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--- a +++ b/docs/reference/custom_moves.html @@ -0,0 +1,243 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Customise samplers for outbreaker — custom_moves • outbreaker2</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + + +<meta property="og:title" content="Customise samplers for outbreaker — custom_moves" /> +<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:" /> + + + + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">outbreaker2</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html"> + <span class="fas fa-home fa-lg"></span> + + </a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/customisation.html">Using custom priors, likelihood, or movements in outbreaker2</a> + </li> + <li> + <a href="../articles/introduction.html">Introduction to outbreaker2</a> + </li> + <li> + <a href="../articles/overview.html">outbreaker2: package overview</a> + </li> + <li> + <a href="../articles/Rcpp_API.html">outbreaker2: Rcpp API</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">Changelog</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <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> + + </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> + + + <footer> + <div class="copyright"> + <p>Developed by Thibaut Jombart, Finlay Campbell, Rich Fitzjohn.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + +