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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'><-</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'><-</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'><-</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'><-</span> <span class='va'>fake_outbreak</span> +<span class='va'>data</span> <span class='op'><-</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'><-</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> + +