Merge pull request #43 from grunwaldlab/southen_APS_2021

Updates for APS Southern 2021. Thanks Zach for rebuilding the caches and verifying images and code output display correctly
grunwaldlab · Feb 11, 2021 · 79d6866 · 79d6866
2 parents e29f7d8 + 42077ed
commit 79d6866
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diff --git a/AMOVA_cache/html/unnamed-chunk-8_37b059c3e0898a13167ab7283b8bfaf9.RData b/AMOVA_cache/html/unnamed-chunk-8_37b059c3e0898a13167ab7283b8bfaf9.RData
diff --git a/AMOVA_cache/html/unnamed-chunk-8_37b059c3e0898a13167ab7283b8bfaf9.rdb b/AMOVA_cache/html/unnamed-chunk-8_37b059c3e0898a13167ab7283b8bfaf9.rdb
diff --git a/AMOVA_cache/html/unnamed-chunk-8_37b059c3e0898a13167ab7283b8bfaf9.rdx b/AMOVA_cache/html/unnamed-chunk-8_37b059c3e0898a13167ab7283b8bfaf9.rdx
diff --git a/AMOVA_files/figure-html/Aeut_clonecorrect_random_plot-1.png b/AMOVA_files/figure-html/Aeut_clonecorrect_random_plot-1.png
diff --git a/AMOVA_files/figure-html/Aeut_random_plot-1.png b/AMOVA_files/figure-html/Aeut_random_plot-1.png
diff --git a/AMOVA_files/figure-html/randomized_strata_plot-1.png b/AMOVA_files/figure-html/randomized_strata_plot-1.png
diff --git a/Authors.html b/Authors.html
@@ -20,6 +20,9 @@
 <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
 <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
+<script src="site_libs/accessible-code-block-0.0.1/empty-anchor.js"></script>
+<link href="site_libs/anchor-sections-1.0/anchor-sections.css" rel="stylesheet" />
+<script src="site_libs/anchor-sections-1.0/anchor-sections.js"></script>
 <!-- Global Site Tag (gtag.js) - Google Analytics -->
 <script async src="https://www.googletagmanager.com/gtag/js?id=UA-107144798-3"></script>
 <script>
@@ -30,6 +33,15 @@
   gtag('config', 'UA-107144798-3');
 </script>
 
+<style type="text/css">
+  code{white-space: pre-wrap;}
+  span.smallcaps{font-variant: small-caps;}
+  span.underline{text-decoration: underline;}
+  div.column{display: inline-block; vertical-align: top; width: 50%;}
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+  ul.task-list{list-style: none;}
+    </style>
+
 
 
 
@@ -347,28 +359,53 @@
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Workshop
+    Workshops
 
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="workshop.html">Workshop</a>
-    </li>
-    <li>
-      <a href="intro_vcf.html">Introduction</a>
-    </li>
-    <li>
-      <a href="reading_vcf.html">VCF data</a>
-    </li>
-    <li>
-      <a href="quality_control.html">Quality control</a>
-    </li>
-    <li>
-      <a href="gbs_analysis.html">Analysis of GBS data</a>
+    <li class="dropdown-submenu">
+      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ICPP</a>
+      <ul class="dropdown-menu" role="menu">
+        <li>
+          <a href="workshop_icpp.html">Preparation</a>
+        </li>
+        <li>
+          <a href="intro_vcf.html">Introduction</a>
+        </li>
+        <li>
+          <a href="reading_vcf.html">VCF data</a>
+        </li>
+        <li>
+          <a href="quality_control.html">Quality control</a>
+        </li>
+        <li>
+          <a href="gbs_analysis.html">Analysis of GBS data</a>
+        </li>
+        <li>
+          <a href="analysis_of_genome.html">Analysis of genome data</a>
+        </li>
+      </ul>
     </li>
-    <li>
-      <a href="analysis_of_genome.html">Analysis of genome data</a>
+    <li class="dropdown-submenu">
+      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">APS Southern Division</a>
+      <ul class="dropdown-menu" role="menu">
+        <li>
+          <a href="workshop_southernAPS.html">Preparation</a>
+        </li>
+        <li>
+          <a href="intro_vcf.html">Introduction</a>
+        </li>
+        <li>
+          <a href="reading_vcf.html">VCF data</a>
+        </li>
+        <li>
+          <a href="quality_control.html">Quality control</a>
+        </li>
+        <li>
+          <a href="gbs_analysis.html">Analysis of GBS data</a>
+        </li>
+      </ul>
     </li>
   </ul>
 </li>
@@ -538,7 +575,7 @@ <h1>
 
