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likelihoods and movement functions) and explores the space of plausible
transmission trees of a densely sampled outbreaks." />




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    <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>
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