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    <h1>Phylogenetic uncertainty - Trait Evolution Discrete Characters</h1>
    <small class="dont-index">Source: <a href='https://github.com/paternogbc/sensiPhy/blob/master/R/tree_Discrete.R'><code>R/tree_Discrete.R</code></a></small>
    <div class="hidden name"><code>tree_discrete.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Fits models for trait evolution of discrete (binary) characters, 
evaluating phylogenetic uncertainty.</p>
    </div>

    <pre class="usage"><span class='fu'>tree_discrete</span>(
  <span class='no'>data</span>,
  <span class='no'>phy</span>,
  <span class='kw'>n.tree</span> <span class='kw'>=</span> <span class='fl'>10</span>,
  <span class='no'>model</span>,
  <span class='kw'>transform</span> <span class='kw'>=</span> <span class='st'>"none"</span>,
  <span class='kw'>bounds</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(),
  <span class='kw'>n.cores</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
  <span class='kw'>track</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
  <span class='no'>...</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>data</th>
      <td><p>Data vector for a single binary trait, with names matching tips in <code>phy</code>.</p></td>
    </tr>
    <tr>
      <th>phy</th>
      <td><p>Phylogenies (class 'multiPhylo', see ?<code>ape</code>).</p></td>
    </tr>
    <tr>
      <th>n.tree</th>
      <td><p>Number of times to repeat the analysis with n different trees picked 
randomly in the multiPhylo file. If NULL, <code>n.tree</code> = 10</p></td>
    </tr>
    <tr>
      <th>model</th>
      <td><p>The Mkn model to use (see Details).</p></td>
    </tr>
    <tr>
      <th>transform</th>
      <td><p>The evolutionary model to transform the tree (see Details). Default is <code>none</code>.</p></td>
    </tr>
    <tr>
      <th>bounds</th>
      <td><p>settings to constrain parameter estimates. See <code><a href='https://rdrr.io/pkg/geiger/man/fitDiscrete.html'>fitDiscrete</a></code></p></td>
    </tr>
    <tr>
      <th>n.cores</th>
      <td><p>number of cores to use. If 'NULL', number of cores is detected.</p></td>
    </tr>
    <tr>
      <th>track</th>
      <td><p>Print a report tracking function progress (default = TRUE)</p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>Further arguments to be passed to <code><a href='https://rdrr.io/pkg/geiger/man/fitDiscrete.html'>fitDiscrete</a></code></p></td>
    </tr>
    </table>

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

    <p>The function <code>tree_discrete</code> returns a list with the following
components:</p>
<p><code>call</code>: The function call</p>
<p><code>data</code>: The original full data vector</p>
<p><code>sensi.estimates</code>: Parameter estimates (transition rates q12 and q21), 
AICc and the optimised value of the phylogenetic transformation parameter (e.g. <code>lambda</code>) 
for each analysis with a different phylogenetic tree.</p>
<p><code>N.tree</code>: Number of trees <code>n.tree</code> analysed</p>
<p><code>stats</code>: Main statistics for model parameters, i.e. minimum, maximum, mean, median and sd-values</p>
<p><code>optpar</code>: Transformation parameter used (e.g. <code>lambda</code>, <code>kappa</code> etc.)</p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>This function fits different models of discrete character evolution using <code><a href='https://rdrr.io/pkg/geiger/man/fitDiscrete.html'>fitDiscrete</a></code>
to n trees, randomly picked in a multiPhylo file. Currently, only binary discrete traits are supported</p>
<p>Different character model from <code>fitDiscrete</code> can be used, including <code>ER</code> (equal-rates), 
<code>SYM</code> (symmetric), <code>ARD</code> (all-rates-different) and <code>meristic</code> (stepwise fashion).</p>
<p>All transformations to the phylogenetic tree from <code>fitDiscrete</code> can be used, i.e. <code>none</code>,
<code>EB</code>, <code>lambda</code>, <code>kappa</code> and<code>delta</code>.</p>
<p>See <code><a href='https://rdrr.io/pkg/geiger/man/fitDiscrete.html'>fitDiscrete</a></code> for more details on character models and tree transformations.</p>
<p>Output can be visualised using <code>sensi_plot</code>.</p>
    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