 // add bootstrap table styles to pandoc tables
 function bootstrapStylePandocTables() {
-  $('tr.header').parent('thead').parent('table').addClass('table table-condensed');
+  $('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
 }
 $(document).ready(function () {
   bootstrapStylePandocTables();

diff --git a/DAPC.html b/DAPC.html
diff --git a/DAPC_cache/html/Pramhide_139815d38286c724c65ceb7119c05f91.RData b/DAPC_cache/html/Pramhide_139815d38286c724c65ceb7119c05f91.RData
diff --git a/DAPC_cache/html/Pramhide_139815d38286c724c65ceb7119c05f91.rdb b/DAPC_cache/html/Pramhide_139815d38286c724c65ceb7119c05f91.rdb
diff --git a/DAPC_cache/html/Pramhide_139815d38286c724c65ceb7119c05f91.rdx b/DAPC_cache/html/Pramhide_139815d38286c724c65ceb7119c05f91.rdx
diff --git a/DAPC_cache/html/Pramhide_3e52e15c05a4148e39d7f85e6dab96eb.RData b/DAPC_cache/html/Pramhide_3e52e15c05a4148e39d7f85e6dab96eb.RData
diff --git a/DAPC_cache/html/Pramhide_3e52e15c05a4148e39d7f85e6dab96eb.rdb b/DAPC_cache/html/Pramhide_3e52e15c05a4148e39d7f85e6dab96eb.rdb
diff --git a/DAPC_cache/html/Pramhide_3e52e15c05a4148e39d7f85e6dab96eb.rdx b/DAPC_cache/html/Pramhide_3e52e15c05a4148e39d7f85e6dab96eb.rdx
diff --git a/DAPC_cache/html/__packages b/DAPC_cache/html/__packages
@@ -6,6 +6,6 @@ ade4
 adegenet
 poppr
 vcfR
-igraph
-RColorBrewer
-ape
+reshape2
+ggplot2
+ggpubr
diff --git a/DAPC_cache/html/unnamed-chunk-2_b14a4f8e64a6988878802d61e77e9c3f.RData b/DAPC_cache/html/unnamed-chunk-2_b14a4f8e64a6988878802d61e77e9c3f.RData
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diff --git a/DAPC_cache/html/unnamed-chunk-3_2e2269bcf050bfb4ec4207dd647aab2a.RData b/DAPC_cache/html/unnamed-chunk-3_2e2269bcf050bfb4ec4207dd647aab2a.RData
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diff --git a/DAPC_cache/html/unnamed-chunk-6_58bf8bb86aa000ad68c700b4d113a347.rdx b/DAPC_cache/html/unnamed-chunk-6_58bf8bb86aa000ad68c700b4d113a347.rdx
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diff --git a/DAPC_cache/html/unnamed-chunk-8_f0c1365850b7de8ff8c62277b736ccb2.RData b/DAPC_cache/html/unnamed-chunk-8_f0c1365850b7de8ff8c62277b736ccb2.RData
diff --git a/DAPC_cache/html/unnamed-chunk-8_f0c1365850b7de8ff8c62277b736ccb2.rdx b/DAPC_cache/html/unnamed-chunk-8_f0c1365850b7de8ff8c62277b736ccb2.rdx
diff --git a/DAPC_files/figure-html/Pramhide-1.png b/DAPC_files/figure-html/Pramhide-1.png
diff --git a/DAPC_files/figure-html/unnamed-chunk-2-1.png b/DAPC_files/figure-html/unnamed-chunk-2-1.png
diff --git a/DAPC_files/figure-html/unnamed-chunk-3-1.png b/DAPC_files/figure-html/unnamed-chunk-3-1.png
diff --git a/DAPC_files/figure-html/unnamed-chunk-5-1.png b/DAPC_files/figure-html/unnamed-chunk-5-1.png
diff --git a/DAPC_files/figure-html/unnamed-chunk-6-1.png b/DAPC_files/figure-html/unnamed-chunk-6-1.png
diff --git a/DAPC_files/figure-html/unnamed-chunk-7-1.png b/DAPC_files/figure-html/unnamed-chunk-7-1.png
diff --git a/DAPC_files/figure-html/unnamed-chunk-8-1.png b/DAPC_files/figure-html/unnamed-chunk-8-1.png
diff --git a/Data_Preparation.html b/Data_Preparation.html
@@ -20,6 +20,9 @@
 <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
 <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
+<script src="site_libs/accessible-code-block-0.0.1/empty-anchor.js"></script>
+<link href="site_libs/anchor-sections-1.0/anchor-sections.css" rel="stylesheet" />
+<script src="site_libs/anchor-sections-1.0/anchor-sections.js"></script>
 <!-- Global Site Tag (gtag.js) - Google Analytics -->
 <script async src="https://www.googletagmanager.com/gtag/js?id=UA-107144798-3"></script>
 <script>
@@ -30,12 +33,21 @@
   gtag('config', 'UA-107144798-3');
 </script>
 
