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<meta property="og:description" content="This package provides a statistical platform for reconstructing transmission
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reimplements, as a particular case, the model of 'outbreaker' (see
references). 'outbreaker2' extends and replaces 'outbreaker'. " />
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<h1>outbreaker2: a platform for disease outbreak reconstruction</h1>
<div class="hidden name"><code>outbreaker_package.Rd</code></div>
</div>
<div class="ref-description">
<p>This package provides a statistical platform for reconstructing transmission
trees ('who infects whom') in densely sampled disease outbreaks. It
reimplements, as a particular case, the model of 'outbreaker' (see
references). 'outbreaker2' extends and replaces 'outbreaker'. <br /></p>
</div>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The emphasis of 'outbreaker2' is on modularity, which enables customisation
of priors, likelihoods and even movements of parameters and augmented data by
the user. This the dedicated vignette on this topic
<code>vignette("outbreaker2_custom")</code>.<br /></p>
<p>The main functions of the package are:</p><ul>
<li><p><code><a href='outbreaker.html'>outbreaker</a></code>: main function to run analyses</p></li>
<li><p><code><a href='outbreaker_data.html'>outbreaker_data</a></code>: function to process input data</p></li>
<li><p><code><a href='create_config.html'>create_config</a></code>: function to create default and customise
configuration settings</p></li>
<li><p><code><a href='custom_priors.html'>custom_priors</a></code>: function to specify customised prior
functions</p></li>
<li><p><code><a href='custom_likelihoods.html'>custom_likelihoods</a></code>: function to specify customised likelihoods
functions</p></li>
<li><p><code><a href='custom_moves.html'>custom_moves</a></code>: function to create default and customise movement
functions</p></li>
</ul>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Thibaut Jombart <a href='mailto:thibautjombart@gmail.com'>thibautjombart@gmail.com</a></p>
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Datasets
Models
