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+    <div class="page-header">
+    <h1>Basic methods for processing outbreaker results</h1>
+    
+    <div class="hidden name"><code>outbreaker_chains.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Several methods are defined for instances of the class
+<code>outbreaker_chains</code>, returned by <code><a href='outbreaker.html'>outbreaker</a></code>, including:
+<code>print</code>, <code>plot</code>, <code>summary</code></p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for outbreaker_chains</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>, n_row <span class='op'>=</span> <span class='fl'>3</span>, n_col <span class='op'>=</span> <span class='fl'>8</span>, <span class='va'>...</span><span class='op'>)</span>
+
+<span class='co'># S3 method for outbreaker_chains</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  y <span class='op'>=</span> <span class='st'>"post"</span>,
+  type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"trace"</span>, <span class='st'>"hist"</span>, <span class='st'>"density"</span>, <span class='st'>"alpha"</span>, <span class='st'>"t_inf"</span>, <span class='st'>"kappa"</span>, <span class='st'>"network"</span><span class='op'>)</span>,
+  group <span class='op'>=</span> <span class='cn'>NULL</span>,
+  burnin <span class='op'>=</span> <span class='fl'>0</span>,
+  min_support <span class='op'>=</span> <span class='fl'>0.1</span>,
+  labels <span class='op'>=</span> <span class='cn'>NULL</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for outbreaker_chains</span>
+<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, burnin <span class='op'>=</span> <span class='fl'>0</span>, method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mpa"</span>, <span class='st'>"decycle"</span><span class='op'>)</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>x</th>
+      <td><p>an <code>outbreaker_chains</code> object as returned by <code>outbreaker</code>.</p></td>
+    </tr>
+    <tr>
+      <th>n_row</th>
+      <td><p>the number of rows to display in head and tail; defaults to 3.</p></td>
+    </tr>
+    <tr>
+      <th>n_col</th>
+      <td><p>the number of columns to display; defaults to 8.</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>further arguments to be passed to other methods</p></td>
+    </tr>
+    <tr>
+      <th>y</th>
+      <td><p>a character string indicating which element of an
+<code>outbreaker_chains</code> object to plot</p></td>
+    </tr>
+    <tr>
+      <th>type</th>
+      <td><p>a character string indicating the kind of plot to be used (see details)</p></td>
+    </tr>
+    <tr>
+      <th>group</th>
+      <td><p>a vector of character strings indicating the parameters to display, 
+or "all" to display all global parameters (non node-specific parameters).</p></td>
+    </tr>
+    <tr>
+      <th>burnin</th>
+      <td><p>the number of iterations to be discarded as burnin</p></td>
+    </tr>
+    <tr>
+      <th>min_support</th>
+      <td><p>a number between 0 and 1 indicating the minimum support of
+ancestries to be plotted; only used if 'type' is 'network'</p></td>
+    </tr>
+    <tr>
+      <th>labels</th>
+      <td><p>a vector of length N indicating the case labels (must be
+provided in the same order used for dates of symptom onset)</p></td>
+    </tr>
+    <tr>
+      <th>object</th>
+      <td><p>an <code>outbreaker_chains</code> object as returned by <code>outbreaker</code>.</p></td>
+    </tr>
+    <tr>
+      <th>method</th>
+      <td><p>the method used to determine consensus ancestries. 'mpa'
+(maximum posterior ancestry) simply returns the posterior ancestry with the
+highest posterior support for each case, even if this includes
+cycles. 'decycle' will return the maximum posterior ancestry, except when
+cycles are detected, in which case the link in the cycle with the lowest
+support is pruned and the tree recalculated.</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p><code>type</code> indicates the type of graphic to plot:</p>
+<ul>
+<li><p><code>trace</code> to visualise MCMC traces for parameters or augmented data (plots the
+log-likelihood by default)</p></li>
+<li><p><code>hist</code> to plot histograms of quantitative values</p></li>
+<li><p><code>density</code> to plot kernel density estimations of quantitative values</p></li>
+<li><p><code>alpha</code> to visualise the posterior frequency of ancestries</p></li>
+<li><p><code>network</code> to visualise the transmission tree; note that
+ this opens up an interactive plot and requires a web browser with
+ Javascript enabled; the argument `min_support` is useful to select only the
+ most supported ancestries and avoid displaying too many links</p></li>
+<li><p><code>kappa</code> to visualise the distributions generations between cases and their
+ancestor/infector</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/introduction.html#graphics'>introduction vignette</a> for detailed examples on how to visualise <code>outbreaker_chains</code> objects.</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>
+
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