+<style type="text/css">
+  code{white-space: pre-wrap;}
+  span.smallcaps{font-variant: small-caps;}
+  span.underline{text-decoration: underline;}
+  div.column{display: inline-block; vertical-align: top; width: 50%;}
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+  ul.task-list{list-style: none;}
+    </style>
+
 
 <style type="text/css">code{white-space: pre;}</style>
 <style type="text/css" data-origin="pandoc">
-a.sourceLine { display: inline-block; line-height: 1.25; }
-a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+code.sourceCode > span { display: inline-block; line-height: 1.25; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 div.sourceCode { margin: 1em 0; }
@@ -45,14 +57,16 @@
 }
 @media print {
 code.sourceCode { white-space: pre-wrap; }
-a.sourceLine { text-indent: -1em; padding-left: 1em; }
-}
-pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
-pre.numberSource a.sourceLine::before
-  { content: attr(data-line-number);
+code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
     position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    border: none; display: inline-block;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -61,9 +75,9 @@
   }
 pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
 div.sourceCode
-  { background-color: #f8f8f8; }
+  {  background-color: #f8f8f8; }
 @media screen {
-a.sourceLine::before { text-decoration: underline; }
+code.sourceCode > span > a:first-child::before { text-decoration: underline; }
 }
 code span.al { color: #ef2929; } /* Alert */
 code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
@@ -437,28 +451,53 @@
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Workshop
+    Workshops
 
