Updated PoMoBalance tutorial to run on the dev_PoMo_bs_master branch

revbayes · Apr 22, 2024 · 3264d85 · 3264d85
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diff --git a/developer/index.html b/developer/index.html
@@ -96,23 +96,23 @@ <h3 id="developers-guide">Developer’s Guide</h3>
 </div>
 
 <div class="tutorial">
-<a class="title" href="/developer/automated_builds/"><p>Automated building and testing in RevBayes</p>
+<a class="title" href="/developer/docker/"><p>Using Docker with RevBayes</p>
 </a>
-<p class="subtitle"><p>Quick automated feedback on code changes</p>
+<p class="subtitle"><p>Containerized debugging and executeables</p>
 </p>
 </div>
 
 <div class="tutorial">
-<a class="title" href="/developer/best_practices/"><p>Best practices in RevBayes</p>
+<a class="title" href="/developer/tests/"><p>Integration Tests in RevBayes</p>
 </a>
-<p class="subtitle"><p>Coding and documentation guidelines</p>
+<p class="subtitle"><p>Ensuring that code changes did not unexpectedly alter the software</p>
 </p>
 </div>
 
 <div class="tutorial">
-<a class="title" href="/developer/docker/"><p>Using Docker with RevBayes</p>
+<a class="title" href="/developer/tutorial/"><p>Contributing a RevBayes tutorial</p>
 </a>
-<p class="subtitle"><p>Containerized debugging and executeables</p>
+<p class="subtitle"><p>How to write and host a tutorial on this website</p>
 </p>
 </div>
 
@@ -124,16 +124,16 @@ <h3 id="developers-guide">Developer’s Guide</h3>
 </div>
 
 <div class="tutorial">
-<a class="title" href="/developer/tests/"><p>Integration Tests in RevBayes</p>
+<a class="title" href="/developer/best_practices/"><p>Best practices in RevBayes</p>
 </a>
-<p class="subtitle"><p>Ensuring that code changes did not unexpectedly alter the software</p>
+<p class="subtitle"><p>Coding and documentation guidelines</p>
 </p>
 </div>
 
 <div class="tutorial">
-<a class="title" href="/developer/tutorial/"><p>Contributing a RevBayes tutorial</p>
+<a class="title" href="/developer/automated_builds/"><p>Automated building and testing in RevBayes</p>
 </a>
-<p class="subtitle"><p>How to write and host a tutorial on this website</p>
+<p class="subtitle"><p>Quick automated feedback on code changes</p>
 </p>
 </div>
 

diff --git a/developer/setup/netbeans.html b/developer/setup/netbeans.html
@@ -55,7 +55,7 @@
 	<h1 class="maintitle"></h1>
 
 	<h4 class="authors"></h4>
-  <h5>Last modified on March 11, 2018</h5>
+  <h5>Last modified on March 10, 2018</h5>
 </div>
 
 <p>Conventions: File paths are relative to the repository root.</p>

diff --git a/developer/setup/vim.html b/developer/setup/vim.html
@@ -55,7 +55,7 @@
 	<h1 class="maintitle">Setting up vim for RevBayes development</h1>
 
 	<h4 class="authors"></h4>
-  <h5>Last modified on March 11, 2018</h5>
+  <h5>Last modified on March 10, 2018</h5>
 </div>
 
 <p><a href="http://www.vim.org">Vim</a> is a text editor that some people love.

diff --git a/developer/tutorial/index.html b/developer/tutorial/index.html
@@ -55,7 +55,7 @@
 	<h1 class="maintitle">Contributing a RevBayes tutorial</h1>
 
 	<h4 class="authors"></h4>
-  <h5>Last modified on May 31, 2019</h5>
+  <h5>Last modified on May 30, 2019</h5>
 </div>
 
 <div class="sidebar no-print">

diff --git a/tutorials/biogeo/biogeo_dating.html b/tutorials/biogeo/biogeo_dating.html
@@ -55,7 +55,7 @@
 	<h1 class="maintitle">Biogeographic Dating of Divergence Times</h1>
 	<h3 class="subtitle">Estimating divergence times with molecular, biogeographic, and paleogeographic evidence under the Dispersal-Extirpation-Cladogenesis (DEC) model</h3>
 	<h4 class="authors">Michael J. Landis</h4>
-  <h5>Last modified on February 28, 2022</h5>
+  <h5>Last modified on February 27, 2022</h5>
 </div>
 
