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updating pps_morpho
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laumul committed Jan 31, 2024
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28 changes: 14 additions & 14 deletions developer/index.html
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Expand Up @@ -96,51 +96,51 @@ <h3 id="developers-guide">Developer’s Guide</h3>
</div>

<div class="tutorial">
<a class="title" href="/developer/tutorial/"><p>Contributing a RevBayes tutorial</p>
<a class="title" href="/developer/docker/"><p>Using Docker with RevBayes</p>
</a>
<p class="subtitle"><p>How to write and host a tutorial on this website</p>
<p class="subtitle"><p>Containerized debugging and executeables</p>
</p>
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<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>
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<div class="tutorial">
<a class="title" href="/developer/implementation/"><p>Implementing functions, distributions, and moves</p>
<a class="title" href="/developer/tutorial/"><p>Contributing a RevBayes tutorial</p>
</a>
<p class="subtitle"><p>Getting started with RevBayes development</p>
<p class="subtitle"><p>How to write and host a tutorial on this website</p>
</p>
</div>

<div class="tutorial">
<a class="title" href="/developer/docker/"><p>Using Docker with RevBayes</p>
<a class="title" href="/developer/implementation/"><p>Implementing functions, distributions, and moves</p>
</a>
<p class="subtitle"><p>Containerized debugging and executeables</p>
<p class="subtitle"><p>Getting started with RevBayes development</p>
</p>
</div>

<div class="tutorial">
<a class="title" href="/developer/validation/"><p>Validation Scripts in RevBayes</p>
<a class="title" href="/developer/best_practices/"><p>Best practices in RevBayes</p>
</a>
<p class="subtitle"><p>Ensuring correct performance of models and methods using simulations</p>
<p class="subtitle"><p>Coding and documentation guidelines</p>
</p>
</div>

<div class="tutorial">
<a class="title" href="/developer/tests/"><p>Integration Tests in RevBayes</p>
<a class="title" href="/developer/automated_builds/"><p>Automated building and testing in RevBayes</p>
</a>
<p class="subtitle"><p>Ensuring that code changes did not unexpectedly alter the software</p>
<p class="subtitle"><p>Quick automated feedback on code changes</p>
</p>
</div>

<div class="tutorial">
<a class="title" href="/developer/automated_builds/"><p>Automated building and testing in RevBayes</p>
<a class="title" href="/developer/validation/"><p>Validation Scripts in RevBayes</p>
</a>
<p class="subtitle"><p>Quick automated feedback on code changes</p>
<p class="subtitle"><p>Ensuring correct performance of models and methods using simulations</p>
</p>
</div>

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2 changes: 1 addition & 1 deletion developer/setup/eclipse.html
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<h1 class="maintitle">Setting up Eclipse for RevBayes development</h1>

<h4 class="authors"></h4>
<h5>Last modified on August 31, 2018</h5>
<h5>Last modified on September 1, 2018</h5>
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<p>Eclipse is a Java-based, cross-platform IDE with lots of nice features that make it convenient for RevBayes development. First, it’s cross-platform, and unlike Xcode, you can use any compiler you like (not just <code class="language-plaintext highlighter-rouge">clang</code>).</p>
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2 changes: 1 addition & 1 deletion developer/setup/netbeans.html
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<h1 class="maintitle"></h1>

<h4 class="authors"></h4>
<h5>Last modified on March 10, 2018</h5>
<h5>Last modified on March 11, 2018</h5>
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<p>Conventions: File paths are relative to the repository root.</p>
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2 changes: 1 addition & 1 deletion developer/setup/vim.html
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<h1 class="maintitle">Setting up vim for RevBayes development</h1>

<h4 class="authors"></h4>
<h5>Last modified on March 10, 2018</h5>
<h5>Last modified on March 11, 2018</h5>
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<p><a href="http://www.vim.org">Vim</a> is a text editor that some people love.
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2 changes: 1 addition & 1 deletion developer/tutorial/index.html
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<h1 class="maintitle">Contributing a RevBayes tutorial</h1>

<h4 class="authors"></h4>
<h5>Last modified on May 30, 2019</h5>
<h5>Last modified on May 31, 2019</h5>
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2 changes: 1 addition & 1 deletion tutorials/biogeo/biogeo_dating.html
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<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 27, 2022</h5>
<h5>Last modified on February 28, 2022</h5>
</div>


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2 changes: 1 addition & 1 deletion tutorials/biogeo/biogeo_simple.html
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<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 27, 2022</h5>
<h5>Last modified on February 28, 2022</h5>
</div>