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="workshop.html">Workshop</a>
-    </li>
-    <li>
-      <a href="intro_vcf.html">Introduction</a>
-    </li>
-    <li>
-      <a href="reading_vcf.html">VCF data</a>
-    </li>
-    <li>
-      <a href="quality_control.html">Quality control</a>
-    </li>
-    <li>
-      <a href="gbs_analysis.html">Analysis of GBS data</a>
+    <li class="dropdown-submenu">
+      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ICPP</a>
+      <ul class="dropdown-menu" role="menu">
+        <li>
+          <a href="workshop_icpp.html">Preparation</a>
+        </li>
+        <li>
+          <a href="intro_vcf.html">Introduction</a>
+        </li>
+        <li>
+          <a href="reading_vcf.html">VCF data</a>
+        </li>
+        <li>
+          <a href="quality_control.html">Quality control</a>
+        </li>
+        <li>
+          <a href="gbs_analysis.html">Analysis of GBS data</a>
+        </li>
+        <li>
+          <a href="analysis_of_genome.html">Analysis of genome data</a>
+        </li>
+      </ul>
     </li>
-    <li>
-      <a href="analysis_of_genome.html">Analysis of genome data</a>
+    <li class="dropdown-submenu">
+      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">APS Southern Division</a>
+      <ul class="dropdown-menu" role="menu">
+        <li>
+          <a href="workshop_southernAPS.html">Preparation</a>
+        </li>
+        <li>
+          <a href="intro_vcf.html">Introduction</a>
+        </li>
+        <li>
+          <a href="reading_vcf.html">VCF data</a>
+        </li>
+        <li>
+          <a href="quality_control.html">Quality control</a>
+        </li>
+        <li>
+          <a href="gbs_analysis.html">Analysis of GBS data</a>
+        </li>
+      </ul>
     </li>
   </ul>
 </li>
@@ -532,9 +571,9 @@ <h3>GenAlEx formatted data</h3>
 <p>Note that <code>*.csv</code> stands for comma-separated-value. This can be opened in a text editor or excel. <code>*.csv</code> is a good format for portability into R.</p>
 </blockquote>
 <p>To import GenAlEx formatted data into <em>poppr</em>, you should use the function <code>read.genalex</code>. Below is an example using <strong>monpop.csv</strong>.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(<span class="st">&quot;poppr&quot;</span>)</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2">monpop &lt;-<span class="st"> </span><span class="kw">read.genalex</span>(<span class="st">&quot;~/Downloads/monpop.csv&quot;</span>)</a>
-<a class="sourceLine" id="cb1-3" data-line-number="3">monpop</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw">library</span>(<span class="st">&quot;poppr&quot;</span>)</span>
+<span id="cb1-2"><a href="#cb1-2"></a>monpop &lt;-<span class="st"> </span><span class="kw">read.genalex</span>(<span class="st">&quot;~/Downloads/monpop.csv&quot;</span>)</span>
+<span id="cb1-3"><a href="#cb1-3"></a>monpop</span></code></pre></div>
 <pre><code>## 
 ## This is a genclone object
 ## -------------------------
@@ -550,7 +589,7 @@ <h3>GenAlEx formatted data</h3>
 ##     12 populations defined - 
 ## 7_09_BB, 26_09_BB, 26_09_FR, ..., 45_10_FR, 26_11_BB, 26_11_FR</code></pre>
 <blockquote>
-<p>There are other options for genalex formatted data, such as xy coordinates. We won’t cover the other options, but type <code>help(&quot;read.genalex&quot;)</code> in your R console for details.</p>
+<p>There are other options for genalex formatted data, such as xy coordinates. We won’t cover the other options, but type <code>help("read.genalex")</code> in your R console for details.</p>
 </blockquote>
 </div>
 <div id="other-data-formats" class="section level3">
@@ -562,7 +601,7 @@ <h3>Other data formats</h3>
 <li><strong>GENEPOP</strong> (file.gen)</li>
 <li><strong>STRUCTURE</strong> (file.str)</li>
 </ul>
-<p>The <em>adegenet</em> function <code>import2genind</code> will import all of these formats. If you have sequence data, you can use the <code>read.FASTA</code> function from the <em>ape</em> package. If your data is in any other format, type <code>help(&quot;df2genind&quot;)</code> for guidance.</p>
+<p>The <em>adegenet</em> function <code>import2genind</code> will import all of these formats. If you have sequence data, you can use the <code>read.FASTA</code> function from the <em>ape</em> package. If your data is in any other format, type <code>help("df2genind")</code> for guidance.</p>
 </div>
 </div>
 <div id="genalex-data-format" class="section level2">
@@ -601,12 +640,12 @@ <h3>Basic Format</h3>
 </tbody>
 </table>
 <div class="figure">
-<img src="images/monpop.png" alt="monpop" />
+<img src="images/monpop.png" alt="" />
 <p class="caption">monpop</p>
 </div>
 <p>The columns of the metadata beyond those three rows define the number of individuals contained within each population. Since this data is redundant with the second column, it is not necessary. Notice, also, that the second column, reserved for the population assignments, has a pattern of underscores in the populations. This will be important at the end of this section. Below is a modified version of the input format that should make it easier to format.</p>
 <div class="figure">
-<img src="images/monpop_ideal.png" alt="monpop_ideal" />
+<img src="images/monpop_ideal.png" alt="" />
 <p class="caption">monpop_ideal</p>
