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uncertainty in trees topology." />
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    <h1>Phylogenetic uncertainty - Phylogenetic Linear Regression</h1>
    <small class="dont-index">Source: <a href='https://github.com/paternogbc/sensiPhy/blob/master/R/tree_phylm.R'><code>R/tree_phylm.R</code></a></small>
    <div class="hidden name"><code>tree_phylm.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Performs Phylogenetic linear regression evaluating
uncertainty in trees topology.</p>
    </div>

    <pre class="usage"><span class='fu'>tree_phylm</span>(<span class='no'>formula</span>, <span class='no'>data</span>, <span class='no'>phy</span>, <span class='kw'>n.tree</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"lambda"</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>formula</th>
      <td><p>The model formula</p></td>
    </tr>
    <tr>
      <th>data</th>
      <td><p>Data frame containing species traits with species as row names.</p></td>
    </tr>
    <tr>
      <th>phy</th>
      <td><p>A phylogeny (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> = 2</p></td>
    </tr>
    <tr>
      <th>model</th>
      <td><p>The phylogenetic model to use (see Details). Default is <code>lambda</code>.</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>phylolm</code></p></td>
    </tr>
    </table>

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

    <p>The function <code>tree_phylm</code> returns a list with the following
components:</p>
<p><code>formula</code>: The formula</p>
<p><code>data</code>: Original full dataset</p>
<p><code>sensi.estimates</code>: Coefficients, aic and the optimised
value of the phylogenetic parameter (e.g. <code>lambda</code>) for each regression with a 
different phylogenetic tree.</p>
<p><code>N.obs</code>: Size of the dataset after matching it with tree tips and removing NA's.</p>
<p><code>stats</code>: Main statistics for model parameters.<code>CI_low</code> and <code>CI_high</code> are the lower 
and upper limits of the 95<!-- % confidence interval. --></p>
<p><code>all.stats</code>: Complete statistics for model parameters. <code>sd_intra</code> is the standard deviation 
due to intraspecific variation. <code>CI_low</code> and <code>CI_high</code> are the lower and upper limits 
of the 95<!-- % confidence interval. --></p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>This function fits a phylogenetic linear regression model using <code><a href='https://rdrr.io/pkg/phylolm/man/phylolm.html'>phylolm</a></code>
to n trees, randomly picked in a multiPhylo file.</p>
<p>All phylogenetic models from <code>phylolm</code> can be used, i.e. <code>BM</code>,
<code>OUfixedRoot</code>, <code>OUrandomRoot</code>, <code>lambda</code>, <code>kappa</code>,
<code>delta</code>, <code>EB</code> and <code>trend</code>. See ?<code>phylolm</code> for details.</p>
<p>Currently, this function can only implement simple linear models (i.e. \(trait~
predictor\)). In the future we will implement more complex models.</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>Donoghue, M.J. &amp; Ackerly, D.D. (1996). Phylogenetic Uncertainties and 
Sensitivity Analyses in Comparative Biology. Philosophical Transactions:
 Biological Sciences, pp. 1241-1249.</p> 
<p>Ho, L. S. T. and Ane, C. 2014. "A linear-time algorithm for 
Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.</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/phylolm/man/phylolm.html'>phylolm</a></code>, <code><a href='sensi_plot.html'>sensi_plot</a></code>, <code><a href='tree_phyglm.html'>tree_phyglm</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='co'># Load data:</span>
<span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>alien</span>)
<span class='co'># This analysis needs a multiphylo file:</span>
<span class='fu'><a href='https://rdrr.io/r/base/class.html'>class</a></span>(<span class='no'>alien</span>$<span class='no'>phy</span>)</div><div class='output co'>#&gt; [1] "multiPhylo"</div><div class='input'><span class='no'>alien</span>$<span class='no'>phy</span></div><div class='output co'>#&gt; 101 phylogenetic trees</div><div class='input'><span class='co'># run PGLS accounting for phylogenetic uncertain:</span>
<span class='no'>tree</span> <span class='kw'>&lt;-</span> <span class='fu'>tree_phylm</span>(<span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='no'>gestaLen</span>) ~ <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='no'>adultMass</span>), <span class='kw'>phy</span> <span class='kw'>=</span> <span class='no'>alien</span>$<span class='no'>phy</span>,
<span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>alien</span>$<span class='no'>data</span>, <span class='kw'>n.tree</span> <span class='kw'>=</span> <span class='fl'>30</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: NA's in response or predictor, rows with NA's were removed</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Some phylo tips do not match species in data (this can be due to NA removal) species were dropped from phylogeny or data</span></div><div class='output co'>#&gt; <span class='message'>Used dataset has  84  species that match data and phylogeny</span></div><div class='output co'>#&gt; 
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  |======================================================================| 100%</div><div class='input'><span class='co'># To check summary results:</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>tree</span>)</div><div class='output co'>#&gt;                 mean CI_low CI_high
#&gt; intercept      2.327  2.315   2.339
#&gt; se.intercept   0.343  0.342   0.344
#&gt; pval.intercept 0.000  0.000   0.000
#&gt; estimate       0.152  0.150   0.153
#&gt; se.estimate    0.022  0.022   0.022
#&gt; pval.estimate  0.000  0.000   0.000</div><div class='input'><span class='co'># Visual diagnostics</span>
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree</span>)</div><div class='img'><img src='tree_phylm-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># You can specify which graph to print: </span>
<span class='fu'><a href='sensi_plot.html'>sensi_plot</a></span>(<span class='no'>tree</span>, <span class='kw'>graphs</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='img'><img src='tree_phylm-2.png' alt='' width='700' height='433' /></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>Caterina Penone &amp; Pablo Ariel Martinez</p>
  </div>
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