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<meta property="og:description" content="Phylogenetic trees depict the evolutionary relationships between different
species. Each branch in a phylogenetic tree represents a period of
evolutionary history. Species that are connected to the same branch
both share that same period of evolutionary history. This function creates
a matrix that shows which species are connected with branch. In other words,
it creates a matrix that shows which periods of evolutionary history
each species have experienced." />
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<h1>Branch matrix</h1>
<small class="dont-index">Source: <a href='https://github.com/prioritizr/prioritizr/blob/master/R/branch_matrix.R'><code>R/branch_matrix.R</code></a></small>
<div class="hidden name"><code>branch_matrix.Rd</code></div>
</div>
<div class="ref-description">
<p>Phylogenetic trees depict the evolutionary relationships between different
species. Each branch in a phylogenetic tree represents a period of
evolutionary history. Species that are connected to the same branch
both share that same period of evolutionary history. This function creates
a matrix that shows which species are connected with branch. In other words,
it creates a matrix that shows which periods of evolutionary history
each species have experienced.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>branch_matrix</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'># S3 method for default</span>
<span class='fu'>branch_matrix</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'># S3 method for phylo</span>
<span class='fu'>branch_matrix</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></code></pre></div>
<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><code><a href='https://rdrr.io/pkg/ape/man/read.tree.html'>ape::phylo()</a></code> tree object.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p><code><a href='https://rdrr.io/pkg/Matrix/man/dgCMatrix-class.html'>dgCMatrix</a></code> sparse matrix object. Each row
corresponds to a different species. Each column corresponds to a different
branch. Species that inherit from a given branch are denoted with a one.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='r-in'><span class='co'># load data</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>sim_phylogeny</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'># generate species by branch matrix</span></span>
<span class='r-in'><span class='va'>m</span> <span class='op'><-</span> <span class='fu'>branch_matrix</span><span class='op'>(</span><span class='va'>sim_phylogeny</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'># plot data</span></span>
<span class='r-in'><span class='co'># \dontrun{</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/r/graphics/par.html'>par</a></span><span class='op'>(</span>mfrow <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='fl'>1</span>,<span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='va'>sim_phylogeny</span>, main <span class='op'>=</span> <span class='st'>"phylogeny"</span><span class='op'>)</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/raster.html'>raster</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/as.matrix.html'>as.matrix</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span><span class='op'>)</span>, main <span class='op'>=</span> <span class='st'>"branch matrix"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>,</span>
<span class='r-in'> box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-plt'><img src='branch_matrix-1.png' alt='' width='700' height='433' /></span>
<span class='r-in'><span class='co'># }</span></span>
</code></pre></div>
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