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<meta property="og:description" content="This function is used to specify customised movement functions
(a.k.a. samplers) for outbreaker. Custom functions are specified as a named
list or series of comma-separated, named arguments, indicating which type of
movement they implement. Values currently available are:" />
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<h1>Customise samplers for outbreaker</h1>
<div class="hidden name"><code>custom_moves.Rd</code></div>
</div>
<div class="ref-description">
<p>This function is used to specify customised movement functions
(a.k.a. samplers) for outbreaker. Custom functions are specified as a named
list or series of comma-separated, named arguments, indicating which type of
movement they implement. Values currently available are:</p>
</div>
<pre class="usage"><span class='fu'>custom_moves</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for outbreaker_moves</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</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>...</th>
<td><p>A list or a series of named, comma-separated functions
implementing movements of parameters or augmented data.</p></td>
</tr>
<tr>
<th>x</th>
<td><p>an <code>outbreaker_moves</code> object as returned by <code>create_moves</code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list of movement functions with a single argument 'param', with
class <code>outbreaker_moves</code>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<ul>
<li><p><code>mu</code>: movement of the mutation rate; by default, the function
<code>cpp_move_mu</code> is used.</p></li>
<li><p><code>pi</code>: movement of the reporting probability; by default, the function
<code>cpp_move_pi</code> is used.</p></li>
<li><p><code>eps</code>: movement of the contact reporting coverage; by default, the
function <code>cpp_move_eps</code> is used.</p></li>
<li><p><code>lambda</code>: the movement of the non-infectious contact rate; the
function <code>cpp_move_lambda</code> is used.</p></li>
<li><p><code>alpha</code>: movement of the transmission tree, by randomly proposing
infectors in the pool of cases infected before; by default, the function
<code>cpp_move_alpha</code> is used.</p></li>
<li><p><code>swap_cases</code>: movement of the transmission tree, by swapping
infectors and infected cases; by default, the function
<code>cpp_move_swap_cases</code> is used.</p></li>
<li><p><code>t_inf</code>: movement of the date of infection; by default, the
function <code>cpp_move_t_inf</code> is used.</p></li>
<li><p><code>kappa</code>: movement of the number generations between cases; by
default, the function <code>cpp_move_kappa</code> is used.</p></li>
</ul>
<p>Movement functions must have an argument <code>param</code>, which is a list of
parameters and augmented data of the class <code><a href='create_param.html'>create_param</a></code>.
Each movement function will be enclosed with its other arguments, so that the
resulting function will have a single argument 'param'. For non-standard
movements (i.e. none of the names specified above), the closure will contain:</p>
<ul>
<li><p><code>data</code>: a list of named items containing input data as returned by
<code><a href='outbreaker_data.html'>outbreaker_data</a></code></p></li>
<li><p><code>config</code>: a list of named items containing input data as returned by
<code><a href='create_config.html'>create_config</a></code></p></li>
<li><p><code>likelihoods</code>: a list of named custom likelihood functions as returned by
<code><a href='custom_likelihoods.html'>custom_likelihoods</a></code></p></li>
<li><p><code>priors</code>: a list of named custom prior functions as returned by
<code><a href='custom_priors.html'>custom_priors</a></code></p></li>
</ul>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>See <a href='http://www.repidemicsconsortium.org/outbreaker2/articles/customisation.html#customising-movements'>customization vignette</a> for detailed examples on how to customise movement functions.</p></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>
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