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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Welcome to DateLife’s R package GitHub repository! • datelife</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.1.0/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.1.0/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Welcome to DateLife’s R package GitHub repository!"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small>
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<img src="" class="logo" alt=""><h1>Welcome to DateLife’s R package GitHub repository!</h1>
<small class="dont-index">Source: <a href="https://github.com/phylotastic/datelife/blob/HEAD/README.knit.md" class="external-link"><code>README.knit.md</code></a></small>
</div>
<p><img src="reference/figures/datelife-hexsticker-ai.png" align="right" style="width:150px"></p>
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<p><img src="https://img.shields.io/github/r-package/v/phylotastic/datelife?color=green" alt="GitHub R package version"><a href="https://app.codecov.io/gh/phylotastic/datelife" class="external-link"><img src="https://codecov.io/gh/phylotastic/datelife/branch/master/graph/badge.svg" alt="codecov"></a> <a href="https://github.com/phylotastic/datelife/issues" class="external-link"><img src="https://img.shields.io/github/issues-raw/phylotastic/datelife.svg" alt="Github Open Issues"></a> <a href="https://github.com/phylotastic/datelife/issues?q=is%3Aissue+is%3Aclosed" class="external-link"><img src="https://img.shields.io/github/issues-closed-raw/phylotastic/datelife.svg" alt="Github Closed Issues"></a> <a href="https://zenodo.org/badge/latestdoi/23036/phylotastic/datelife" class="external-link"><img src="https://zenodo.org/badge/23036/phylotastic/datelife.svg" alt="DOI"></a> <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1458603" class="external-link"><img src="https://img.shields.io/badge/NSF-1458603-white.svg" alt="NSF-1458603"></a> <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=0905606" class="external-link"><img src="https://img.shields.io/badge/NSF-0905606-white.svg" alt="NSF-0905606"></a> <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1458572" class="external-link"><img src="https://img.shields.io/badge/NSF-1458572-white.svg" alt="NSF-1458572"></a> <a href="https://github.com/phylotastic/datelife/actions" class="external-link"><img src="https://github.com/phylotastic/datelife/workflows/R-CMD-check/badge.svg" alt="R-CMD-check"></a> <!-- badges: end --></p>
<div id="welcome-to-datelifes-r-package-github-repository" class="section level1">
<p>Get a phylogenetic tree with branch lengths proportional to geologic time (aka a <em><strong>chronogram</strong></em>) of any two or more lineages of interest to you.</p>
<p>Use the <code>datelife</code> R package locally, or through <a href="http://datelife.org/query/" class="external-link">DateLife’s website</a> to search for chronograms available for your lineages in <a href="https://tree.opentreeoflife.org/curator" class="external-link">Open Tree of Life’s tree store</a>.</p>
<p>You can also date a phylogenetic tree of your own making (or choosing one from the literature), using node ages from chronograms found with <code>datelife</code>, using the congruification method (<a href="https://doi.org/10.1111/2041-210X.12051" class="external-link">Eastman et al. 2013</a>) implemented with <em>geiger</em> (<a href="https://doi.org/10.1093/bioinformatics/btm538" class="external-link">Harmon et al. 2008</a>).</p>
<p><code>datelife</code> has been developed as part of the <a href="http://phylotastic.org/" class="external-link">phylotastic</a> (NSF-funded) project, and is still under development.</p>
<ol style="list-style-type: decimal"><li><a href="#installation">Installation</a></li>
<li><a href="#citation">Citation</a></li>
<li><a href="#feedback">Feedback and info for developers</a></li>
<li><a href="#license">License</a></li>
</ol><div class="section level2">
<h2 id="installation">1. Installation<a class="anchor" aria-label="anchor" href="#installation"></a></h2>
<p>Once accepted on CRAN, <code>datelife</code>s stable version will be available for installation with:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"datelife"</span><span class="op">)</span></code></pre></div>
<p>For now, you can install the development version from the GitHub repository:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"phylotastic/datelife"</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level2">
<h2 id="citation">2. Citation<a class="anchor" aria-label="anchor" href="#citation"></a></h2>
<p>If you use <code>datelife</code> for a publication, please cite the R package and the accompanying paper:</p>
<p>
O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright A, Schliep K, Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M (2022). <em>datelife: Go from a List of Taxa or a Tree to a Chronogram using Open Scientific Data on Time of Lineage Divergence</em>. R package version 0.5.0.
</p>
<p>
Sanchez-Reyes L, O’Meara B (2019). “datelife: Leveraging databases and analytical tools to reveal the dated Tree of Life.” <em>bioRxiv</em>, <b>782094</b>. doi: <a href="https://doi.org/10.1101/782094" class="external-link">10.1101/782094</a>.