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2 changes: 1 addition & 1 deletion tutorials/chromo/index.html
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<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 27, 2022</h5>
<h5>Last modified on February 28, 2022</h5>
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8 changes: 4 additions & 4 deletions tutorials/cont_traits/relaxed_bm.html
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Expand Up @@ -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>


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<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>

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8 changes: 4 additions & 4 deletions tutorials/cont_traits/relaxed_ou.html
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<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>


Expand All @@ -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>
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8 changes: 4 additions & 4 deletions tutorials/cont_traits/simple_bm.html
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Expand Up @@ -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>


Expand All @@ -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>
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8 changes: 4 additions & 4 deletions tutorials/cont_traits/simple_ou.html
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Expand Up @@ -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>

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Expand All @@ -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>
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4 changes: 2 additions & 2 deletions tutorials/divrate/branch_specific.html
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Expand Up @@ -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>
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8 changes: 4 additions & 4 deletions tutorials/divrate/div_rate_intro.html
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Expand Up @@ -357,14 +357,14 @@ <h3 class="subsection" id="the-birth-death-branching-process">The birth-death br
<li><span id="Condamine2018">Condamine F.L., Rolland J., Höhna S., Sperling F.A.H., Sanmartín I. 2018. Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies. Systematic Biology. 67:940–964.</span>

</li>
<li><span id="Hoehna2013">Höhna S. 2013. Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes. Bioinformatics. 29:1367–1374.</span>
<li><span id="Hoehna2014a">Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.</span>

<a href="https://doi.org/10.1093/bioinformatics/btt153">10.1093/bioinformatics/btt153</a>
<a href="https://doi.org/10.1371/journal.pone.0084184">10.1371/journal.pone.0084184</a>

</li>
<li><span id="Hoehna2014a">Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.</span>
<li><span id="Hoehna2013">Höhna S. 2013. Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes. Bioinformatics. 29:1367–1374.</span>

<a href="https://doi.org/10.1371/journal.pone.0084184">10.1371/journal.pone.0084184</a>
<a href="https://doi.org/10.1093/bioinformatics/btt153">10.1093/bioinformatics/btt153</a>

</li>
<li><span id="Hoehna2015a">Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.</span>
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10 changes: 5 additions & 5 deletions tutorials/divrate/ebd.html
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<li><a href="/tutorials/divrate/data/primates.tre">primates.tre</a></li>

<li><a href="/tutorials/intro/data/primates.tre">primates.tre</a></li>

<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/divrate/data/primates.tre">primates.tre</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>

<li><a href="/tutorials/biogeo/data/primates_tree.nex">primates_tree.nex</a></li>

</ul>


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6 changes: 3 additions & 3 deletions tutorials/divrate/env.html
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Expand Up @@ -101,14 +101,14 @@ <h2>Data files and scripts</h2>

<li><a href="/tutorials/intro/data/primates.tre">primates.tre</a></li>

<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/biogeo/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/intro/data/primates_tree.nex">primates_tree.nex</a></li>

</ul>


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2 changes: 1 addition & 1 deletion tutorials/divrate/sampling.html
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<h1 class="maintitle">Diversification Rate Estimation with Missing Taxa</h1>
<h3 class="subtitle">How to estimate diversification rates with incomplete taxon sampling</h3>
<h4 class="authors">Sebastian Höhna, Will Freyman and Mike May</h4>
<h5>Last modified on February 27, 2022</h5>
<h5>Last modified on February 28, 2022</h5>
</div>


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4 changes: 2 additions & 2 deletions tutorials/divrate/simple.html
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<li><a href="/tutorials/divrate/data/primates.tre">primates.tre</a></li>

<li><a href="/tutorials/intro/data/primates.tre">primates.tre</a></li>

<li><a href="/tutorials/divrate/data/primates.tre">primates.tre</a></li>

<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>
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2 changes: 1 addition & 1 deletion tutorials/fbd/fbd_specimen.html
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<h1 class="maintitle">Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Extant Taxa and Fossil Specimens</h1>
<h3 class="subtitle">Joint inference of divergence times and phylogenetic relationships of fossil and extant taxa</h3>
<h4 class="authors">Tracy A. Heath, April M. Wright, and Walker Pett</h4>
<h5>Last modified on April 8, 2020</h5>
<h5>Last modified on April 9, 2020</h5>
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2 changes: 1 addition & 1 deletion tutorials/fbd_range/index.html
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<h1 class="maintitle">Macroevolutionary Analysis of Stratigraphic Range Data</h1>
<h3 class="subtitle">Inference of diversification rates using the fossilized birth-death range process</h3>
<h4 class="authors">Rachel Warnock and Walker Pett</h4>
<h5>Last modified on February 27, 2022</h5>
<h5>Last modified on February 28, 2022</h5>
</div>


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