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<meta name="description" content="Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well as other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.">
<title>R package for diversity dynamics • divDyn</title>
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<img src="logo.png" class="logo" alt=""><h1 id="divdyn-diversity-dynamics-">divDyn: Diversity Dynamics <a class="anchor" aria-label="anchor" href="#divdyn-diversity-dynamics-"></a>
</h1>
</div>
<p><a href="https://github.com/divDyn/divDyn" class="external-link"><img src="https://img.shields.io/badge/devel%20version-0.8.2-green.svg"></a> <a href="https://cran.r-project.org/package=divDyn" class="external-link"><img src="https://www.r-pkg.org/badges/version/divDyn?color=blue"></a> <a href="https://cran.r-project.org/package=divDyn" class="external-link"><img src="http://cranlogs.r-pkg.org/badges/grand-total/divDyn?color=yellow"></a> <a href="https://cran.r-project.org/web/checks/check_results_divDyn.html" class="external-link"><img src="https://badges.cranchecks.info/summary/divDyn.svg" alt="CRAN checks"></a></p>
<div class="section level3">
<h3 id="diversity-dynamics-using-fossil-occurrence-data">Diversity Dynamics using fossil occurrence data<a class="anchor" aria-label="anchor" href="#diversity-dynamics-using-fossil-occurrence-data"></a>
</h3>
<p>Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well as other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <a href="doi:10.1101/423780" class="uri">doi:10.1101/423780</a>.</p>
<p><br></p>
</div>
<div class="section level2">
<h2 id="site-contents">Site Contents<a class="anchor" aria-label="anchor" href="#site-contents"></a>
</h2>
<hr>
<p>The site is getting filled with the following content:</p>
<div class="section level4">
<h4 id="tutorials-with-the-pbdb-coral-data-from-2015">Tutorials with the PBDB coral data from 2015<a class="anchor" aria-label="anchor" href="#tutorials-with-the-pbdb-coral-data-from-2015"></a>
</h4>
<ul><li>This particular dataset is used to ensure interface stability and consistency.</li></ul>
</div>
<div class="section level4">
<h4 id="the-ddphanero-analysis-from-the-miee-paper">The ‘ddPhanero’ analysis (from the MiEE paper)<a class="anchor" aria-label="anchor" href="#the-ddphanero-analysis-from-the-miee-paper"></a>
</h4>
<ul><li>Execute up-to-date versions</li></ul>
</div>
<div class="section level4"><h4 id="function-reference-and-technical-material">Function reference and technical material<a class="anchor" aria-label="anchor" href="#function-reference-and-technical-material"></a>
</h4></div>
<div class="section level4">
<h4 id="additional-material">Additional material<a class="anchor" aria-label="anchor" href="#additional-material"></a>
</h4>
<ul><li>How-to guides on combining the package’s capabilities with other packages are deposited on the <a href="https://www.evolv-ed.net/" class="external-link">evolvED blog</a>.</li></ul>
<p><br></p>
</div>
</div>
<div class="section level2">
<h2 id="example-output">Example output<a class="anchor" aria-label="anchor" href="#example-output"></a>
</h2>
<hr>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># attach library</span></span>
<span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">divDyn</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># import example data</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">corals</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">stages</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># calculate metrics of diversity dynamics</span></span>
<span> <span class="va">dd</span> <span class="op"><-</span> <span class="fu"><a href="reference/divDyn.html">divDyn</a></span><span class="op">(</span><span class="va">corals</span>, tax<span class="op">=</span><span class="st">"genus"</span>, bin<span class="op">=</span><span class="st">"stg"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># plotting</span></span>
<span> <span class="fu"><a href="reference/tsplot.html">tsplot</a></span><span class="op">(</span><span class="va">stages</span>, shading<span class="op">=</span><span class="st">"series"</span>, boxes<span class="op">=</span><span class="st">"sys"</span>, xlim<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">260</span>,<span class="fl">0</span><span class="op">)</span>, </span>