</p>
<p>You can get these citations and the bibtex entry with:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/citation.html" class="external-link">citation</a></span><span class="op">(</span><span class="st">"datelife"</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/utils/toLatex.html" class="external-link">toBibtex</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/citation.html" class="external-link">citation</a></span><span class="op">(</span><span class="st">"datelife"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>.bibtex files are available</p>
</div>
<div class="section level2">
<h2 id="feedback-and-information-for-developers">3. Feedback and Information for Developers<a class="anchor" aria-label="anchor" href="#feedback-and-information-for-developers"></a></h2>
<p>We welcome and encourage to post a <a href="https://github.com/phylotastic/datelife/issues/new" class="external-link">GitHub issue</a> with any comments, ideas and questions about <code>datelife</code>’s software and website. If you want to contribute with code directly, we welcome and encourage <a href="https://github.com/phylotastic/datelife/pulls" class="external-link">pull requests</a>.</p>
<div class="section level4">
<h4 id="function-documentation">Function documentation:<a class="anchor" aria-label="anchor" href="#function-documentation"></a></h4>
<p>Package and function documentation was generated with <a href="https://CRAN.R-project.org/package=roxygen2" class="external-link">roxygen2</a>:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">roxygen2</span><span class="fu">::</span><span class="fu"><a href="https://roxygen2.r-lib.org/reference/roxygenize.html" class="external-link">roxygenise</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level4">
<h4 id="styling-code">Styling code:<a class="anchor" aria-label="anchor" href="#styling-code"></a></h4>
<p>We used the package <a href="https://CRAN.R-project.org/package=lintr" class="external-link">lintr</a> to check for coding style:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">lintr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/lintr/man/lint_package.html" class="external-link">lint_package</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level4">
<h4 id="calculating-test-coverage">Calculating test coverage:<a class="anchor" aria-label="anchor" href="#calculating-test-coverage"></a></h4>
<p>Code coverage was calculated with the package <a href="https://CRAN.R-project.org/package=covr" class="external-link">covr</a>:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">cov</span> <span class="op"><-</span> <span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/package_coverage.html" class="external-link">package_coverage</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu">usethis</span><span class="fu">::</span><span class="fu"><a href="https://usethis.r-lib.org/reference/use_data.html" class="external-link">use_data</a></span><span class="op">(</span><span class="va">cov</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>You can see an interactive report of testing coverage:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/report.html" class="external-link">report</a></span><span class="op">(</span><span class="va">cov</span><span class="op">)</span></code></pre></div>
<p>And, find code with zero coverage:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/zero_coverage.html" class="external-link">zero_coverage</a></span><span class="op">(</span><span class="va">cov</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level4">
<h4 id="releasing-to-cran">Releasing to CRAN:<a class="anchor" aria-label="anchor" href="#releasing-to-cran"></a></h4>
<p>To be able to release to CRAN, the first step is to pass a check. To run a local check, you can use the command <code>R CMD check</code> from your terminal. For that, change directories to the one above your working clone of the <code>datelife</code> repo:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="bu">cd</span> ../</a></code></pre></div>
<p>Generate a tar ball for your package by running <code>R CMD build package-name</code>:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="ex">R</span> CMD build datelife</a></code></pre></div>
<p>Finally, run <code>R CMD check package-tar-ball</code> on the tar ball that you just generated:</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="ex">R</span> CMD check datelife_0.6.0.tar.gz</a></code></pre></div>
<p>If you do not have access to different OS to test your package on, the <a href="https://CRAN.R-project.org/package=rhub" class="external-link">rhub</a> package allows remote testing on a variety of OS with the command:</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">rhub</span><span class="fu">::</span><span class="fu"><a href="https://r-hub.github.io/rhub/reference/check_for_cran.html" class="external-link">check_for_cran</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level4">
<h4 id="generating-datelifes-hexsticker">Generating <code>datelife</code>’s hexsticker:<a class="anchor" aria-label="anchor" href="#generating-datelifes-hexsticker"></a></h4>
<p>Code used to generate current <code>datelife</code>’s logo hexsticker is in <a href="https://github.com/phylotastic/datelife/blob/master/data-raw/hexsticker-current.R" class="external-link">data-raw/hexsticker-current.R</a></p>
</div>
<div class="section level4">
<h4 id="rendering-the-vignettes">Rendering the vignettes:<a class="anchor" aria-label="anchor" href="#rendering-the-vignettes"></a></h4>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/knit.html" class="external-link">knit</a></span><span class="op">(</span><span class="st">"vignettes/Getting_started_with_datelife.Rmd"</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level4">
<h4 id="creating-a-website-for-the-package">Creating a website for the package<a class="anchor" aria-label="anchor" href="#creating-a-website-for-the-package"></a></h4>
<p>Using <code>pkgdown</code> for this is quite straightforwrd and fun:</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">usethis</span><span class="fu">::</span><span class="fu"><a href="https://usethis.r-lib.org/reference/use_pkgdown.html" class="external-link">use_pkgdown</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level4">
<h4 id="submitting-to-cran">Submitting to CRAN<a class="anchor" aria-label="anchor" href="#submitting-to-cran"></a></h4>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/release.html" class="external-link">release</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
</div>
<div class="section level2">
<h2 id="license">4. License<a class="anchor" aria-label="anchor" href="#license"></a></h2>
<p>This package is free and open source software, licensed under GPL.</p>
</div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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<p></p><p>Developed by Brian O’Meara, Jonathan Eastman, Tracy Heath, April Wright, Klaus Schliep, Scott Chamberlain, Peter Midford, Luke Harmon, Joseph Brown, Matt Pennell, Mike Alfaro, Luna L. Sanchez Reyes.</p>
</div>
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
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