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    <h1>Initializes outputs for outbreaker</h1>





  
  

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    <div class="hidden name"><code>create_param.Rd</code></div>





  
  

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    <p>This function creates initial outputs and parameter states for outbreaker.</p>





  
  

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    <pre class="usage"><span class='fu'>create_param</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><span class='op'>)</span></pre>





  
  

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    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>





  
  

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    <table class="ref-arguments">





  
  

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    <colgroup><col class="name" /><col class="desc" /></colgroup>





  
  

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    <tr>





  
  

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      <th>data</th>





  
  

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      <td><p>A list of data items as returned by <code>outbreaker_data</code>, or





  
  

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arguments passed to this function.</p></td>





  
  

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    </tr>





  
  

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    <tr>





  
  

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      <th>config</th>





  
  

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      <td><p>A list of settings as returned by <code>create_config</code>, or





  
  

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arguments passed to this function.</p></td>





  
  

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    </tr>





  
  

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    </table>





  
  

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    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>





  
  

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    <p>A list containing two components <code>$store</code> and





  
  

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<code>$current</code>. <code>store</code> is a list with the class





  
  

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<code>outbreaker_store</code>, used for storing 'saved' states of the





  
  

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MCMC. <code>current</code> is a list with the class <code>outbreaker_param</code>, used





  
  

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for storing 'current' states of the MCMC. <br /> <br /></p>





  
  

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<p><code>outbreaker_store</code> class content:</p><ul>





  
  

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<li><p><code>size</code>: The length of the list, corresponding to the number of





  
  

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samples saved from the MCMC.</p></li>





  
  

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<li><p><code>step</code>: A vector of integers of length <code>size</code>, storing the





  
  

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steps of the MCMC corresponding to the saved samples.</p></li>





  
  

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<li><p><code>post</code>: A numeric vector of length <code>size</code>, storing





  
  

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log-posterior values.</p></li>





  
  

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<li><p><code>like</code>: A numeric vector of length <code>size</code>, storing





  
  

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log-likelihood values.</p></li>





  
  

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<li><p><code>prior</code>: A numeric vector of length <code>size</code>,





  
  

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storing log-prior values.</p></li>





  
  

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<li><p><code>alpha</code>: A list of length <code>size</code>. Each item of the list is





  
  

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an integer vector of length <code>data$N</code>, storing indices (from 1 to N) of





  
  

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infectors for each case.</p></li>





  
  

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<li><p><code>t_inf</code>: A list of length <code>size</code>. Each item of the list is





  
  

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an integer vector of length <code>data$N</code>, storing dates of infections for





  
  

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each case.</p></li>





  
  

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<li><p><code>mu</code>: A numeric vector of length <code>size</code>, storing values of





  
  

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the mutation rate.</p></li>





  
  

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<li><p><code>kappa</code>: A list of length <code>size</code>. Each item of the list is





  
  

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an integer vector of length <code>data$N</code>, storing the number of generations





  
  

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before the last sampled ancestor for each case.</p></li>





  
  

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<li><p><code>pi</code>: A numeric vector of length <code>size</code>, storing values of





  
  

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the reporting probability.</p></li>





  
  

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<li><p><code>eps</code>: A numeric vector of length <code>size</code>, storing values of





  
  

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the contact reporting coverage.</p></li>





  
  

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<li><p><code>lambda</code>: A numeric vector of length <code>size</code>, storing values of





  
  

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the non-infectious contact rate.</p></li>





  
  

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<li><p><code>counter</code>: A counter used to keep track of the current iteration





  
  

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of the MCMC (used internally).</p></li>





  
  

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</ul>





  
  

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<p><code>outbreaker_param</code> class content:</p><ul>





  
  

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<li><p><code>alpha</code>: An integer vector of length <code>data$N</code>, storing





  
  

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indices (from 1 to N) of infectors for each case.</p></li>





  
  

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<li><p><code>t_inf</code>: An integer vector of length <code>data$N</code>, storing dates





  
  

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of infections for each case.</p></li>





  
  

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<li><p><code>mu</code>: The value of the mutation rate.</p></li>





  
  

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<li><p><code>kappa</code>: An integer vector of length <code>data$N</code>, storing the





  
  

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number of generations before the last sampled ancestor for each case.</p></li>





  
  

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<li><p><code>pi</code>: The value of the reporting probability.</p></li>





  
  

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<li><p><code>eps</code>: The value of the contact reporting coverage.</p></li>





  
  

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<li><p><code>lambda</code>: The value of the non-infectious contact rate.</p></li>





  
  

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</ul>





  
  

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    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>





  
  

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    <p>Thibaut Jombart (<a href='mailto:thibautjombart@gmail.com'>thibautjombart@gmail.com</a>)</p>





  
  

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    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>





  
  

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    <pre class="examples"><div class='input'>





  
  

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<span class='co'>## load data</span>





  
  

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<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='va'>fake_outbreak</span>





  
  

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<span class='va'>data</span> <span class='op'>&lt;-</span> <span class='fu'><a href='outbreaker_data.html'>outbreaker_data</a></span><span class='op'>(</span>dates <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>sample</span>, dna <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>dna</span>, w_dens <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>w</span><span class='op'>)</span>





  
  

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<span class='co'>## modify config settings</span>





  
  

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<span class='va'>config</span> <span class='op'>&lt;-</span> <span class='fu'><a href='create_config.html'>create_config</a></span><span class='op'>(</span>move_alpha <span class='op'>=</span> <span class='cn'>FALSE</span>, n_iter <span class='op'>=</span> <span class='fl'>2e5</span>, sample_every <span class='op'>=</span> <span class='fl'>1000</span><span class='op'>)</span>





  
  

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<span class='co'>## create param object</span>





  
  

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<span class='va'>param</span> <span class='op'>&lt;-</span> <span class='fu'>create_param</span><span class='op'>(</span>data <span class='op'>=</span> <span class='va'>data</span>, config <span class='op'>=</span> <span class='va'>config</span><span class='op'>)</span>





  
  

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