 </div>
 <p>Highlighted in blue is the cell that defines the number of columns highlighted in red. If we set this number to <code>1</code>, then we do not have to enter in any information in those columns. Try it for yourself.</p>
@@ -615,15 +654,15 @@ <h3>Basic Format</h3>
 <h3>Diploids</h3>
 <p>Diploid data is only different in the fact that you will have two alleles per locus. This is coded such that each allele is in a separate column. Below is an example of the <code>nancycats</code> data set (from the <em>adegenet</em> package), exported like above. Highlighted in blue and red are the first and second loci, respectively.</p>
 <div class="figure">
-<img src="images/diploid.png" alt="diploid" />
+<img src="images/diploid.png" alt="" />
 <p class="caption">diploid</p>
 </div>
 </div>
 <div id="polyploids" class="section level3">
 <h3>Polyploids</h3>
 <p>GenAlEx does not handle polyploids, but since poppr can do it, we have set up a scheme to allow import of polyploids via this format. The limitation is that all of your loci have to have the same observed ploidy. Below is the example of <em>Phytophthora infestans</em> in the data set <code>Pinf</code> where some genotypes had observed tetraploid loci <span class="citation">(Goss et al., 2014)</span>.</p>
 <div class="figure">
-<img src="images/tetraploid.png" alt="tetraploid" />
+<img src="images/tetraploid.png" alt="" />
 <p class="caption">tetraploid</p>
 </div>
 <p>Highlighted in blue is the first locus and highlighted in red are two samples at that locus, an observed diploid and observed triploid. Note the extra zeroes needed to make the genotype tetraploid.</p>
@@ -755,8 +794,8 @@ <h2>Population strata</h2>
 <p>If you do not want to concatenate your population factors into one row, save them as a separate csv file and use the functions <code>read.table</code> and <code>strata</code> after you’ve imported your genetic data to achieve the same result.</p>
 </blockquote>
 <p>The data imported this way can be accessed with the function <code>splitStrata</code>:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># using monpop from above</span></a>
-<a class="sourceLine" id="cb3-2" data-line-number="2">monpop <span class="co"># Before (One level, Pop)</span></a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="co"># using monpop from above</span></span>
+<span id="cb3-2"><a href="#cb3-2"></a>monpop <span class="co"># Before (One level, Pop)</span></span></code></pre></div>
 <pre><code>## 
 ## This is a genclone object
 ## -------------------------
@@ -771,8 +810,8 @@ <h2>Population strata</h2>
 ##      1 stratum - Pop
 ##     12 populations defined - 
 ## 7_09_BB, 26_09_BB, 26_09_FR, ..., 45_10_FR, 26_11_BB, 26_11_FR</code></pre>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw">splitStrata</span>(monpop) &lt;-<span class="st"> </span><span class="er">~</span>Tree<span class="op">/</span>Year<span class="op">/</span>Symptom</a>
-<a class="sourceLine" id="cb5-2" data-line-number="2">monpop <span class="co"># After (Three distinct levels)</span></a></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw">splitStrata</span>(monpop) &lt;-<span class="st"> </span><span class="er">~</span>Tree<span class="op">/</span>Year<span class="op">/</span>Symptom</span>
+<span id="cb5-2"><a href="#cb5-2"></a>monpop <span class="co"># After (Three distinct levels)</span></span></code></pre></div>
 <pre><code>## 
 ## This is a genclone object
 ## -------------------------
@@ -794,10 +833,10 @@ <h2>References</h2>
 <!------>
 <div id="refs" class="references">
 <div id="ref-everhart2014finescale">
-<p>Everhart S., Scherm H. 2015. Fine-scale genetic structure of <em>Monilinia fructicola</em> during brown rot epidemics within individual peach tree canopies. <em>Phytopathology</em> 105:542–549. Available at: <a href="https://doi.org/10.1094/PHYTO-03-14-0088-R" class="uri">https://doi.org/10.1094/PHYTO-03-14-0088-R</a></p>
+<p>Everhart S., Scherm H. 2015. Fine-scale genetic structure of <em>Monilinia fructicola</em> during brown rot epidemics within individual peach tree canopies. <em>Phytopathology</em> 105:542–549. Available at: <a href="https://doi.org/10.1094/PHYTO-03-14-0088-R">https://doi.org/10.1094/PHYTO-03-14-0088-R</a></p>
 </div>
 <div id="ref-goss2014irish">
-<p>Goss EM., Tabima JF., Cooke DEL., Restrepo S., Fry WE., Forbes GA., Fieland VJ., Cardenas M., Grünwald NJ. 2014. The Irish potato famine pathogen <em>phytophthora infestans</em> originated in central mexico rather than the andes. <em>Proceedings of the National Academy of Sciences</em> 111:8791–8796. Available at: <a href="http://www.pnas.org/content/early/2014/05/29/1401884111.abstract" class="uri">http://www.pnas.org/content/early/2014/05/29/1401884111.abstract</a></p>
+<p>Goss EM., Tabima JF., Cooke DEL., Restrepo S., Fry WE., Forbes GA., Fieland VJ., Cardenas M., Grünwald NJ. 2014. The Irish potato famine pathogen <em>phytophthora infestans</em> originated in central mexico rather than the andes. <em>Proceedings of the National Academy of Sciences</em> 111:8791–8796. Available at: <a href="http://www.pnas.org/content/early/2014/05/29/1401884111.abstract">http://www.pnas.org/content/early/2014/05/29/1401884111.abstract</a></p>
 </div>
 </div>
 </div>
@@ -811,7 +850,7 @@ <h2>References</h2>
 
