36 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
 
-      <h1>clustur: What the Package Does in One 'Title Case' Line</h1>
-
+      <h1>clustur: Clustering</h1>
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/clustur-package.R" class="external-link"><code>R/clustur-package.R</code></a></small>
       <div class="d-none name"><code>clustur-package.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>One paragraph description of what the package does as one or more full sentences.</p>
+    <p>A tool that implements the clustering algorithms from mothur (Schloss PD et al. (2009) <a href="https://doi.org/10.1128/AEM.01541-09" class="external-link">doi:10.1128/AEM.01541-09</a>
+). Clustur make use of the 'cluster' and 'make.shared' command from mothur. The cluster command has five different algorithms implemented: 'opticlust', 'furthest', 'nearest', 'average', and 'weighted'. Opticlust is an optimized OTU clustering algorithm, and you can learn more here, (Westcott SL, Schloss PD (2017) <a href="https://doi.org/10.1128/mspheredirect.00073-17" class="external-link">doi:10.1128/mspheredirect.00073-17</a>
+). The 'make.shared' command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.</p>
     </div>
 
 
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
     <div class="dont-index"><p>Useful links:</p><ul><li><p><a href="http://www.schlosslab.org/Clustur/">http://www.schlosslab.org/Clustur/</a></p></li>
+<li><p>Report bugs at <a href="https://github.com/SchlossLab/Clustur/issues" class="external-link">https://github.com/SchlossLab/Clustur/issues</a></p></li>
 </ul></div>
     </div>
+    <div class="section level2">
+    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
+    <p><strong>Maintainer</strong>: Patrick Schloss <a href="mailto:pschloss@umich.edu">pschloss@umich.edu</a> (<a href="https://orcid.org/0000-0002-6935-4275" class="external-link">ORCID</a>) [copyright holder]</p>
+<p>Authors:</p><ul><li><p>Gregory Johnson <a href="mailto:grejoh@umich.edu">grejoh@umich.edu</a> (<a href="https://orcid.org/0009-0008-3890-0297" class="external-link">ORCID</a>)</p></li>
+</ul></div>
 
-  </main></div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/create_sparse_matrix.html b/reference/create_sparse_matrix.html
index 0fd8e93..bc1a607 100644
--- a/reference/create_sparse_matrix.html
+++ b/reference/create_sparse_matrix.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,6 +23,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -38,7 +39,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Create Sparse Matrix</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/Cluster.R" class="external-link"><code>R/Cluster.R</code></a></small>
       <div class="d-none name"><code>create_sparse_matrix.Rd</code></div>
     </div>
 
@@ -71,13 +72,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>a sparse matrix.</p>
+    <p>a `dgTMatrix` from the `Matrix` library.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># This will return the path to our example file</span></span></span>
-<span class="r-in"><span> <span class="va">i_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">100</span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">i_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">100</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">j_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">100</span>, <span class="fl">100</span>, <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">x_values</span> <span class="op">&lt;-</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="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">s_matrix</span> <span class="op">&lt;-</span> <span class="fu">create_sparse_matrix</span><span class="op">(</span><span class="va">i_values</span>, <span class="va">j_values</span>, <span class="va">x_values</span><span class="op">)</span></span></span>
@@ -89,7 +89,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/example_path.html b/reference/example_path.html
index 4a5c0e0..cedf30a 100644
--- a/reference/example_path.html
+++ b/reference/example_path.html
@@ -1,9 +1,9 @@
 <!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, shrink-to-fit=no"><title>Example Path — example_path • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example Path — example_path"><meta name="description" content="This function was created as a helper function to generate file paths to our
- internal data. You are able to access this function if you
- want to follow along with the example."><meta property="og:description" content="This function was created as a helper function to generate file paths to our
- internal data. You are able to access this function if you
- want to follow along with the example."></head><body>
+ internal data. You should use this function if you
+ want to follow along with the example, or intereact with the data"><meta property="og:description" content="This function was created as a helper function to generate file paths to our
+ internal data. You should use this function if you
+ want to follow along with the example, or intereact with the data"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,6 +23,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -38,14 +39,14 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Example Path</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/Cluster.R" class="external-link"><code>R/Cluster.R</code></a></small>
       <div class="d-none name"><code>example_path.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>This function was created as a helper function to generate file paths to our
- internal data. You are able to access this function if you
- want to follow along with the example.</p>
+ internal data. You should use this function if you
+ want to follow along with the example, or intereact with the data</p>
     </div>
 
     <div class="section level2">
@@ -58,12 +59,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-file">file<a class="anchor" aria-label="anchor" href="#arg-file"></a></dt>
-<dd><p>The data of the path you are looking to find.</p></dd>
+<dd><p>The file name of the data</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>the path inside of the package of the file.</p>
+    <p>the path to the file as a `chr`.</p>
     </div>
 
     <div class="section level2">
@@ -79,7 +80,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_clusters.html b/reference/get_clusters.html
index 7faf420..f843fcd 100644
--- a/reference/get_clusters.html
+++ b/reference/get_clusters.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, shrink-to-fit=no"><title>Get Clusters — get_clusters • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Clusters — get_clusters"><meta name="description" content="This function returns the cluster data.frame of the cluster object"><meta property="og:description" content="This function returns the cluster data.frame of the cluster object"></head><body>
+<!-- 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, shrink-to-fit=no"><title>Get Clusters — get_clusters • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Clusters — get_clusters"><meta name="description" content="GetClusters returns a `data.frame` of the generated
+clusters from the `cluster()` function."><meta property="og:description" content="GetClusters returns a `data.frame` of the generated
+clusters from the `cluster()` function."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -34,12 +37,13 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Get Clusters</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/cluster_object-getters.R" class="external-link"><code>R/cluster_object-getters.R</code></a></small>
       <div class="d-none name"><code>get_clusters.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This function returns the cluster data.frame of the cluster object</p>
+    <p>GetClusters returns a `data.frame` of the generated
+clusters from the `cluster()` function.</p>
     </div>
 
     <div class="section level2">
@@ -52,12 +56,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-cluster-data">cluster_data<a class="anchor" aria-label="anchor" href="#arg-cluster-data"></a></dt>
-<dd><p>The cluster method output</p></dd>
+<dd><p>The output from the `cluster()` function.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>the cluster data.frame</p>
+    <p>the created cluster `data.frame`.</p>
     </div>
 
     <div class="section level2">
@@ -77,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_count_table.html b/reference/get_count_table.html
index 04542bd..bff13ea 100644
--- a/reference/get_count_table.html
+++ b/reference/get_count_table.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -36,7 +37,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Get Count Table</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/distance_object-getters.R" class="external-link"><code>R/distance_object-getters.R</code></a></small>
       <div class="d-none name"><code>get_count_table.Rd</code></div>
     </div>
 
