--- a
+++ b/docs/reference/fake_outbreak.html
@@ -0,0 +1,263 @@
+<!-- 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>Small simulated outbreak — fake_outbreak • 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="Small simulated outbreak — fake_outbreak" />
+<meta property="og:description" content="This dataset is a small (30 cases) simulated outbreak originally used to
+illustrate outbreaker, and used for the same purposes in
+outbreaker2.  This list contains the following:" />
+
+
+
+
+<!-- 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>Small simulated outbreak</h1>
+    
+    <div class="hidden name"><code>fake_outbreak.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>This dataset is a small (30 cases) simulated outbreak originally used to
+illustrate <code>outbreaker</code>, and used for the same purposes in
+<code>outbreaker2</code>.  This list contains the following:</p>
+    </div>
+
+    <pre class="usage"><span class='va'>fake_outbreak</span></pre>
+
+
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <p>An object of class <code>list</code> of length 6.</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    
+<ul>
+<li><p><code>$onset</code>: A vector of integers representing dates of onset.</p></li>
+<li><p><code>$sample</code>: A vector of integers representing the dates of isolation.</p></li>
+<li><p><code>$dna</code>: A DNAbin matrix of pathogen genome sequences.</p></li>
+<li><p><code>$w</code>: A numeric vector giving the empirical distribution of the
+generation time.</p></li>
+<li><p><code>$ances</code>: A vector of integers indicating, for each case, the true
+infectors. <code>NA</code> represents imported cases.</p></li>
+</ul>
+
+    <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='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>fake_outbreak</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; [1] "onset"  "sample" "dna"    "w"      "ances"  "ctd"   </div><div class='input'><span class='va'>fake_outbreak</span>
+</div><div class='output co'>#&gt; $onset
+#&gt;  [1]  0  2  4  4  6  6  6  7  7  8  8  8  8  9  9  9  9 10 10 10 10 10 10 10 10
+#&gt; [26] 10 10 10 11 11
+#&gt; 
+#&gt; $sample
+#&gt;  [1]  3  5  6  6  7  9  8  9  9  9 11 10 10 10 10 11 11 12 11 13 12 13 11 12 11
+#&gt; [26] 11 13 12 14 14
+#&gt; 
+#&gt; $dna
+#&gt; 30 DNA sequences in binary format stored in a matrix.
+#&gt; 
+#&gt; All sequences of same length: 10000 
+#&gt; 
+#&gt; Labels:
+#&gt; ...
+#&gt; 
+#&gt; Base composition:
+#&gt;     a     c     g     t 
+#&gt; 0.251 0.242 0.251 0.256 
+#&gt; (Total: 300 kb)
+#&gt; 
+#&gt; $w
+#&gt; [1] 0.04255319 0.21276596 0.42553191 0.31914894
+#&gt; 
+#&gt; $ances
+#&gt;  [1] NA  1  2 NA  3  4  4  5  6  6  7  8  9  5  5  7  7  8  9 10 11 11 13 13 13
+#&gt; [26] 17 17 NA 10 13
+#&gt; 
+#&gt; $ctd
+#&gt;     i  j
+#&gt; 1   4  7
+#&gt; 2  10 29
+#&gt; 3  13 30
+#&gt; 4  11 22
+#&gt; 5  13 25
+#&gt; 6  16  7
+#&gt; 7  13 23
+#&gt; 8  10  6
+#&gt; 9  18  8
+#&gt; 10 14  5
+#&gt; 11 17 26
+#&gt; 12 11 21
+#&gt; 13  3  5
+#&gt; 14 17 27
+#&gt; 15  2  3
+#&gt; 16 17  7
+#&gt; 17 19  9
+#&gt; 18 12  8
+#&gt; 19 22  6
+#&gt; 20 30  9
+#&gt; 21 17 20
+#&gt; 22 21 29
+#&gt; 23 11 14
+#&gt; 24 18  9
+#&gt; 25 25 29
+#&gt; 26  1 17
+#&gt; 27 23  7
+#&gt; 28 25  3
+#&gt; 29  3  9
+#&gt; 30  1  4
+#&gt; 31 13  4
+#&gt; 32 21 27
+#&gt; 33 16  2
+#&gt; 34 29  3
+#&gt; 35 21  5
+#&gt; </div><div class='input'>
+</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>
+
+