outbreaker2 / Git / [dfe06d] /docs/reference/custom

Models:
MarcoTheBlack/
outbreaker2
Downloads: 1
[dfe06d]: / docs / reference / custom_likelihoods.html
History
Download this file
259 lines (197 with data), 12.5 kB

<!-- 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 likelihood functions for outbreaker — custom_likelihoods • 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 likelihood functions for outbreaker — custom_likelihoods" />
<meta property="og:description" content="This function is used to specify customised likelihood functions for
outbreaker. Custom functions are specified as a named list or series of
comma-separated, named arguments, indicating which log-likelihood component
they compute. 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 likelihood functions for outbreaker</h1>
    
    <div class="hidden name"><code>custom_likelihoods.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function is used to specify customised likelihood functions for
outbreaker. Custom functions are specified as a named list or series of
comma-separated, named arguments, indicating which log-likelihood component
they compute. Values currently available are:</p>
    </div>

    <pre class="usage"><span class='fu'>custom_likelihoods</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span>

<span class='co'># S3 method for custom_likelihoods</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 named list of functions, each computing a log-likelihood component.</p></td>
    </tr>
    <tr>
      <th>x</th>
      <td><p>an <code>outbreaker_config</code> object as returned by <code>create_config</code>.</p></td>
    </tr>
    </table>

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

    <p>A named list of list(function, arity) pairs with the class
    <code>custom_likelihood</code>, each function implementing a customised
    log-likelihood component of outbreaker. Functions which are not
    customised will result in a list(NULL, 0) component. Any function with
    arity 3 must have the third parameter default to NULL.</p>
<p>a list of named functions</p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    
<ul>
<li><p><code>genetic</code>: the genetic likelihood; by default, the function
<code>cpp_ll_genetic</code> is used.</p></li>
<li><p><code>timing_sampling</code>: the likelihood of sampling times; by default, the function
<code>cpp_ll_timing_sampling</code> is used.</p></li>
<li><p><code>timing_infections</code>: the likelihood of infection times; by default, the function
<code>cpp_ll_timing_infections</code> is used.</p></li>
<li><p><code>reporting</code>: the likelihood of the reporting process; by default,
the function <code>cpp_ll_reporting</code> is used.</p></li>
<li><p><code>contact</code>: the likelihood of the contact tracing data; by default,
the function <code>cpp_ll_contact</code> is used.</p></li>
</ul>

<p>All log-likelihood functions should have the following arguments, in this
order:</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>param</code>: a list of parameters with the class
<code><a href='create_param.html'>create_param</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#customizing-likelihood'>customization vignette</a> for detailed examples on how to customize likelihoods.</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>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>
<span class='co'>## specify a null model by disabling all likelihood components</span>
<span class='va'>f_null</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>data</span>, <span class='va'>param</span><span class='op'>)</span> <span class='op'>{</span>
  <span class='kw'><a href='https://rdrr.io/r/base/function.html'>return</a></span><span class='op'>(</span><span class='fl'>0.0</span><span class='op'>)</span>
<span class='op'>}</span>

<span class='va'>null_model</span> <span class='op'>&lt;-</span> <span class='fu'>custom_likelihoods</span><span class='op'>(</span>genetic <span class='op'>=</span> <span class='va'>f_null</span>,
                                timing_sampling <span class='op'>=</span> <span class='va'>f_null</span>,
                                timing_infections <span class='op'>=</span> <span class='va'>f_null</span>,
                                reporting <span class='op'>=</span> <span class='va'>f_null</span>,
                                contact <span class='op'>=</span> <span class='va'>f_null</span><span class='op'>)</span>

<span class='va'>null_config</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>find_import <span class='op'>=</span> <span class='cn'>FALSE</span>,
                    n_iter <span class='op'>=</span> <span class='fl'>200</span>,
                    sample_every <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>

<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='va'>res_null</span> <span class='op'>&lt;-</span> <span class='fu'><a href='outbreaker.html'>outbreaker</a></span><span class='op'>(</span>data <span class='op'>=</span> <span class='va'>data</span>,
                       config <span class='op'>=</span> <span class='va'>null_config</span>,
                       likelihoods <span class='op'>=</span> <span class='va'>null_model</span><span class='op'>)</span>

<span class='co'>## visualise ancestries to see if all transmission trees have been explored</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>res_null</span>, type <span class='op'>=</span> <span class='st'>"alpha"</span><span class='op'>)</span>
</div><div class='img'><img src='custom_likelihoods-1.png' alt='' width='700' height='433' /></div></pre>
  </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>