@@ -55,12 +56,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-distance-object">distance_object<a class="anchor" aria-label="anchor" href="#arg-distance-object"></a></dt>
-<dd><p>The read.dist output object</p></dd>
+<dd><p>The output from the `read.dist()` function.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>a count table data.frame</p>
+    <p>a count_table `data.frame`.</p>
     </div>
 
     <div class="section level2">
@@ -79,7 +80,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_cutoff.html b/reference/get_cutoff.html
index a32f66d..72905d3 100644
--- a/reference/get_cutoff.html
+++ b/reference/get_cutoff.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, shrink-to-fit=no"><title>Get Cutoff — get_cutoff • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Cutoff — get_cutoff"><meta name="description" content="This function returns the cutoff of the cluster object"><meta property="og:description" content="This function returns the cutoff of the cluster object"></head><body>
+<!-- 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, shrink-to-fit=no"><title>Get Cutoff — get_cutoff • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Cutoff — get_cutoff"><meta name="description" content="GetCutoff returns the cutoff of the cluster object from
+the `cluster()` function."><meta property="og:description" content="GetCutoff returns the cutoff of the cluster object from
+the `cluster()` function."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -34,12 +37,13 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Get Cutoff</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/cluster_object-getters.R" class="external-link"><code>R/cluster_object-getters.R</code></a></small>
       <div class="d-none name"><code>get_cutoff.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This function returns the cutoff of the cluster object</p>
+    <p>GetCutoff returns the cutoff of the cluster object from
+the `cluster()` function.</p>
     </div>
 
     <div class="section level2">
@@ -52,12 +56,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-cluster-data">cluster_data<a class="anchor" aria-label="anchor" href="#arg-cluster-data"></a></dt>
-<dd><p>The cluster method output</p></dd>
+<dd><p>The output from the `cluster()` function.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>the cutoff value</p>
+    <p>the cutoff value as a `dbl`</p>
     </div>
 
     <div class="section level2">
@@ -77,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_distance_data_frame.html b/reference/get_distance_data_frame.html
index 405f503..01f90ff 100644
--- a/reference/get_distance_data_frame.html
+++ b/reference/get_distance_data_frame.html
@@ -1,6 +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, shrink-to-fit=no"><title>Get Distance Data Frame — get_distance_data_frame • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Distance Data Frame — get_distance_data_frame"><meta name="description" content="This function will generate a data.frame that contains the distances
-of all the indexes."><meta property="og:description" content="This function will generate a data.frame that contains the distances
+<!-- 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, shrink-to-fit=no"><title>Get Distance Data Frame — get_distance_data_frame • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Distance Data Frame — get_distance_data_frame"><meta name="description" content="This function will generate a `data.frame` that contains the distances
+of all the indexes."><meta property="og:description" content="This function will generate a `data.frame` that contains the distances
 of all the indexes."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -36,12 +37,12 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Get Distance Data Frame</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/distance_object-getters.R" class="external-link"><code>R/distance_object-getters.R</code></a></small>
       <div class="d-none name"><code>get_distance_data_frame.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This function will generate a data.frame that contains the distances
+    <p>This function will generate a `data.frame` that contains the distances
 of all the indexes.</p>
     </div>
 
@@ -55,12 +56,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-distance-object">distance_object<a class="anchor" aria-label="anchor" href="#arg-distance-object"></a></dt>
-<dd><p>The read.dist output object</p></dd>
+<dd><p>The output from the `read.dist()` function.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>a distance data.frame</p>
+    <p>a distance `data.frame`.</p>
     </div>
 
     <div class="section level2">
@@ -79,7 +80,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_metrics.html b/reference/get_metrics.html
index 24bb9f9..f5a3bca 100644
--- a/reference/get_metrics.html
+++ b/reference/get_metrics.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, shrink-to-fit=no"><title>Get Metrics — get_metrics • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Metrics — get_metrics"><meta name="description" content="This function returns the all of the metrics from the cluster object"><meta property="og:description" content="This function returns the all of the metrics from the cluster object"></head><body>
+<!-- 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, shrink-to-fit=no"><title>Get Metrics — get_metrics • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Metrics — get_metrics"><meta name="description" content="GetMetrics returns the generated metrics `data.frame` from the
+`cluster()` function."><meta property="og:description" content="GetMetrics returns the generated metrics `data.frame` from the
+`cluster()` function."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -34,12 +37,13 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Get Metrics</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/cluster_object-getters.R" class="external-link"><code>R/cluster_object-getters.R</code></a></small>
       <div class="d-none name"><code>get_metrics.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This function returns the all of the metrics from the cluster object</p>
+    <p>GetMetrics returns the generated metrics `data.frame` from the
+`cluster()` function.</p>
     </div>
 
     <div class="section level2">
@@ -52,7 +56,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-cluster-data">cluster_data<a class="anchor" aria-label="anchor" href="#arg-cluster-data"></a></dt>
-<dd><p>The cluster method output</p></dd>
+<dd><p>The output from the `cluster()` function.</p></dd>
 
 </dl></div>
     <div class="section level2">
@@ -77,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_shared.html b/reference/get_shared.html
index 93bd6ed..103a4c9 100644
--- a/reference/get_shared.html
+++ b/reference/get_shared.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, shrink-to-fit=no"><title>Get Shared — get_shared • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Shared — get_shared"><meta name="description" content="This function returns the shared data.frame of the cluster object"><meta property="og:description" content="This function returns the shared data.frame of the cluster object"></head><body>
+<!-- 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, shrink-to-fit=no"><title>Get Shared — get_shared • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Shared — get_shared"><meta name="description" content="GetShared retuns the generated abundance `data.frame`
+from the `cluster()` function"><meta property="og:description" content="GetShared retuns the generated abundance `data.frame`
+from the `cluster()` function"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -34,12 +37,13 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Get Shared</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/cluster_object-getters.R" class="external-link"><code>R/cluster_object-getters.R</code></a></small>
       <div class="d-none name"><code>get_shared.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This function returns the shared data.frame of the cluster object</p>
+    <p>GetShared retuns the generated abundance `data.frame`
+from the `cluster()` function</p>
     </div>
 
     <div class="section level2">
@@ -52,7 +56,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-cluster-data">cluster_data<a class="anchor" aria-label="anchor" href="#arg-cluster-data"></a></dt>
-<dd><p>The cluster method output</p></dd>
+<dd><p>The output from the `cluster()` function.</p></dd>
 
 </dl></div>
     <div class="section level2">
@@ -77,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/index.html b/reference/index.html
index db77187..7712927 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +19,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -152,13 +153,19 @@ <h2 id="helper-functions">Helper Functions<a class="anchor" aria-label="anchor"
 
         </dt>
         <dd>Create Sparse Matrix</dd>
+      </dl><dl><dt>
+
+          <code><a href="split_clusters_to_list.html">split_clusters_to_list()</a></code>
+
+        </dt>
+        <dd>Split Clusters to List</dd>
       </dl></div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/read_count.html b/reference/read_count.html
index bfd609d..938a676 100644
--- a/reference/read_count.html
+++ b/reference/read_count.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -36,7 +37,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Read Count</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/Cluster.R" class="external-link"><code>R/Cluster.R</code></a></small>
       <div class="d-none name"><code>read_count.Rd</code></div>
     </div>
 
@@ -60,12 +61,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>a count table data frame.</p>
+    <p>a count table `data.frame`.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># This will return the path to our example file</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">count_table</span> <span class="op">&lt;-</span> <span class="fu">read_count</span><span class="op">(</span><span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon.count_table"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
@@ -75,7 +76,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/read_dist.html b/reference/read_dist.html
index 978a69a..a7cbb43 100644
--- a/reference/read_dist.html
+++ b/reference/read_dist.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,6 +19,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -34,7 +35,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Read Dist Description</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/Cluster.R" class="external-link"><code>R/Cluster.R</code></a></small>
       <div class="d-none name"><code>read_dist.Rd</code></div>
     </div>
 
@@ -44,7 +45,7 @@ <h1>Read Dist Description</h1>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_dist</span><span class="op">(</span><span class="va">distance_file</span>, <span class="va">count_table</span>, <span class="va">cutoff</span>, <span class="va">is_simularity_matrix</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_dist</span><span class="op">(</span><span class="va">distance_file</span>, <span class="va">count_table</span>, <span class="va">cutoff</span>, is_simularity_matrix <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -61,8 +62,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg-cutoff">cutoff<a class="anchor" aria-label="anchor" href="#arg-cutoff"></a></dt>
-<dd><p>The value you wish to use as a cutoff when clustering.
-opti, furthest, nearest, average, or weighted.</p></dd>
+<dd><p>The value you wish to use as a cutoff when clustering.</p></dd>
 
 
 <dt id="arg-is-simularity-matrix">is_simularity_matrix<a class="anchor" aria-label="anchor" href="#arg-is-simularity-matrix"></a></dt>
@@ -72,29 +72,29 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A distance object that contains all your distance information</p>
+    <p>A distance `externalptr` object that contains all your
+distance information.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
-<span class="r-in"><span> <span class="co"># Convert Phylip or column file to a sparse matrix</span></span></span>
-<span class="r-in"><span> <span class="co"># spMatrix requires the use of the matrix library</span></span></span>
-<span class="r-in"><span> <span class="va">i_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">100</span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">i_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">100</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">j_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">100</span>, <span class="fl">100</span>, <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">x_values</span> <span class="op">&lt;-</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="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">s_matrix</span> <span class="op">&lt;-</span> <span class="fu"><a href="create_sparse_matrix.html">create_sparse_matrix</a></span><span class="op">(</span><span class="va">i_values</span>, <span class="va">j_values</span>, <span class="va">x_values</span><span class="op">)</span></span></span>
-<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="va">sparse_count</span> <span class="op">&lt;-</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>
+<span class="r-in"><span>                 Representative_Sequence <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">100</span>,</span></span>
+<span class="r-in"><span>                 total <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span>, times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span> <span class="va">column_path</span> <span class="op">&lt;-</span> <span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon_column.dist"</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">phylip_path</span> <span class="op">&lt;-</span> <span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon_phylip.dist"</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">count_table</span> <span class="op">&lt;-</span> <span class="fu"><a href="read_count.html">read_count</a></span><span class="op">(</span><span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon.count_table"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="va">data_column</span> <span class="op">&lt;-</span> <span class="fu">read_dist</span><span class="op">(</span><span class="va">column_path</span>, <span class="va">count_table</span>, <span class="fl">0.2</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">data_column</span> <span class="op">&lt;-</span> <span class="fu">read_dist</span><span class="op">(</span><span class="va">column_path</span>, <span class="va">count_table</span>, <span class="fl">0.2</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> This is a column file. Processing now...</span>
-<span class="r-in"><span><span class="va">data_phylip</span> <span class="op">&lt;-</span> <span class="fu">read_dist</span><span class="op">(</span><span class="va">phylip_path</span>, <span class="va">count_table</span>, <span class="fl">0.2</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">data_phylip</span> <span class="op">&lt;-</span> <span class="fu">read_dist</span><span class="op">(</span><span class="va">phylip_path</span>, <span class="va">count_table</span>, <span class="fl">0.2</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> This is a phylip file. Processing now...</span>
-<span class="r-in"><span><span class="va">data_sparse</span> <span class="op">&lt;-</span> <span class="fu">read_dist</span><span class="op">(</span><span class="va">s_matrix</span>, <span class="va">count_table</span>, <span class="fl">0.2</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">data_sparse</span> <span class="op">&lt;-</span> <span class="fu">read_dist</span><span class="op">(</span><span class="va">s_matrix</span>, <span class="va">sparse_count</span>, <span class="fl">0.2</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
@@ -104,7 +104,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/split_clusters_to_list.html b/reference/split_clusters_to_list.html
new file mode 100644
index 0000000..6d5ffac
--- /dev/null
+++ b/reference/split_clusters_to_list.html
@@ -0,0 +1,102 @@
+<!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, shrink-to-fit=no"><title>Split Clusters to List — split_clusters_to_list • clustur</title><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split Clusters to List — split_clusters_to_list"><meta name="description" content="`split_clusters_to_list()` will extract clusters from the
+cluster generated `data.frame`. It will then turn those clusters
+into a list. This allows users to more easily visualize their data."><meta property="og:description" content="`split_clusters_to_list()` will extract clusters from the
+cluster generated `data.frame`. It will then turn those clusters
+into a list. This allows users to more easily visualize their data."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top " aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">clustur</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
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+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/clustur.html">clustur</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
+  <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="dark"><span class="fa fa-moon"></span> Dark</button></li>
+    <li><button class="dropdown-item" data-bs-theme-value="auto"><span class="fa fa-adjust"></span> Auto</button></li>
+  </ul></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Split Clusters to List</h1>
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/cluster_data_converters.R" class="external-link"><code>R/cluster_data_converters.R</code></a></small>
+      <div class="d-none name"><code>split_clusters_to_list.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>`split_clusters_to_list()` will extract clusters from the
+cluster generated `data.frame`. It will then turn those clusters
+into a list. This allows users to more easily visualize their data.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">split_clusters_to_list</span><span class="op">(</span><span class="va">cluster</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-cluster">cluster<a class="anchor" aria-label="anchor" href="#arg-cluster"></a></dt>
+<dd><p>The output generated from the `cluster()` function.</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>a named `list` of clusters.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="va">cutoff</span> <span class="op">&lt;-</span> <span class="fl">0.2</span></span></span>
+<span class="r-in"><span> <span class="va">count_table</span> <span class="op">&lt;-</span> <span class="fu"><a href="read_count.html">read_count</a></span><span class="op">(</span><span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon.count_table"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">distance_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="read_dist.html">read_dist</a></span><span class="op">(</span><span class="fu"><a href="example_path.html">example_path</a></span><span class="op">(</span><span class="st">"amazon_column.dist"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                            <span class="va">count_table</span>, <span class="va">cutoff</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> This is a column file. Processing now...</span>
+<span class="r-in"><span> <span class="va">cluster_results</span> <span class="op">&lt;-</span> <span class="fu"><a href="cluster.html">cluster</a></span><span class="op">(</span><span class="va">distance_data</span>, method <span class="op">=</span> <span class="st">"opti"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="va">cluster_list</span> <span class="op">&lt;-</span> <span class="fu">split_clusters_to_list</span><span class="op">(</span><span class="va">cluster_results</span><span class="op">)</span></span></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/validate_count_table.html b/reference/validate_count_table.html
index 2ec0e50..65b422a 100644
--- a/reference/validate_count_table.html
+++ b/reference/validate_count_table.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">clustur</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,6 +21,7 @@
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/SchlossLab/Clustur/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-lightswitch" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true" aria-label="Light switch"><span class="fa fa-sun"></span></button>
   <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="dropdown-lightswitch"><li><button class="dropdown-item" data-bs-theme-value="light"><span class="fa fa-sun"></span> Light</button></li>
@@ -36,7 +37,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
 
