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+<meta property="og:description" content="The function outbreaker is the main function of the package. It runs
+processes various inputs (data, configuration settings, custom priors,
+likelihoods and movement functions) and explores the space of plausible
+transmission trees of a densely sampled outbreaks." />
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+      <a href="../articles/customisation.html">Using custom priors, likelihood, or movements in outbreaker2</a>
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+      <a href="../articles/introduction.html">Introduction to outbreaker2</a>
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+    <li>
+      <a href="../articles/overview.html">outbreaker2: package overview</a>
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+    <div class="page-header">
+    <h1>outbreaker2: main function for reconstructing disease outbreaks</h1>
+    
+    <div class="hidden name"><code>outbreaker.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>The function <code>outbreaker</code> is the main function of the package. It runs
+processes various inputs (data, configuration settings, custom priors,
+likelihoods and movement functions) and explores the space of plausible
+transmission trees of a densely sampled outbreaks.<br /></p>
+    </div>
+
+    <pre class="usage"><span class='fu'>outbreaker</span><span class='op'>(</span>
+  data <span class='op'>=</span> <span class='fu'><a href='outbreaker_data.html'>outbreaker_data</a></span><span class='op'>(</span><span class='op'>)</span>,
+  config <span class='op'>=</span> <span class='fu'><a href='create_config.html'>create_config</a></span><span class='op'>(</span><span class='op'>)</span>,
+  priors <span class='op'>=</span> <span class='fu'><a href='custom_priors.html'>custom_priors</a></span><span class='op'>(</span><span class='op'>)</span>,
+  likelihoods <span class='op'>=</span> <span class='fu'><a href='custom_likelihoods.html'>custom_likelihoods</a></span><span class='op'>(</span><span class='op'>)</span>,
+  moves <span class='op'>=</span> <span class='fu'><a href='custom_moves.html'>custom_moves</a></span><span class='op'>(</span><span class='op'>)</span>
+<span class='op'>)</span></pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>data</th>
+      <td><p>a list of named items containing input data as returned by
+<code><a href='outbreaker_data.html'>outbreaker_data</a></code></p></td>
+    </tr>
+    <tr>
+      <th>config</th>
+      <td><p>a set of settings as returned by <code><a href='create_config.html'>create_config</a></code></p></td>
+    </tr>
+    <tr>
+      <th>priors</th>
+      <td><p>a set of log-prior functions as returned by
+<code><a href='custom_priors.html'>custom_priors</a></code></p></td>
+    </tr>
+    <tr>
+      <th>likelihoods</th>
+      <td><p>a set of log-likelihood functions as returned by
+<code><a href='custom_likelihoods.html'>custom_likelihoods</a></code></p></td>
+    </tr>
+    <tr>
+      <th>moves</th>
+      <td><p>a set of movement functions as returned by
+<code><a href='custom_moves.html'>custom_moves</a></code></p></td>
+    </tr>
+    </table>
+
+    <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>
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson
+    N (2014).  Bayesian reconstruction of disease outbreaks by combining
+    epidemiologic and genomic data. PLoS Computational Biology.</p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p><code><a href='outbreaker_data.html'>outbreaker_data</a></code> to process input data, and
+    <code><a href='create_config.html'>create_config</a></code> to process/set up parameters</p>
+<ul>
+<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>
+</div>
+    <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>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'>
+<span class='co'>## get data</span>
+<span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>fake_outbreak</span><span class='op'>)</span>
+<span class='va'>dat</span> <span class='op'>&lt;-</span> <span class='va'>fake_outbreak</span>
+
+<span class='kw'>if</span> <span class='op'>(</span><span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>{</span>
+<span class='co'>## run outbreaker</span>
+<span class='va'>out</span> <span class='op'>&lt;-</span> <span class='fu'>outbreaker</span><span class='op'>(</span>data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>dna <span class='op'>=</span> <span class='va'>dat</span><span class='op'>$</span><span class='va'>dna</span>, dates <span class='op'>=</span> <span class='va'>dat</span><span class='op'>$</span><span class='va'>onset</span>, w_dens <span class='op'>=</span> <span class='va'>dat</span><span class='op'>$</span><span class='va'>w</span><span class='op'>)</span>,
+config <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>n_iter <span class='op'>=</span> <span class='fl'>2e4</span>, sample_every <span class='op'>=</span> <span class='fl'>200</span><span class='op'>)</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>out</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span><span class='op'>(</span><span class='va'>out</span><span class='op'>)</span>
+
+<span class='co'>## run outbreaker, no DNA sequences</span>
+<span class='va'>out2</span> <span class='op'>&lt;-</span> <span class='fu'>outbreaker</span><span class='op'>(</span>data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>dates <span class='op'>=</span> <span class='va'>dat</span><span class='op'>$</span><span class='va'>onset</span>, w_dens <span class='op'>=</span> <span class='va'>w</span><span class='op'>)</span>,
+config <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>n_iter <span class='op'>=</span> <span class='fl'>2e4</span>, sample_every <span class='op'>=</span> <span class='fl'>200</span><span class='op'>)</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>out2</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span><span class='op'>(</span><span class='va'>out2</span><span class='op'>)</span>
+
+<span class='op'>}</span>
+</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
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+      <footer>
+      <div class="copyright">
+  <p>Developed by Thibaut Jombart, Finlay Campbell, Rich Fitzjohn.</p>
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