    <p>Paterno, G. B., Penone, C. Werner, G. D. A. 
<a href='http://doi.wiley.com/10.1111/2041-210X.12990'>sensiPhy: 
An r-package for sensitivity analysis in phylogenetic 
comparative methods.</a> Methods in Ecology and Evolution 
2018, 9(6):1461-1467</p>
<p>Yang Z. 2006. Computational Molecular Evolution. Oxford University Press: Oxford.</p>
<p>Harmon Luke J, Jason T Weir, Chad D Brock, Richard E Glor, and Wendell Challenger. 2008.
GEIGER: investigating evolutionary radiations. Bioinformatics 24:129-131.</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='https://rdrr.io/pkg/geiger/man/fitDiscrete.html'>fitDiscrete</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='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>#Load data:</span>
<span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='st'>"primates"</span>)
<span class='co'>#Create a binary trait factor </span>
<span class='no'>adultMass_binary</span><span class='kw'>&lt;-</span><span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>primates</span>$<span class='no'>data</span>$<span class='no'>adultMass</span> <span class='kw'>&gt;</span> <span class='fl'>7350</span>, <span class='st'>"big"</span>, <span class='st'>"small"</span>)
<span class='no'>adultMass_binary</span><span class='kw'>&lt;-</span><span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='no'>adultMass_binary</span>))
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>adultMass_binary</span>)<span class='kw'>&lt;-</span><span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>primates</span>$<span class='no'>data</span>)
<span class='co'>#Model trait evolution accounting for phylogenetic uncertainty</span>
<span class='no'>tree_binary</span><span class='kw'>&lt;-</span><span class='fu'>tree_discrete</span>(<span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>adultMass_binary</span>,<span class='kw'>phy</span> <span class='kw'>=</span> <span class='no'>primates</span>$<span class='no'>phy</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"ARD"</span>,<span class='kw'>transform</span> <span class='kw'>=</span> <span class='st'>"none"</span>,<span class='kw'>n.tree</span> <span class='kw'>=</span> <span class='fl'>30</span>,<span class='kw'>n.cores</span> <span class='kw'>=</span> <span class='fl'>2</span>,<span class='kw'>track</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'>#Print summary statistics</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>tree_binary</span>)
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree_binary</span>)
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree_binary</span>,<span class='kw'>graphs</span><span class='kw'>=</span><span class='st'>"q12"</span>)
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree_binary</span>,<span class='kw'>graphs</span><span class='kw'>=</span><span class='st'>"q21"</span>)
<span class='co'>#Use a different evolutionary model or transformation.</span>
<span class='no'>tree_binary_lambda</span><span class='kw'>&lt;-</span><span class='fu'>tree_discrete</span>(<span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>adultMass_binary</span>,<span class='kw'>phy</span> <span class='kw'>=</span> <span class='no'>primates</span>$<span class='no'>phy</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SYM"</span>,<span class='kw'>transform</span> <span class='kw'>=</span> <span class='st'>"lambda"</span>,<span class='kw'>n.tree</span> <span class='kw'>=</span> <span class='fl'>30</span>,<span class='kw'>n.cores</span> <span class='kw'>=</span> <span class='fl'>2</span>,<span class='kw'>track</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>tree_binary_lambda</span>) <span class='co'>#Using Pagel's Lambda</span>
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree_binary_lambda</span>)
<span class='co'>#Symmetrical rates, with an Early Burst (EB) model of trait evolution</span>
<span class='no'>tree_binary_SYM_EB</span><span class='kw'>&lt;-</span><span class='fu'>tree_discrete</span>(<span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>adultMass_binary</span>,<span class='kw'>phy</span> <span class='kw'>=</span> <span class='no'>primates</span>$<span class='no'>phy</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SYM"</span>,<span class='kw'>transform</span> <span class='kw'>=</span> <span class='st'>"EB"</span>,<span class='kw'>n.tree</span> <span class='kw'>=</span> <span class='fl'>30</span>,<span class='kw'>n.cores</span> <span class='kw'>=</span> <span class='fl'>2</span>,<span class='kw'>track</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>tree_binary_SYM_EB</span>)
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree_binary_SYM_EB</span>)
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree_binary_SYM_EB</span>,<span class='kw'>graphs</span><span class='kw'>=</span><span class='st'>"optpar"</span>)
}</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="#details">Details</a></li>
      <li><a href="#references">References</a></li>
      <li><a href="#see-also">See also</a></li>
      <li><a href="#examples">Examples</a></li>
    </ul>

    <h2>Author</h2>
    <p>Gijsbert Werner &amp; Caterina Penone</p>
  </div>
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