       <h1>Validate Count Table</h1>
-
+      <small class="dont-index">Source: <a href="https://github.com/SchlossLab/Clustur/blob/master/R/Cluster.R" class="external-link"><code>R/Cluster.R</code></a></small>
       <div class="d-none name"><code>validate_count_table.Rd</code></div>
     </div>
 
@@ -55,12 +56,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-count-table-df">count_table_df<a class="anchor" aria-label="anchor" href="#arg-count-table-df"></a></dt>
-<dd><p>The count table dataframe object.</p></dd>
+<dd><p>The count table `data.frame` object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A validated count table.</p>
+    <p>A validated count table `data.frame`</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -79,7 +80,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Gregory Johnson.</p>
+  <p>Developed by Gregory Johnson, Patrick Schloss.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/search.json b/search.json
index 9e2243a..38f5836 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"starting-up","dir":"Articles","previous_headings":"","what":"Starting Up","title":"clustur","text":"clustur developed similar mothur implementation written C++, however differences note. order cluster data, requiring users build sparse matrix (also support phylip files) count table R mothur. objects built can call cluster function. currently support 5 cluster methods mothur: furthest, nearest, weighted, average neighbor opticlust, mothur’s default. methods produce data comparable mothur. speed clustur mothur comparable. show create sparse matrix count table. count table, clustur can produce one , assume abundance sequence one cluster sequences distance matrix.","code":"# install via cran install.packages(\"clustur\") # install via github remotes::install_github(\"SchlossLab/Clustur\")"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"read-count-files","dir":"Articles","previous_headings":"Starting Up","what":"Read count files","title":"clustur","text":"mothur used produce tabular count table now produces compressed verion, clustur read formats figure …","code":"count_table <- read_count(example_path(\"amazon.count_table\")) #should be a tsv or mothur-native count file count_table_sparse <- read_count(example_path(\"count_table.sparse.count_table\")) #should be a tsv or mothur-native count file"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"read-distance-matrix-file","dir":"Articles","previous_headings":"Starting Up","what":"Read distance matrix file","title":"clustur","text":"mothur produces column/sparse distance matrix Phylip-formatted distance matrix files. clustur read formats figure . return value distance_data memory address. want data frame version distances, can use get_distances(distance_data).","code":"distance_data <- read_dist(example_path(\"amazon_column.dist\"), count_table, cutoff = 0.03, FALSE) #> This is a column file. Processing now... distance_data <- read_dist(example_path(\"amazon_phylip.dist\"), count_table, cutoff = 0.03, FALSE) #> This is a phylip file. Processing now..."},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"cluster-data","dir":"Articles","previous_headings":"Starting Up","what":"Cluster data","title":"clustur","text":"opticlust default","code":"cluster_data <- cluster(distance_data, method = \"opti\") # this needs to make sure that dist_data and count_table are compatible"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"selecting-different-clustering-methods","dir":"Articles","previous_headings":"Starting Up > Cluster data","what":"Selecting different clustering methods","title":"clustur","text":"","code":"cluster_data <- cluster(distance_data, method = \"furthest\") cluster_data <- cluster(distance_data, method = \"nearest\") cluster_data <- cluster(distance_data, method = \"average\") cluster_data <- cluster(distance_data, method = \"weighted\")"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"output-data-from-clustering","dir":"Articles","previous_headings":"Starting Up","what":"Output data from clustering","title":"clustur","text":"methods produce list object indicator cutoff used (cutoff), well cluster (clusters) shared (shared) data frames. clusters data frame shows sequence cluster together column cluster identifiers (cluster) column lists indicating identifiers within cluster (identifiers). shared data frame contains columns indicating cluster sample identifiers abundance cluster sample; cluster identifier shared data frame clusters data frame. metrics data frame. OptiClust method also includes metrics data frame, describe optimization value iteration fitting process; data clusters shared taken last iteration. clustur provides getter functions, get_cutoff(), get_clusters(), get_shared(), get_metrics(), demonstrated .","code":"clusters <- cluster(distance_data, method = \"opti\")  get_cutoff(clusters) #> [1] 0.03 get_clusters(clusters) #>       label                        bins   otu #> 85 0.030000 U68618,U68638,U68658,U68620 otu85 #> 88 0.030000 U68663,U68688,U68679,U68665 otu88 #> 87 0.030000        U68641,U68673,U68667 otu87 #> 84 0.030000               U68615,U68680 otu84 #> 86 0.030000               U68631,U68636 otu86 #>  [ reached 'max' / getOption(\"max.print\") -- omitted 83 rows ] get_shared(clusters) #>      label  samples  otu abundance #> 1 0.030000 no_group OTU1         1 #> 2 0.030000 no_group OTU2         1 #> 3 0.030000 no_group OTU3         1 #>  [ reached 'max' / getOption(\"max.print\") -- omitted 85 rows ] get_metrics(clusters) #> $metrics #>      label   cutoff specificity      ppv       ttp  f1score          tn #> 1 0.030000 0.030000    1.000000 1.000000 17.000000 1.000000 4736.000000 #>        mcc       fn       fp sensitivity      npv      fdr accuracy #> 1 1.000000 0.000000 0.000000    1.000000 1.000000 1.000000 1.000000 #>  #> $other_metrics #>      mcc accuracy fdr iter cutoff specificity ppv time f1score tn label tp #>      num_otus fn fp sensitivity npv #>  [ reached 'max' / getOption(\"max.print\") -- omitted 3 rows ]"},{"path":"http://www.schlosslab.org/Clustur/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Gregory Johnson. Maintainer.","code":""},{"path":"http://www.schlosslab.org/Clustur/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Johnson G (2024). clustur: Package One 'Title Case' Line. R package version 1.0, http://www.schlosslab.org/Clustur/.","code":"@Manual{,   title = {clustur: What the Package Does in One 'Title Case' Line},   author = {Gregory Johnson},   year = {2024},   note = {R package version 1.0},   url = {http://www.schlosslab.org/Clustur/}, }"},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"mothur","dir":"","previous_headings":"","what":"What the Package Does in One Title Case Line","title":"What the Package Does in One Title Case Line","text":"mothur open-sourced software used analysis ecological data. strong presence use analyzing 16S rRNA gene sequences. mothur plethora features, , clustering based genetic similarity, sequence alignment, taxomic assignment, alpha beta diversity, phylotype analysis. numerous publications using software individuals intuitions alike. plan take advantage power mothur, isolate clustering feature. believe allow scientist work familiar tool give rise creation pipelines utilizing package.","code":""},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"clustur","dir":"","previous_headings":"","what":"clustur","title":"What the Package Does in One Title Case Line","text":"clustur developed two main reasons: allow developers easily create pipelines mothur code R, give users powerful clustering algorithm mothur without download . mothur built using rcpp, benefits speed c++ usability R. Additionally, since clustur open source, developers can modify package needed. help us continue create high quality packages, allow everyone take advantage foundation already built.","code":""},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"What the Package Does in One Title Case Line","text":"","code":"# install via cran install.packages(\"clustur\") # install via github remotes::install_github(\"SchlossLab/Clustur\")"},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting Started","title":"What the Package Does in One Title Case Line","text":"get started, look “Getting started” page.","code":""},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"contributions","dir":"","previous_headings":"","what":"Contributions","title":"What the Package Does in One Title Case Line","text":"feature requrest please visit issue page github use feature tag. like contribute pull request welcomed!","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":null,"dir":"Reference","previous_headings":"","what":"Cluster Description — cluster","title":"Cluster Description — cluster","text":"Detailed description function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cluster Description — cluster","text":"","code":"cluster(distance_object, method, random_seed = 123)"},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cluster Description — cluster","text":"distance_object distance object created using read_dist function. method type cluster wish conduct; opti, furthest, nearest, average, weighted. random_seed random seed wish use, defaulted 123.