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--- a +++ b/docs/reference/index.html @@ -0,0 +1,267 @@ +<!-- 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>Function reference • 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> + +<!-- 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data-target="#toc"> + <div class="container template-reference-index"> + <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="contents col-md-9"> + <div class="page-header"> + <h1>Reference</h1> + </div> + + <table class="ref-index"> + + <colgroup> + + <col class="alias" /> + <col class="title" /> + </colgroup> + + <tbody> + <tr> + <th colspan="2"> + <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2> + <p class="section-desc"></p> + </th> + </tr> + + + </tbody><tbody> + + + <tr> + + <td> + <p><code><a href="bind_to_function.html">bind_to_function()</a></code> </p> + </td> + <td><p>Encloses argument in a function's environment</p></td> + </tr><tr> + + <td> + <p><code><a href="create_config.html">create_config()</a></code> <code><a href="create_config.html">print(<i><outbreaker_config></i>)</a></code> </p> + </td> + <td><p>Set and check parameter settings of outbreaker</p></td> + </tr><tr> + + <td> + <p><code><a href="create_param.html">create_param()</a></code> </p> + </td> + <td><p>Initializes outputs for outbreaker</p></td> + </tr><tr> + + <td> + <p><code><a href="custom_likelihoods.html">custom_likelihoods()</a></code> <code><a href="custom_likelihoods.html">print(<i><custom_likelihoods></i>)</a></code> </p> + </td> + <td><p>Customise likelihood functions for outbreaker</p></td> + </tr><tr> + + <td> + <p><code><a href="custom_moves.html">custom_moves()</a></code> <code><a href="custom_moves.html">print(<i><outbreaker_moves></i>)</a></code> </p> + </td> + <td><p>Customise samplers for outbreaker</p></td> + </tr><tr> + + <td> + <p><code><a href="custom_priors.html">custom_priors()</a></code> <code><a href="custom_priors.html">print(<i><custom_priors></i>)</a></code> </p> + </td> + <td><p>Customise priors for outbreaker</p></td> + </tr><tr> + + <td> + <p><code><a href="fake_outbreak.html">fake_outbreak</a></code> </p> + </td> + <td><p>Small simulated outbreak</p></td> + </tr><tr> + + <td> + <p><code><a href="get_cpp_api.html">get_cpp_api()</a></code> </p> + </td> + <td><p>Access internal C++ rountines used in outbreaker2</p></td> + </tr><tr> + + <td> + <p><code><a href="outbreaker.html">outbreaker()</a></code> </p> + </td> + <td><p>outbreaker2: main function for reconstructing disease outbreaks</p></td> + </tr><tr> + + <td> + <p><code><a href="outbreaker_chains.html">print(<i><outbreaker_chains></i>)</a></code> <code><a href="outbreaker_chains.html">plot(<i><outbreaker_chains></i>)</a></code> <code><a href="outbreaker_chains.html">summary(<i><outbreaker_chains></i>)</a></code> </p> + </td> + <td><p>Basic methods for processing outbreaker results</p></td> + </tr><tr> + + <td> + <p><code><a href="outbreaker_data.html">outbreaker_data()</a></code> </p> + </td> + <td><p>Process input data for outbreaker</p></td> + </tr><tr> + + <td> + <p><code><a href="outbreaker_package.html">outbreaker_package</a></code> </p> + </td> + <td><p>outbreaker2: a platform for disease outbreak reconstruction</p></td> + </tr><tr> + + <td> + <p><code><a href="palettes.html">chains_pal()</a></code> <code><a href="palettes.html">cases_pal()</a></code> </p> + </td> + <td><p>Color palettes used in outbreaker</p></td> + </tr><tr> + + <td> + <p><code><a href="sim_ctd.html">sim_ctd()</a></code> </p> + </td> + <td><p>Simulate contact data from a transmission tree</p></td> + </tr> + </tbody> + </table> + </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> + +