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    <h1>Initializes outputs for outbreaker</h1>
    
    <div class="hidden name"><code>create_param.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function creates initial outputs and parameter states for outbreaker.</p>
    </div>

    <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>

    <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 data items as returned by <code>outbreaker_data</code>, or
arguments passed to this function.</p></td>
    </tr>
    <tr>
      <th>config</th>
      <td><p>A list of settings as returned by <code>create_config</code>, or
arguments passed to this function.</p></td>
    </tr>
    </table>

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

    <p>A list containing two components <code>$store</code> and
<code>$current</code>. <code>store</code> is a list with the class
<code>outbreaker_store</code>, used for storing 'saved' states of the
MCMC. <code>current</code> is a list with the class <code>outbreaker_param</code>, used
for storing 'current' states of the MCMC. <br /> <br /></p>
<p><code>outbreaker_store</code> class content:</p><ul>
<li><p><code>size</code>: The length of the list, corresponding to the number of
samples saved from the MCMC.</p></li>
<li><p><code>step</code>: A vector of integers of length <code>size</code>, storing the
steps of the MCMC corresponding to the saved samples.</p></li>
<li><p><code>post</code>: A numeric vector of length <code>size</code>, storing
log-posterior values.</p></li>
<li><p><code>like</code>: A numeric vector of length <code>size</code>, storing
log-likelihood values.</p></li>
<li><p><code>prior</code>: A numeric vector of length <code>size</code>,
storing log-prior values.</p></li>
<li><p><code>alpha</code>: A list of length <code>size</code>. Each item of the list is
an integer vector of length <code>data$N</code>, storing indices (from 1 to N) of
infectors for each case.</p></li>
<li><p><code>t_inf</code>: A list of length <code>size</code>. Each item of the list is
an integer vector of length <code>data$N</code>, storing dates of infections for
each case.</p></li>
<li><p><code>mu</code>: A numeric vector of length <code>size</code>, storing values of
the mutation rate.</p></li>
<li><p><code>kappa</code>: A list of length <code>size</code>. Each item of the list is
an integer vector of length <code>data$N</code>, storing the number of generations
before the last sampled ancestor for each case.</p></li>
<li><p><code>pi</code>: A numeric vector of length <code>size</code>, storing values of
the reporting probability.</p></li>
<li><p><code>eps</code>: A numeric vector of length <code>size</code>, storing values of
the contact reporting coverage.</p></li>
<li><p><code>lambda</code>: A numeric vector of length <code>size</code>, storing values of
the non-infectious contact rate.</p></li>
<li><p><code>counter</code>: A counter used to keep track of the current iteration
of the MCMC (used internally).</p></li>
</ul>


<p><code>outbreaker_param</code> class content:</p><ul>
<li><p><code>alpha</code>: An integer vector of length <code>data$N</code>, storing
indices (from 1 to N) of infectors for each case.</p></li>
<li><p><code>t_inf</code>: An integer vector of length <code>data$N</code>, storing dates
of infections for each case.</p></li>
<li><p><code>mu</code>: The value of the mutation rate.</p></li>
<li><p><code>kappa</code>: An integer vector of length <code>data$N</code>, storing the
number of generations before the last sampled ancestor for each case.</p></li>
<li><p><code>pi</code>: The value of the reporting probability.</p></li>
<li><p><code>eps</code>: The value of the contact reporting coverage.</p></li>
<li><p><code>lambda</code>: The value of the non-infectious contact rate.</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>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>
<span class='co'>## load data</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='va'>fake_outbreak</span>
<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>

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

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

</div></pre>
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