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cluster Description — cluster","text":"list dataframes contain abundance, clustering results.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cluster Description — cluster","text":"","code":"# Convert Phylip of column file to a sparse matrix  cutoff <- 0.2  count_table <- read_count(example_path(\"amazon.count_table\"))  distance_data <- read_dist(example_path(\"amazon_column.dist\"),                             count_table, cutoff, FALSE) #> This is a column file. Processing now...   # The clustur using one of the 5 methods  # opti  cluster_results <- cluster(distance_data, method = \"opti\")  # furthest  cluster_results <- cluster(distance_data, method = \"furthest\")  # nearest  cluster_results <- cluster(distance_data, method = \"nearest\")  # average  cluster_results <- cluster(distance_data, method = \"average\")  # weighted  cluster_results <- cluster(distance_data, method = \"weighted\")"},{"path":"http://www.schlosslab.org/Clustur/reference/clustur-package.html","id":null,"dir":"Reference","previous_headings":"","what":"clustur: What the Package Does in One 'Title Case' Line — clustur-package","title":"clustur: What the Package Does in One 'Title Case' Line — clustur-package","text":"One paragraph description package one full sentences.","code":""},{"path":[]},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Sparse Matrix — create_sparse_matrix","title":"Create Sparse Matrix — create_sparse_matrix","text":"Given list indexs, j indexes, distances values, can create sparse distance matrix . vector must size.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Sparse Matrix — create_sparse_matrix","text":"","code":"create_sparse_matrix(i_index, j_index, distances)"},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Sparse Matrix — create_sparse_matrix","text":"i_index list indexes, must numeric j_index list j indexes, must numeric distances list distance j index","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Sparse Matrix — create_sparse_matrix","text":"sparse matrix.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Sparse Matrix — create_sparse_matrix","text":"","code":"# This will return the path to our example file  i_values <- as.integer(1:100)  j_values <- as.integer(sample(1:100, 100, TRUE))  x_values <- as.numeric(runif(100, 0, 1))  s_matrix <- create_sparse_matrix(i_values, j_values, x_values)"},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Example Path — example_path","title":"Example Path — example_path","text":"function created helper function generate file paths  internal data. able access function  want follow along example.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example Path — example_path","text":"","code":"example_path(file = NULL)"},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Example Path — example_path","text":"file data path looking find.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Example Path — example_path","text":"path inside package file.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example Path — example_path","text":"","code":"# This will return the path to our example file example_path(\"amazon_phylip.dist\") #> [1] \"/home/runner/work/_temp/Library/clustur/extdata/amazon_phylip.dist\""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clusters — get_clusters","title":"Get Clusters — get_clusters","text":"function returns cluster data.frame cluster object","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clusters — get_clusters","text":"","code":"get_clusters(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clusters — get_clusters","text":"cluster_data cluster method output","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clusters — get_clusters","text":"cluster data.frame","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clusters — get_clusters","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") clusters <- get_clusters(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Count Table — get_count_table","title":"Get Count Table — get_count_table","text":"function returns count table used generate distance object.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Count Table — get_count_table","text":"","code":"get_count_table(distance_object)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Count Table — get_count_table","text":"distance_object read.dist output object","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Count Table — get_count_table","text":"count table data.frame","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Count Table — get_count_table","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... count_table <- get_count_table(distance_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Cutoff — get_cutoff","title":"Get Cutoff — get_cutoff","text":"function returns cutoff cluster object","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Cutoff — get_cutoff","text":"","code":"get_cutoff(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Cutoff — get_cutoff","text":"cluster_data cluster method output","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Cutoff — get_cutoff","text":"cutoff value","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Cutoff — get_cutoff","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") cutoff <- get_cutoff(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Distance Data Frame — get_distance_data_frame","title":"Get Distance Data Frame — get_distance_data_frame","text":"function generate data.frame contains distances indexes.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Distance Data Frame — get_distance_data_frame","text":"","code":"get_distance_data_frame(distance_object)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Distance Data Frame — get_distance_data_frame","text":"distance_object read.dist output object","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Distance Data Frame — get_distance_data_frame","text":"distance data.frame","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Distance Data Frame — get_distance_data_frame","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                                         count_table, cutoff, FALSE) #> This is a column file. Processing now... count_table <- get_count_table(distance_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Metrics — get_metrics","title":"Get Metrics — get_metrics","text":"function returns metrics cluster object","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Metrics — get_metrics","text":"","code":"get_metrics(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Metrics — get_metrics","text":"cluster_data cluster method output","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Metrics — get_metrics","text":"list metric data.frames","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Metrics — get_metrics","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") list_of_metrics <- get_metrics(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Shared — get_shared","title":"Get Shared — get_shared","text":"function returns shared data.frame cluster object","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Shared — get_shared","text":"","code":"get_shared(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Shared — get_shared","text":"cluster_data cluster method output","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Shared — get_shared","text":"shared data.frame","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Shared — get_shared","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") shared <- get_shared(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Count — read_count","title":"Read Count — read_count","text":"function read return count table. can take sparse normal count tables.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Count — read_count","text":"","code":"read_count(count_table_path)"},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Count — read_count","text":"count_table_path file path count table.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Count — read_count","text":"count table data frame.