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    <h1>Extract a clade from phylogenetic tree</h1>
    
    <div class="hidden name"><code>PCMTreeExtractClade.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Extract a clade from phylogenetic tree</p>
    </div>

    <pre class="usage"><span class='fu'>PCMTreeExtractClade</span>(
  <span class='no'>tree</span>,
  <span class='no'>cladeRootNode</span>,
  <span class='kw'>tableAncestors</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
  <span class='kw'>X</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
  <span class='kw'>returnList</span> <span class='kw'>=</span> !<span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span>(<span class='no'>X</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>tree</th>
      <td><p>a PCMTree object.</p></td>
    </tr>
    <tr>
      <th>cladeRootNode</th>
      <td><p>a character string denoting the label or an integer denoting a node in the tree.</p></td>
    </tr>
    <tr>
      <th>tableAncestors</th>
      <td><p>an integer matrix returned by a previous call to PCMTreeTableAncestors(tree) or NULL.</p></td>
    </tr>
    <tr>
      <th>X</th>
      <td><p>an optional k x N matrix with trait value vectors for each tip in tree.</p></td>
    </tr>
    <tr>
      <th>returnList</th>
      <td><p>logical indicating if only the phylo object associated
with the clade should be returned. Defaults to <code>!is.null(X)</code></p></td>
    </tr>
    </table>

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

    <p>If returnList is FALSE, a phylo object associated with the clade,
 otherwise, a list with two named members :</p><ul>
<li><p>treethe phylo object associated with the clade</p></li>
<li><p>Xthe submatrix of X with columns corresponding to the tips in the clade</p></li>
</ul>

    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

    <div class='dont-index'><p>PCMTreeSpliAtNode PCMTreeDropClade</p></div>

    <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/Random.html'>set.seed</a></span>(<span class='fl'>1</span>, <span class='kw'>kind</span> <span class='kw'>=</span> <span class='st'>"Mersenne-Twister"</span>, <span class='kw'>normal.kind</span> <span class='kw'>=</span> <span class='st'>"Inversion"</span>)
<span class='no'>tree</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='PCMTree.html'>PCMTree</a></span>(<span class='kw pkg'>ape</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ape/man/rtree.html'>rtree</a></span>(<span class='fl'>25</span>))
<span class='fu'><a href='PCMTreeSetPartRegimes.html'>PCMTreeSetPartRegimes</a></span>(
  <span class='no'>tree</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>`26`</span><span class='kw'>=</span><span class='st'>"a"</span>, <span class='kw'>`28`</span><span class='kw'>=</span><span class='st'>"b"</span>, <span class='kw'>`45`</span><span class='kw'>=</span><span class='st'>"c"</span>), <span class='kw'>setPartition</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'># \donttest{</span>
<span class='fu'><a href='PCMTreePlot.html'>PCMTreePlot</a></span>(<span class='no'>tree</span>, <span class='kw'>palette</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>a</span> <span class='kw'>=</span> <span class='st'>"red"</span>, <span class='kw'>b</span> <span class='kw'>=</span> <span class='st'>"green"</span>, <span class='kw'>c</span> <span class='kw'>=</span> <span class='st'>"blue"</span>)) +
  <span class='kw pkg'>ggtree</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ggtree/man/geom_nodelab.html'>geom_nodelab</a></span>(<span class='kw'>angle</span> <span class='kw'>=</span> <span class='fl'>45</span>) + <span class='kw pkg'>ggtree</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ggtree/man/geom_tiplab.html'>geom_tiplab</a></span>(<span class='kw'>angle</span> <span class='kw'>=</span> <span class='fl'>45</span>)</div><div class='img'><img src='PCMTreeExtractClade-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
<span class='no'>blueTree</span> <span class='kw'>&lt;-</span> <span class='fu'>PCMTreeExtractClade</span>(<span class='no'>tree</span>, <span class='fl'>45</span>)
<span class='fu'><a href='PCMTreeGetPartRegimes.html'>PCMTreeGetPartRegimes</a></span>(<span class='no'>blueTree</span>)</div><div class='output co'>#&gt;  45 
#&gt; "c" </div><div class='input'><span class='co'># \donttest{</span>
<span class='fu'><a href='PCMTreePlot.html'>PCMTreePlot</a></span>(<span class='no'>blueTree</span>, <span class='kw'>palette</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>a</span> <span class='kw'>=</span> <span class='st'>"red"</span>, <span class='kw'>b</span> <span class='kw'>=</span> <span class='st'>"green"</span>, <span class='kw'>c</span> <span class='kw'>=</span> <span class='st'>"blue"</span>)) +
  <span class='kw pkg'>ggtree</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ggtree/man/geom_nodelab.html'>geom_nodelab</a></span>(<span class='kw'>angle</span> <span class='kw'>=</span> <span class='fl'>45</span>) + <span class='kw pkg'>ggtree</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ggtree/man/geom_tiplab.html'>geom_tiplab</a></span>(<span class='kw'>angle</span> <span class='kw'>=</span> <span class='fl'>45</span>)</div><div class='img'><img src='PCMTreeExtractClade-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
<span class='co'># we need to use the label here, because the node 29 in tree is not the same</span>
<span class='co'># id in redGreenTree:</span>
<span class='no'>blueTree2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='PCMTreeDropClade.html'>PCMTreeDropClade</a></span>(<span class='no'>blueTree</span>, <span class='st'>"48"</span>)
<span class='co'># \donttest{</span>
<span class='fu'><a href='PCMTreePlot.html'>PCMTreePlot</a></span>(<span class='no'>blueTree2</span>, <span class='kw'>palette</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>a</span> <span class='kw'>=</span> <span class='st'>"red"</span>, <span class='kw'>b</span> <span class='kw'>=</span> <span class='st'>"green"</span>, <span class='kw'>c</span> <span class='kw'>=</span> <span class='st'>"blue"</span>)) +
  <span class='kw pkg'>ggtree</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ggtree/man/geom_nodelab.html'>geom_nodelab</a></span>(<span class='kw'>angle</span> <span class='kw'>=</span> <span class='fl'>45</span>) + <span class='kw pkg'>ggtree</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ggtree/man/geom_tiplab.html'>geom_tiplab</a></span>(<span class='kw'>angle</span> <span class='kw'>=</span> <span class='fl'>45</span>)</div><div class='img'><img src='PCMTreeExtractClade-3.png' alt='' width='700' height='433' /></div><div class='input'># }

</div></pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      <li><a href="#arguments">Arguments</a></li>
      <li><a href="#value">Value</a></li>
      <li><a href="#see-also">See also</a></li>
      <li><a href="#examples">Examples</a></li>
    </ul>

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