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<h1>Set tip and internal node labels in a tree</h1>
<div class="hidden name"><code>PCMTreeSetLabels.Rd</code></div>
</div>
<div class="ref-description">
<p>Set tip and internal node labels in a tree</p>
</div>
<pre class="usage"><span class='fu'>PCMTreeSetLabels</span>(
<span class='no'>tree</span>,
<span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/character.html'>as.character</a></span>(<span class='fl'>1</span>:<span class='fu'><a href='PCMTreeNumNodes.html'>PCMTreeNumNodes</a></span>(<span class='no'>tree</span>)),
<span class='kw'>inplace</span> <span class='kw'>=</span> <span class='fl'>TRUE</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 phylo object or a PCMTree object. If this is a PCMTree object,
the internal edge.part and part.regime members will be updated accordingly.</p></td>
</tr>
<tr>
<th>labels</th>
<td><p>a character vector in the order 1:PCMTreeNumNodes(tree) as
denoted in the tree$edge matrix.</p></td>
</tr>
<tr>
<th>inplace</th>
<td><p>a logical indicating if the change should be done in place on
the object in the calling environment (in this case tree must not be a
temporary object, e.g. returned by another function call). Default is TRUE.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>if inplace is FALSE, a copy of tree with set or modified
tree$tip.label and tree$node.label. If the original tree has a member
edge.part, the returned tree has tree$edge.part and tree$part.regime updated.
If inplace is TRUE (the default), nothing is returned and the above changes
are made directly on the input tree.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='PCMTree.html'>PCMTree</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>tree</span> <span class='kw'><-</span> <span class='kw pkg'>ape</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/ape/man/rtree.html'>rtree</a></span>(<span class='fl'>5</span>)
<span class='no'>tree</span>$<span class='no'>tip.label</span></div><div class='output co'>#> [1] "t2" "t5" "t1" "t4" "t3"</div><div class='input'><span class='co'># the following three are NULLs</span>
<span class='no'>tree</span>$<span class='no'>node.label</span></div><div class='output co'>#> NULL</div><div class='input'><span class='no'>tree</span>$<span class='no'>edge.part</span></div><div class='output co'>#> NULL</div><div class='input'><span class='no'>tree</span>$<span class='no'>part.regime</span></div><div class='output co'>#> NULL</div><div class='input'>
<span class='no'>tree</span> <span class='kw'><-</span> <span class='fu'><a href='PCMTree.html'>PCMTree</a></span>(<span class='no'>tree</span>)
<span class='fu'><a href='PCMTreeSetPartition.html'>PCMTreeSetPartition</a></span>(<span class='no'>tree</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>6</span>, <span class='fl'>8</span>))
<span class='no'>tree</span>$<span class='no'>tip.label</span></div><div class='output co'>#> [1] "t2" "t5" "t1" "t4" "t3"</div><div class='input'><span class='no'>tree</span>$<span class='no'>node.label</span></div><div class='output co'>#> [1] "6" "7" "8" "9"</div><div class='input'><span class='no'>tree</span>$<span class='no'>edge.part</span></div><div class='output co'>#> [1] "6" "6" "8" "8" "8" "6" "6" "6"</div><div class='input'><span class='no'>tree</span>$<span class='no'>part.regime</span></div><div class='output co'>#> 6 8
#> 1 2 </div><div class='input'>
<span class='fu'>PCMTreeSetLabels</span>(
<span class='no'>tree</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"t"</span>, <span class='fl'>5</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"n"</span>, <span class='fl'>4</span>)), <span class='fu'><a href='PCMTreeGetLabels.html'>PCMTreeGetLabels</a></span>(<span class='no'>tree</span>)))
<span class='fu'><a href='PCMTreeGetLabels.html'>PCMTreeGetLabels</a></span>(<span class='no'>tree</span>)</div><div class='output co'>#> [1] "tt2" "tt5" "tt1" "tt4" "tt3" "n6" "n7" "n8" "n9" </div><div class='input'><span class='no'>tree</span>$<span class='no'>tip.label</span></div><div class='output co'>#> [1] "tt2" "tt5" "tt1" "tt4" "tt3"</div><div class='input'><span class='no'>tree</span>$<span class='no'>node.label</span></div><div class='output co'>#> [1] "n6" "n7" "n8" "n9"</div><div class='input'><span class='no'>tree</span>$<span class='no'>edge.part</span></div><div class='output co'>#> [1] "n6" "n6" "n8" "n8" "n8" "n6" "n6" "n6"</div><div class='input'><span class='no'>tree</span>$<span class='no'>part.regime</span></div><div class='output co'>#> n6 n8
#> 1 2 </div><div class='input'>
</div></pre>
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<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>
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