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Count — read_count","text":"","code":"# This will return the path to our example file count_table <- read_count(example_path(\"amazon.count_table\"))"},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Dist Description — read_dist","title":"Read Dist Description — read_dist","text":"Detailed description function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Dist Description — read_dist","text":"","code":"read_dist(distance_file, count_table, cutoff, is_simularity_matrix)"},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Dist Description — read_dist","text":"distance_file Either phylip column distance file, sparse matrix. count_table table names given abundance per group. cutoff value wish use cutoff clustering. opti, furthest, nearest, average, weighted. is_simularity_matrix using simularity matrix distance matrix?","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Dist Description — read_dist","text":"distance object contains distance information","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Dist Description — read_dist","text":"","code":"# Convert Phylip or column file to a sparse matrix  # spMatrix requires the use of the matrix library  i_values <- as.integer(1:100)  j_values <- as.integer(sample(1:100, 100, TRUE))  x_values <- as.numeric(runif(100, 0, 1))  s_matrix <- create_sparse_matrix(i_values, j_values, x_values)    column_path <- example_path(\"amazon_column.dist\")  phylip_path <- example_path(\"amazon_phylip.dist\")  count_table <- read_count(example_path(\"amazon.count_table\"))  data_column <- read_dist(column_path, count_table, 0.2, FALSE) #> This is a column file. Processing now... data_phylip <- read_dist(phylip_path, count_table, 0.2, FALSE) #> This is a phylip file. Processing now... data_sparse <- read_dist(s_matrix, count_table, 0.2, FALSE)"},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate Count Table — validate_count_table","title":"Validate Count Table — validate_count_table","text":"count table already valid nothing change, otherwise add new group count table file.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate Count Table — validate_count_table","text":"","code":"validate_count_table(count_table_df)"},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate Count Table — validate_count_table","text":"count_table_df count table dataframe object.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate Count Table — validate_count_table","text":"validated count table.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Validate Count Table — validate_count_table","text":"Detailed description function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate Count Table — validate_count_table","text":"","code":"count_table <- read.delim(example_path(\"amazon.count_table\"))  count_table_valid <- validate_count_table(count_table)"}]
+[{"path":"http://www.schlosslab.org/Clustur/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 clustur authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"starting-up","dir":"Articles","previous_headings":"","what":"Starting Up","title":"clustur","text":"clustur developed similar mothur implementation written C++, however differences note. order cluster data, requiring users build sparse matrix (also support phylip files) count table R mothur. objects built can call cluster function. currently support 5 cluster methods mothur: furthest, nearest, weighted, average neighbor opticlust, mothur’s default. methods produce data comparable mothur. speed clustur mothur comparable. show create sparse matrix count table. count table, clustur can produce one , assume abundance sequence one cluster sequences distance matrix.","code":"# install via cran install.packages(\"clustur\") # install via github remotes::install_github(\"SchlossLab/Clustur\")"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"read-count-files","dir":"Articles","previous_headings":"Starting Up","what":"Read count files","title":"clustur","text":"mothur used produce tabular count table now produces compressed verion, clustur read formats figure …","code":"count_table <- read_count(example_path(\"amazon.count_table\")) #should be a tsv or mothur-native count file count_table_sparse <- read_count(example_path(\"count_table.sparse.count_table\")) #should be a tsv or mothur-native count file"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"read-distance-matrix-file","dir":"Articles","previous_headings":"Starting Up","what":"Read distance matrix file","title":"clustur","text":"mothur produces column/sparse distance matrix Phylip-formatted distance matrix files. clustur read formats figure . return value distance_data memory address. want data frame version distances, can use get_distances(distance_data).","code":"distance_data <- read_dist(example_path(\"amazon_column.dist\"), count_table, cutoff = 0.03, FALSE) #> This is a column file. Processing now... distance_data <- read_dist(example_path(\"amazon_phylip.dist\"), count_table, cutoff = 0.03, FALSE) #> This is a phylip file. Processing now..."},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"cluster-data","dir":"Articles","previous_headings":"Starting Up","what":"Cluster data","title":"clustur","text":"opticlust default","code":"cluster_data <- cluster(distance_data, method = \"opti\") # this needs to make sure that dist_data and count_table are compatible"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"selecting-different-clustering-methods","dir":"Articles","previous_headings":"Starting Up > Cluster data","what":"Selecting different clustering methods","title":"clustur","text":"","code":"cluster_data <- cluster(distance_data, method = \"furthest\") cluster_data <- cluster(distance_data, method = \"nearest\") cluster_data <- cluster(distance_data, method = \"average\") cluster_data <- cluster(distance_data, method = \"weighted\")"},{"path":"http://www.schlosslab.org/Clustur/articles/clustur.html","id":"output-data-from-clustering","dir":"Articles","previous_headings":"Starting Up","what":"Output data from clustering","title":"clustur","text":"methods produce list object indicator cutoff used (cutoff), well cluster (clusters) shared (shared) data frames. clusters data frame shows sequence cluster together column cluster identifiers (cluster) column lists indicating identifiers within cluster (identifiers). shared data frame contains columns indicating cluster sample identifiers abundance cluster sample; cluster identifier shared data frame clusters data frame. metrics data frame. OptiClust method also includes metrics data frame, describe optimization value iteration fitting process; data clusters shared taken last iteration. clustur provides getter functions, get_cutoff(), get_clusters(), get_shared(), get_metrics(), demonstrated .","code":"clusters <- cluster(distance_data, method = \"opti\")  get_cutoff(clusters) #> [1] 0.03 get_clusters(clusters) #>       label                        bins   otu #> 85 0.030000 U68618,U68638,U68658,U68620 otu85 #> 88 0.030000 U68663,U68688,U68679,U68665 otu88 #> 87 0.030000        U68641,U68673,U68667 otu87 #> 84 0.030000               U68615,U68680 otu84 #> 86 0.030000               U68631,U68636 otu86 #>  [ reached 'max' / getOption(\"max.print\") -- omitted 83 rows ] get_shared(clusters) #>      label  samples  otu abundance #> 1 0.030000 no_group OTU1         1 #> 2 0.030000 no_group OTU2         1 #> 3 0.030000 no_group OTU3         1 #>  [ reached 'max' / getOption(\"max.print\") -- omitted 85 rows ] get_metrics(clusters) #> $metrics #>      label   cutoff specificity      ppv       ttp  f1score          tn #> 1 0.030000 0.030000    1.000000 1.000000 17.000000 1.000000 4736.000000 #>        mcc       fn       fp sensitivity      npv      fdr accuracy #> 1 1.000000 0.000000 0.000000    1.000000 1.000000 1.000000 1.000000 #>  #> $other_metrics #>      mcc accuracy fdr iter cutoff specificity ppv time f1score tn label tp #>      num_otus fn fp sensitivity npv #>  [ reached 'max' / getOption(\"max.print\") -- omitted 3 rows ]"},{"path":"http://www.schlosslab.org/Clustur/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Gregory Johnson. Author. Patrick Schloss. Author, maintainer, copyright holder.","code":""},{"path":"http://www.schlosslab.org/Clustur/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Johnson G, Schloss P (2024). clustur: Clustering. R package version 0.1, https://github.com/SchlossLab/Clustur, http://www.schlosslab.org/Clustur/.","code":"@Manual{,   title = {clustur: Clustering},   author = {Gregory Johnson and Patrick Schloss},   year = {2024},   note = {R package version 0.1, https://github.com/SchlossLab/Clustur},   url = {http://www.schlosslab.org/Clustur/}, }"},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"mothur","dir":"","previous_headings":"","what":"Clustering","title":"Clustering","text":"mothur open-sourced software used analysis ecological data. strong presence use analyzing 16S rRNA gene sequences. mothur plethora features, , clustering based genetic similarity, sequence alignment, taxomic assignment, alpha beta diversity, phylotype analysis. numerous publications using software