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README.html
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<body>
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<h1 id="tbea">tbea</h1>
<h2 id="overview">Overview</h2>
<p>An R package for pre- and post-processing in phylogenetic and
divergence-times Bayesian inference. Functions are provided for prior
specification in divergence time estimation using fossils as well as
other kinds of data. It provides tools for interacting with the input
and output of Bayesian platforms in evolutionary biology such as
‘BEAST2’, ‘MrBayes’, ‘RevBayes’, or ‘MCMCTree’. It Implements a simple
measure similarity between probability density functions for comparing
prior and posterior Bayesian densities, as well as code for calculating
the combination of distributions using conflation of Hill (2008).
Functions for estimating the origination time in collections of
distributions using the x-intercept (e.g., Draper and Smith, 1998) and
stratigraphic intervals (Marshall 2010) are also available.</p>
<p>Hill, T. 2008. “Conflations of probability distributions”.
Transactions of the American Mathematical Society, 363:3351-3372. <a href="doi:10.48550/arXiv.0808.1808">doi:10.48550/arXiv.0808.1808</a></p>
<p>Draper, N. R. and Smith, H. 1998. “Applied Regression Analysis”.
1–706. Wiley Interscience, New York. <a href="DOI:10.1002/9781118625590">DOI:10.1002/9781118625590</a>,</p>
<p>Marshall, C. R. 2010. “Using confidence intervals to quantify the
uncertainty in the end-points of stratigraphic ranges”. Quantitative
Methods in Paleobiology, 291–316. <a href="DOI:10.1017/S1089332600001911">DOI:10.1017/S1089332600001911</a>.</p>
<h2 id="installation">Installation</h2>
<p>You can now install the stable version from CRAN, and the development
one using <code>remotes</code>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"tbea"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"gaballench/tbea"</span>)</span></code></pre></div>
<h2 id="authorship-and-citation">Authorship and citation</h2>
<p>This package was created and maintained by Gustavo A. Ballen
(@gaballench) and Sandra Reinales (@spreinalesl).</p>
<p>Please cite this package as follows:</p>
<p>Ballen, G.A. & Reinales, S. (2024). tbea: tools for pre- and
post-processing in Bayesian evolutionary analyses. BioRxiv <a href="https://www.biorxiv.org/content/10.1101/2024.06.18.599561">https://www.biorxiv.org/content/10.1101/2024.06.18.599561</a>.</p>
<p>If you use bibtex, use the following entry in your .bib file:</p>
<pre><code>@article {Ballen2024.06.18.599561,
author = {Ballen, Gustavo A. and Reinales, Sandra},
title = {tbea: tools for pre- and post-processing in Bayesian evolutionary analyses},
year = {2024},
doi = {10.1101/2024.06.18.599561},
eprint = {https://www.biorxiv.org/content/early/2024/06/19/2024.06.18.599561.full.pdf},
journal = {bioRxiv}
}</code></pre>
<h2 id="problems">Problems?</h2>
<p>If you find a bug or unexpected behavior, please <a href="https://github.com/gaballench/tbea/issues">file an issue</a>.</p>
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