 

diff --git a/tutorials/biogeo/biogeo_simple.html b/tutorials/biogeo/biogeo_simple.html
@@ -55,7 +55,7 @@
 	<h1 class="maintitle">Simple Phylogenetic Analysis of Historical Biogeography</h1>
 	<h3 class="subtitle">Estimating ancestral ranges using the Dispersal-Extirpation-Cladogenesis (DEC) model</h3>
 	<h4 class="authors">Michael J. Landis</h4>
-  <h5>Last modified on February 28, 2022</h5>
+  <h5>Last modified on February 27, 2022</h5>
 </div>
 
 

diff --git a/tutorials/chromo/index.html b/tutorials/chromo/index.html
@@ -55,7 +55,7 @@
 	<h1 class="maintitle">Chromosome Evolution</h1>
 	<h3 class="subtitle">Modeling chromosome evolution with ChromEvol, BiChroM, and ChromoSSE</h3>
 	<h4 class="authors">William A. Freyman and Sebastian Höhna</h4>
-  <h5>Last modified on February 28, 2022</h5>
+  <h5>Last modified on February 27, 2022</h5>
 </div>
 
 

diff --git a/tutorials/cont_traits/relaxed_bm.html b/tutorials/cont_traits/relaxed_bm.html
@@ -99,14 +99,14 @@ <h2>Data files and scripts</h2>
 
 
 
-          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/divrate/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/intro/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/morph_ase/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 
@@ -121,10 +121,10 @@ <h2>Data files and scripts</h2>
 
           <li><a href="/tutorials/cont_traits/data/primates_cont_traits.nex">primates_cont_traits.nex</a></li>
 
-          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/sse/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 </blockquote>

diff --git a/tutorials/cont_traits/relaxed_ou.html b/tutorials/cont_traits/relaxed_ou.html
@@ -99,14 +99,14 @@ <h2>Data files and scripts</h2>
 
 
 
-          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/divrate/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/intro/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/morph_ase/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 
@@ -121,10 +121,10 @@ <h2>Data files and scripts</h2>
 
           <li><a href="/tutorials/cont_traits/data/primates_cont_traits.nex">primates_cont_traits.nex</a></li>
 
-          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/sse/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 </blockquote>

diff --git a/tutorials/cont_traits/simple_bm.html b/tutorials/cont_traits/simple_bm.html
@@ -97,14 +97,14 @@ <h2>Data files and scripts</h2>
 
 
 
-          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/divrate/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/intro/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/morph_ase/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 
@@ -121,10 +121,10 @@ <h2>Data files and scripts</h2>
 
           <li><a href="/tutorials/cont_traits/data/primates_cont_traits.nex">primates_cont_traits.nex</a></li>
 
-          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/sse/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 </blockquote>

diff --git a/tutorials/cont_traits/simple_ou.html b/tutorials/cont_traits/simple_ou.html
@@ -97,14 +97,14 @@ <h2>Data files and scripts</h2>
 
 
 
-          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/divrate/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/intro/data/primates_tree.nex">primates_tree.nex</a></li>
 
           <li><a href="/tutorials/morph_ase/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 
@@ -123,10 +123,10 @@ <h2>Data files and scripts</h2>
 
           <li><a href="/tutorials/cont_traits/data/primates_cont_traits.nex">primates_cont_traits.nex</a></li>
 
-          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/sse/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/cont_traits/data/primates_tree.nex">primates_tree.nex</a></li>
+
         </ul>
 
 </blockquote>

diff --git a/tutorials/divrate/branch_specific.html b/tutorials/divrate/branch_specific.html
@@ -97,10 +97,10 @@ <h2>Data files and scripts</h2>
 
           <li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>
 
-          <li><a href="/tutorials/divrate/data/primates_tree.nex">primates_tree.nex</a></li>
-
           <li><a href="/tutorials/intro/data/primates_tree.nex">primates_tree.nex</a></li>
 
+          <li><a href="/tutorials/divrate/data/primates_tree.nex">primates_tree.nex</a></li>
+
           <li><a href="/tutorials/morph_ase/data/primates_tree.nex">primates_tree.nex</a></li>
 
         </ul>

diff --git a/tutorials/divrate/data/crocs_taxa.txt b/tutorials/divrate/data/crocs_taxa.txt