individuals intuitions alike. plan take advantage power mothur, isolate clustering feature. believe allow scientist work familiar tool give rise creation pipelines utilizing package.","code":""},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"clustur","dir":"","previous_headings":"","what":"clustur","title":"Clustering","text":"clustur developed two main reasons: allow developers easily create pipelines mothur code R, give users powerful clustering algorithm mothur without download . mothur built using rcpp, benefits speed c++ usability R. Additionally, since clustur open source, developers can modify package needed. help us continue create high quality packages, allow everyone take advantage foundation already built.","code":""},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Clustering","text":"","code":"# install via cran install.packages(\"clustur\") # install via github remotes::install_github(\"SchlossLab/Clustur\")"},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting Started","title":"Clustering","text":"get started, look “Getting started” page.","code":""},{"path":"http://www.schlosslab.org/Clustur/index.html","id":"contributions","dir":"","previous_headings":"","what":"Contributions","title":"Clustering","text":"feature requrest please visit issue page github use feature tag. like contribute pull request welcomed!","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":null,"dir":"Reference","previous_headings":"","what":"Cluster Description — cluster","title":"Cluster Description — cluster","text":"Detailed description function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cluster Description — cluster","text":"","code":"cluster(distance_object, method = \"opti\", random_seed = 123)"},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cluster Description — cluster","text":"distance_object distance object created using `read_dist()` function. method type cluster wish conduct; opti, furthest, nearest, average, weighted. random_seed random seed wish use, defaulted 123.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cluster Description — cluster","text":"list `data.frames` contain abundance, clustering results. used \"opti\", also return clustering metrics.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/cluster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cluster Description — cluster","text":"","code":"cutoff <- 0.2  count_table <- read_count(example_path(\"amazon.count_table\"))  distance_data <- read_dist(example_path(\"amazon_column.dist\"),                             count_table, cutoff, FALSE) #> This is a column file. Processing now...   cluster_results <- cluster(distance_data, method = \"opti\")  cluster_results <- cluster(distance_data, method = \"furthest\")  cluster_results <- cluster(distance_data, method = \"nearest\")  cluster_results <- cluster(distance_data, method = \"average\")  cluster_results <- cluster(distance_data, method = \"weighted\")"},{"path":"http://www.schlosslab.org/Clustur/reference/clustur-package.html","id":null,"dir":"Reference","previous_headings":"","what":"clustur: Clustering — clustur-package","title":"clustur: Clustering — clustur-package","text":"tool implements clustering algorithms mothur (Schloss PD et al. (2009) doi:10.1128/AEM.01541-09 ). Clustur make use 'cluster' 'make.shared' command mothur. cluster command five different algorithms implemented: 'opticlust', 'furthest', 'nearest', 'average', 'weighted'. Opticlust optimized OTU clustering algorithm, can learn , (Westcott SL, Schloss PD (2017) doi:10.1128/mspheredirect.00073-17 ). 'make.shared' command always applied end clustering command. functionality allows us generate create clustering abundance data efficiently.","code":""},{"path":[]},{"path":"http://www.schlosslab.org/Clustur/reference/clustur-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"clustur: Clustering — clustur-package","text":"Maintainer: Patrick Schloss pschloss@umich.edu (ORCID) [copyright holder] Authors: Gregory Johnson grejoh@umich.edu (ORCID)","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Sparse Matrix — create_sparse_matrix","title":"Create Sparse Matrix — create_sparse_matrix","text":"Given list indexs, j indexes, distances values, can create sparse distance matrix . vector must size.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Sparse Matrix — create_sparse_matrix","text":"","code":"create_sparse_matrix(i_index, j_index, distances)"},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Sparse Matrix — create_sparse_matrix","text":"i_index list indexes, must numeric j_index list j indexes, must numeric distances list distance j index","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Sparse Matrix — create_sparse_matrix","text":"`dgTMatrix` `Matrix` library.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Sparse Matrix — create_sparse_matrix","text":"","code":"i_values <- as.integer(1:100)  j_values <- as.integer(sample(1:100, 100, TRUE))  x_values <- as.numeric(runif(100, 0, 1))  s_matrix <- create_sparse_matrix(i_values, j_values, x_values)"},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Example Path — example_path","title":"Example Path — example_path","text":"function created helper function generate file paths  internal data. use function  want follow along example, intereact data","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example Path — example_path","text":"","code":"example_path(file = NULL)"},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Example Path — example_path","text":"file file name data","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Example Path — example_path","text":"path file `chr`.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/example_path.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example Path — example_path","text":"","code":"# This will return the path to our example file example_path(\"amazon_phylip.dist\") #> [1] \"/home/runner/work/_temp/Library/clustur/extdata/amazon_phylip.dist\""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clusters — get_clusters","title":"Get Clusters — get_clusters","text":"GetClusters returns `data.frame` generated clusters `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clusters — get_clusters","text":"","code":"get_clusters(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clusters — get_clusters","text":"cluster_data output `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clusters — get_clusters","text":"created cluster `data.frame`.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_clusters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clusters — get_clusters","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") clusters <- get_clusters(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Count Table — get_count_table","title":"Get Count Table — get_count_table","text":"function returns count table used generate distance object.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Count Table — get_count_table","text":"","code":"get_count_table(distance_object)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Count Table — get_count_table","text":"distance_object output `read.dist()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Count Table — get_count_table","text":"count_table `data.frame`.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_count_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Count Table — get_count_table","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... count_table <- get_count_table(distance_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Cutoff — get_cutoff","title":"Get Cutoff — get_cutoff","text":"GetCutoff returns cutoff cluster object `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Cutoff — get_cutoff","text":"","code":"get_cutoff(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Cutoff — get_cutoff","text":"cluster_data output `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Cutoff — get_cutoff","text":"cutoff value `dbl`","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_cutoff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Cutoff — get_cutoff","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") cutoff <- get_cutoff(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Distance Data Frame — get_distance_data_frame","title":"Get Distance Data Frame — get_distance_data_frame","text":"function generate `data.frame` contains distances indexes.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Distance Data Frame — get_distance_data_frame","text":"","code":"get_distance_data_frame(distance_object)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Distance Data Frame — get_distance_data_frame","text":"distance_object output `read.dist()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Distance Data Frame — get_distance_data_frame","text":"distance `data.frame`.