<span> ylab<span class="op">=</span><span class="st">"Range-through diversity (genera) - 2015"</span>, ylim<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">230</span><span class="op">)</span>,</span>
<span> boxes.col<span class="op">=</span><span class="st">"systemCol"</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/graphics/lines.html" class="external-link">lines</a></span><span class="op">(</span><span class="va">stages</span><span class="op">$</span><span class="va">mid</span>, <span class="va">dd</span><span class="op">$</span><span class="va">divRT</span>, lwd<span class="op">=</span><span class="fl">2</span><span class="op">)</span></span></code></pre></div>
<p><img src="reference/figures/divDyn_example.png"></p>
<p><br></p>
</div>
<div class="section level2">
<h2 id="plans">Plans<a class="anchor" aria-label="anchor" href="#plans"></a>
</h2>
<hr>
<div class="section level4">
<h4 id="near">Near<a class="anchor" aria-label="anchor" href="#near"></a>
</h4>
<ul>
<li>Splitting up vignettes to separate <strong>Tutorials</strong>
</li>
<li>Adding the ddPhanero case study with updates</li>
<li>Package updates</li>
</ul>
</div>
<div class="section level4">
<h4 id="distant">Distant<a class="anchor" aria-label="anchor" href="#distant"></a>
</h4>
<ul><li>Writing a C++ library from the core functionality and porting it to Python and Julia</li></ul>
<p><img alt="The logo of the divDyn project" src="https://github.com/divDyn/assets/raw/master/logo/divDyn_logo_medium.png" width="300"></p>
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<h2 data-toc-skip>Links</h2>
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<li><a href="https://cloud.r-project.org/package=divDyn" class="external-link">View on CRAN</a></li>
<li><a href="https://github.com/divDyn/divDyn/" class="external-link">Browse source code</a></li>
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<li><a href="https://creativecommons.org/licenses/by/4.0" class="external-link">CC BY 4.0</a></li>
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<h2 data-toc-skip>Citation</h2>
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<li><a href="authors.html#citation">Citing divDyn</a></li>
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<h2 data-toc-skip>Developers</h2>
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<li>
<a href="https://palaeobiology.nat.fau.de/people/instructors/kocsis/" class="external-link">Adam T. Kocsis</a> <br><small class="roles"> Maintainer, author </small> <a href="https://orcid.org/0000-0002-9028-665X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://researchers.mq.edu.au/en/persons/john-alroy" class="external-link">John Alroy</a> <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-9882-2111" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.gzn.nat.fau.eu/palaeontologie/team/former-members/reddin/" class="external-link">Carl J. Reddin</a> <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-5930-1164" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.gzn.nat.fau.eu/palaeontologie/team/professors/kiessling/" class="external-link">Wolfgang Kiessling</a> <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-1088-2014" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
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<a href="https://www.gzn.nat.fau.eu/" class="external-link"><img src="https://www.gzn.nat.fau.de/files/2017/05/cropped-gzn-logo.jpg" alt="geozentrum" width="80"></a> <br><small class="roles"> Funder </small> </li>
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<p>Developed by <a href="https://palaeobiology.nat.fau.de/people/instructors/kocsis/" class="external-link">Adam T. Kocsis</a>, <a href="https://researchers.mq.edu.au/en/persons/john-alroy" class="external-link">John Alroy</a>, <a href="https://www.gzn.nat.fau.eu/palaeontologie/team/former-members/reddin/" class="external-link">Carl J. Reddin</a>, <a href="https://www.gzn.nat.fau.eu/palaeontologie/team/professors/kiessling/" class="external-link">Wolfgang Kiessling</a>, <a href="https://www.dfg.de/en/index.jsp" class="external-link"><img src="https://www.dfg.de/includes/bausteine/open_graph_de/dfgfallback.jpg" alt="dfg" width="80"></a>, <a href="https://www.gzn.nat.fau.eu/" class="external-link"><img src="https://www.gzn.nat.fau.de/files/2017/05/cropped-gzn-logo.jpg" alt="geozentrum" width="80"></a>.</p>
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