 // add bootstrap table styles to pandoc tables
 function bootstrapStylePandocTables() {
-  $('tr.header').parent('thead').parent('table').addClass('table table-condensed');
+  $('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
 }
 $(document).ready(function () {
   bootstrapStylePandocTables();

diff --git a/Data_Preparation_cache/html/__packages b/Data_Preparation_cache/html/__packages
@@ -6,6 +6,6 @@ ade4
 adegenet
 poppr
 vcfR
-igraph
-RColorBrewer
-ape
+reshape2
+ggplot2
+ggpubr
diff --git a/Data_Preparation_cache/html/unnamed-chunk-2_e67b734050544fe20b8a51c377820591.RData b/Data_Preparation_cache/html/unnamed-chunk-2_e67b734050544fe20b8a51c377820591.RData
diff --git a/Data_Preparation_cache/html/unnamed-chunk-2_e67b734050544fe20b8a51c377820591.rdx b/Data_Preparation_cache/html/unnamed-chunk-2_e67b734050544fe20b8a51c377820591.rdx
diff --git a/Data_Preparation_cache/html/unnamed-chunk-3_7b158e32bba29fbbd9e80db46b02f520.RData b/Data_Preparation_cache/html/unnamed-chunk-3_7b158e32bba29fbbd9e80db46b02f520.RData
diff --git a/Data_Preparation_cache/html/unnamed-chunk-3_7b158e32bba29fbbd9e80db46b02f520.rdb b/Data_Preparation_cache/html/unnamed-chunk-3_7b158e32bba29fbbd9e80db46b02f520.rdb
diff --git a/Data_Preparation_cache/html/unnamed-chunk-3_7b158e32bba29fbbd9e80db46b02f520.rdx b/Data_Preparation_cache/html/unnamed-chunk-3_7b158e32bba29fbbd9e80db46b02f520.rdx
diff --git a/Data_Preparation_cache/html/unnamed-chunk-4_a4894ba4ff449adfc39735aa454d5472.RData b/Data_Preparation_cache/html/unnamed-chunk-4_a4894ba4ff449adfc39735aa454d5472.RData
diff --git a/Data_Preparation_cache/html/unnamed-chunk-4_a4894ba4ff449adfc39735aa454d5472.rdb b/Data_Preparation_cache/html/unnamed-chunk-4_a4894ba4ff449adfc39735aa454d5472.rdb
diff --git a/Data_Preparation_cache/html/unnamed-chunk-4_a4894ba4ff449adfc39735aa454d5472.rdx b/Data_Preparation_cache/html/unnamed-chunk-4_a4894ba4ff449adfc39735aa454d5472.rdx