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<title>Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic
    and Genomic Data • outbreaker2</title>
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<meta property="og:description" content="Bayesian reconstruction of disease outbreaks using epidemiological
    and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
    C and Ferguson N. 2014. &lt;doi:10.1371/journal.pcbi.1003457&gt;. Campbell, F,
    Cori A, Ferguson N, Jombart T. 2019. &lt;doi:10.1371/journal.pcbi.1006930&gt;.">
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<div id="outbreaker2-a-framework-for-reconstructing-disease-outbreaks" class="section level2">
<h2 class="hasAnchor">
<a href="#outbreaker2-a-framework-for-reconstructing-disease-outbreaks" class="anchor"></a><em>outbreaker2: a framework for reconstructing disease outbreaks</em>
</h2>
<p>Welcome to the project page of <em>outbreaker2</em>, a Bayesian framework for integrating epidemiological and genetic data to reconstruct transmission trees of densely sampled outbreaks. It re-implements, generalises and replaces the model of <a href="https://github.com/thibautjombart/outbreaker"><em>outbreaker</em></a>, and uses a modular approach which enables fine customisation of priors, likelihoods and parameter movements (see <a href="http://www.repidemicsconsortium.org/outbreaker2/articles/customisation.html">customisation vignette</a>).</p>
<div id="note-correction-to-genetic-likelihood" class="section level3">
<h3 class="hasAnchor">
<a href="#note-correction-to-genetic-likelihood" class="anchor"></a>NOTE: Correction to genetic likelihood</h3>
<p>The genetic likelihood of the <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003457">original <em>outbreaker</em> paper</a> was found to contain a minor mistake in accounting for unobserved generations of infection. As of June 7th 2019, <em>outbreaker2</em> will use the correct genetic likelihood published <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006930">here</a>.</p>
<p>The original genetic likelihood was:</p>
<p><img src="https://latex.codecogs.com/svg.latex?%5Cmu%5E%7Bd(s_i,s_%7B%5Calpha_i%7D)%7D(1&amp;space;-&amp;space;%5Cmu)%5E%7B(%5Ckappa_i%5Ctimes&amp;space;l(s_i,&amp;space;s_%7B%5Calpha_i%7D))&amp;space;-&amp;space;d(s_i,s_%7B%5Calpha_i%7D)%7D" title="\mu^{d(s_i,s_{\alpha_i})}(1 - \mu)^{(\kappa_i\times l(s_i, s_{\alpha_i})) - d(s_i,s_{\alpha_i})}"></p>
<p>The corrected genetic likelihood is:</p>
<p><img src="https://latex.codecogs.com/svg.latex?(%5Ckappa_i&amp;space;%5Cmu)%5E%7Bd(s_i,s_%7B%5Calpha_i%7D)%7D(1&amp;space;-&amp;space;%5Ckappa_i&amp;space;%5Cmu)%5E%7Bl(s_i,&amp;space;s_%7B%5Calpha_i%7D)&amp;space;-&amp;space;d(s_i,s_%7B%5Calpha_i%7D)%7D" title="(\kappa_i \mu)^{d(s_i,s_{\alpha_i})}(1 - \mu)^{(\kappa_i\times l(s_i, s_{\alpha_i})) - d(s_i,s_{\alpha_i})}"></p>
<p><br></p>
</div>
</div>
<div id="installation" class="section level2">
<h2 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h2>
<p>To install the stable version from CRAN:</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">install.packages</a></span><span class="op">(</span><span class="st">"outbreaker2"</span><span class="op">)</span></code></pre></div>
<p>To install the development version from github (requires Rtools on windows and GSL headers on all platforms):</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">install_github</a></span><span class="op">(</span><span class="st">"reconhub/outbreaker2"</span><span class="op">)</span></code></pre></div>
<p>To add local copies of the vignettes, you will need to specify:</p>
<div class="sourceCode" id="cb3"><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">install_github</a></span><span class="op">(</span><span class="st">"reconhub/outbreaker2"</span>, build_vignettes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>Then, to load the package, use:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="st">"outbreaker2"</span><span class="op">)</span></code></pre></div>
<p><br></p>
</div>
<div id="documentation" class="section level2">
<h2 class="hasAnchor">
<a href="#documentation" class="anchor"></a>Documentation</h2>
<p><em>outbreaker2</em> is fully documented on a <a href="http://www.repidemicsconsortium.org/outbreaker2/">dedicated website</a>.</p>
<p>It also comes with the following vignettes:</p>
<ul>
<li>
<strong><code>introduction</code></strong>: general introduction using a worked example.</li>
<li>
<strong><code>overview</code></strong>: brief overview of the package’s content.</li>
<li>
<strong><code>customisation</code></strong>: customisation of priors, likelihoods, and movement functions.</li>
<li>
<strong><code>Rcpp_API</code></strong>: documentation for the Rcpp API.</li>
</ul>
<p><br></p>
</div>
<div id="contributors" class="section level2">
<h2 class="hasAnchor">
<a href="#contributors" class="anchor"></a>Contributors</h2>
<ul>
<li><a href="https://github.com/thibautjombart">Thibaut Jombart</a></li>
<li><a href="https://github.com/finlaycampbell">Finlay Campbell</a></li>
<li><a href="https://github.com/richfitz">Rich Fitzjohn</a></li>
<li><a href="https://github.com/gtonkinhill">Gerry Tonkin-Hill</a></li>
<li><a href="https://github.com/alxsrobert">Alexis Robert</a></li>
<li><a href="https://github.com/kreldjarn">Kristjan Eldjarn</a></li>
</ul>
<p>See details of contributions <a href="https://github.com/reconhub/outbreaker2/graphs/contributors">here</a>.</p>
<p>Contributions are welcome via <strong>pull requests</strong>.</p>
<p>Please note that this project is released with a <a href="https://github.com/reconhub/outbreaker2/blob/master/CONDUCT.md">Contributor Code of Conduct</a>. By participating in this project you agree to abide by its terms.</p>
<p><strong>Maintainer:</strong> Finlay Campbell (<a href="mailto:finlaycampbell93@gmail.com" class="email">finlaycampbell93@gmail.com</a>)</p>
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<h2>Links</h2>
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<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=outbreaker2">https://​cloud.r-project.org/​package=outbreaker2</a>
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<h2>License</h2>
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<h2>Developers</h2>
<ul class="list-unstyled">
<li>Thibaut Jombart <br><small class="roles"> Author </small>  </li>
<li>Finlay Campbell <br><small class="roles"> Author, maintainer </small>  </li>
<li>Rich Fitzjohn <br><small class="roles"> Author </small>  </li>
<li><a href="authors.html">All authors...</a></li>
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