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_distance_data_frame.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Distance Data Frame — get_distance_data_frame","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                                         count_table, cutoff, FALSE) #> This is a column file. Processing now... count_table <- get_count_table(distance_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Metrics — get_metrics","title":"Get Metrics — get_metrics","text":"GetMetrics returns generated metrics `data.frame` `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Metrics — get_metrics","text":"","code":"get_metrics(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Metrics — get_metrics","text":"cluster_data output `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Metrics — get_metrics","text":"list metric data.frames","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_metrics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Metrics — get_metrics","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") list_of_metrics <- get_metrics(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Shared — get_shared","title":"Get Shared — get_shared","text":"GetShared retuns generated abundance `data.frame` `cluster()` function","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Shared — get_shared","text":"","code":"get_shared(cluster_data)"},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Shared — get_shared","text":"cluster_data output `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Shared — get_shared","text":"shared data.frame","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/get_shared.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Shared — get_shared","text":"","code":"cutoff <- 0.2 count_table <- read_count(example_path(\"amazon.count_table\")) distance_data <- read_dist(example_path(\"amazon_column.dist\"),                            count_table, cutoff, FALSE) #> This is a column file. Processing now... df_clusters <- cluster(distance_data, method = \"opti\") shared <- get_shared(df_clusters)"},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Count — read_count","title":"Read Count — read_count","text":"function read return count table. can take sparse normal count tables.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Count — read_count","text":"","code":"read_count(count_table_path)"},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Count — read_count","text":"count_table_path file path count table.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Count — read_count","text":"count table `data.frame`.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Count — read_count","text":"","code":"count_table <- read_count(example_path(\"amazon.count_table\"))"},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Dist Description — read_dist","title":"Read Dist Description — read_dist","text":"Detailed description function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Dist Description — read_dist","text":"","code":"read_dist(distance_file, count_table, cutoff, is_simularity_matrix = FALSE)"},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Dist Description — read_dist","text":"distance_file Either phylip column distance file, sparse matrix. count_table table names given abundance per group. cutoff value wish use cutoff clustering. is_simularity_matrix using simularity matrix distance matrix?","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Dist Description — read_dist","text":"distance `externalptr` object contains distance information.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/read_dist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Dist Description — read_dist","text":"","code":"i_values <- as.integer(1:100)  j_values <- as.integer(sample(1:100, 100, TRUE))  x_values <- as.numeric(runif(100, 0, 1))  s_matrix <- create_sparse_matrix(i_values, j_values, x_values)  sparse_count <- data.frame(                  Representative_Sequence = 1:100,                  total = rep(1, times = 100))   column_path <- example_path(\"amazon_column.dist\")  phylip_path <- example_path(\"amazon_phylip.dist\")  count_table <- read_count(example_path(\"amazon.count_table\"))   data_column <- read_dist(column_path, count_table, 0.2, FALSE) #> This is a column file. Processing now...  data_phylip <- read_dist(phylip_path, count_table, 0.2, FALSE) #> This is a phylip file. Processing now...  data_sparse <- read_dist(s_matrix, sparse_count, 0.2, FALSE)"},{"path":"http://www.schlosslab.org/Clustur/reference/split_clusters_to_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Split Clusters to List — split_clusters_to_list","title":"Split Clusters to List — split_clusters_to_list","text":"`split_clusters_to_list()` extract clusters cluster generated `data.frame`. turn clusters list. allows users easily visualize data.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/split_clusters_to_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split Clusters to List — split_clusters_to_list","text":"","code":"split_clusters_to_list(cluster)"},{"path":"http://www.schlosslab.org/Clustur/reference/split_clusters_to_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split Clusters to List — split_clusters_to_list","text":"cluster output generated `cluster()` function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/split_clusters_to_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split Clusters to List — split_clusters_to_list","text":"named `list` clusters.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/split_clusters_to_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split Clusters to List — split_clusters_to_list","text":"","code":"cutoff <- 0.2  count_table <- read_count(example_path(\"amazon.count_table\"))  distance_data <- read_dist(example_path(\"amazon_column.dist\"),                             count_table, cutoff, FALSE) #> This is a column file. Processing now...  cluster_results <- cluster(distance_data, method = \"opti\")   cluster_list <- split_clusters_to_list(cluster_results)"},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate Count Table — validate_count_table","title":"Validate Count Table — validate_count_table","text":"count table already valid nothing change, otherwise add new group count table file.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate Count Table — validate_count_table","text":"","code":"validate_count_table(count_table_df)"},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate Count Table — validate_count_table","text":"count_table_df count table `data.frame` object.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate Count Table — validate_count_table","text":"validated count table `data.frame`","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Validate Count Table — validate_count_table","text":"Detailed description function.","code":""},{"path":"http://www.schlosslab.org/Clustur/reference/validate_count_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate Count Table — validate_count_table","text":"","code":"count_table <- read.delim(example_path(\"amazon.count_table\"))  count_table_valid <- validate_count_table(count_table)"},{"path":"http://www.schlosslab.org/Clustur/news/index.html","id":"clustur-01","dir":"Changelog","previous_headings":"","what":"clustur 0.1","title":"clustur 0.1","text":"Initial CRAN submission.","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index 8758b09..c0d2209 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -1,9 +1,12 @@
 <urlset xmlns = 'http://www.sitemaps.org/schemas/sitemap/0.9'>
 <url><loc>http://www.schlosslab.org/Clustur/404.html</loc></url>
+<url><loc>http://www.schlosslab.org/Clustur/LICENSE-text.html</loc></url>
+<url><loc>http://www.schlosslab.org/Clustur/LICENSE.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/articles/clustur.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/articles/index.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/authors.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/index.html</loc></url>
+<url><loc>http://www.schlosslab.org/Clustur/news/index.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/reference/cluster.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/reference/clustur-package.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/reference/create_sparse_matrix.html</loc></url>
@@ -17,6 +20,7 @@
 <url><loc>http://www.schlosslab.org/Clustur/reference/index.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/reference/read_count.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/reference/read_dist.html</loc></url>
+<url><loc>http://www.schlosslab.org/Clustur/reference/split_clusters_to_list.html</loc></url>
 <url><loc>http://www.schlosslab.org/Clustur/reference/validate_count_table.html</loc></url>
 </urlset>
 
