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PCMLmr.html
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PCMLmr.html
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<h1>Quadratic polynomial parameters L, m, r</h1>
<div class="hidden name"><code>PCMLmr.Rd</code></div>
</div>
<div class="ref-description">
<p>Quadratic polynomial parameters L, m, r</p>
</div>
<pre class="usage"><span class='fu'>PCMLmr</span>(
<span class='no'>X</span>,
<span class='no'>tree</span>,
<span class='no'>model</span>,
<span class='kw'>SE</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='PCMNumTraits.html'>PCMNumTraits</a></span>(<span class='no'>model</span>), <span class='fu'><a href='PCMTreeNumTips.html'>PCMTreeNumTips</a></span>(<span class='no'>tree</span>)),
<span class='kw'>metaI</span> <span class='kw'>=</span> <span class='fu'><a href='PCMInfo.html'>PCMInfo</a></span>(<span class='kw'>X</span> <span class='kw'>=</span> <span class='no'>X</span>, <span class='kw'>tree</span> <span class='kw'>=</span> <span class='no'>tree</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='no'>model</span>, <span class='kw'>SE</span> <span class='kw'>=</span> <span class='no'>SE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='no'>verbose</span>),
<span class='kw'>root.only</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>X</th>
<td><p>a <code>k x N</code> numerical matrix with possible <code>NA</code> and
<code>NaN</code> entries. For <code>i=1,..., N</code>, the column <code>i</code> of X contains
the measured trait values for species <code>i</code> (the tip with integer
identifier equal to <code>i</code> in <code>tree</code>). Missing values can be either
not-available (<code>NA</code>) or not existing (<code>NaN</code>). These two values are
treated differently when calculating likelihoods (see
<code><a href='PCMPresentCoordinates.html'>PCMPresentCoordinates</a></code>).</p></td>
</tr>
<tr>
<th>tree</th>
<td><p>a phylo object with N tips.</p></td>
</tr>
<tr>
<th>model</th>
<td><p>an S3 object specifying both, the model type (class, e.g. "OU") as
well as the concrete model parameter values at which the likelihood is to be
calculated (see also Details).</p></td>
</tr>
<tr>
<th>SE</th>
<td><p>a k x N matrix specifying the standard error for each measurement in
X. Alternatively, a k x k x N cube specifying an upper triangular k x k
factor of the variance covariance matrix for the measurement error
for each tip <code>i=1, ..., N</code>. When <code>SE</code> is a matrix, the k x k
measurement error variance matrix for a tip <code>i</code> is calculated as
<code>VE[, , i] <- diag(SE[, i] * SE[, i], nrow = k)</code>. When <code>SE</code> is a
cube, the way how the measurement variance matrix for a tip <code>i</code> is
calculated depends on the runtime option <code>PCMBase.Transpose.Sigma_x</code>
as follows:</p><dl class='dl-horizontal'>
<dt>if <code>getOption("PCMBase.Transpose.Sigma_x", FALSE) == FALSE</code> (default): </dt><dd><p>VE[, , i] <- SE[, , i] %*% t(SE[, , i])</p></dd>
<dt>if <code>getOption("PCMBase.Transpose.Sigma_x", FALSE) == TRUE</code>: </dt><dd><p>VE[, , i] <- t(SE[, , i]) %*% SE[, , i]</p></dd>
</dl><p>Note that the above behavior is consistent with the treatment of the model
parameters <code>Sigma_x</code>, <code>Sigmae_x</code> and <code>Sigmaj_x</code>, which are
also specified as upper triangular factors.
Default: <code><a href='https://rdrr.io/r/base/matrix.html'>matrix(0.0, PCMNumTraits(model), PCMTreeNumTips(tree))</a></code>.</p></td>
</tr>
<tr>
<th>metaI</th>
<td><p>a list returned from a call to <code><a href='PCMInfo.html'>PCMInfo(X, tree, model, SE)</a></code>,
containing meta-data such as N, M and k. Alternatively, this can be a
character string naming a function or a function object that returns such
a list, e.g. the function<code>PCMInfo</code> or the function <code>PCMInfoCpp</code>
from the <code>PCMBaseCpp</code> package.</p></td>
</tr>
<tr>
<th>root.only</th>
<td><p>logical indicating whether to return the calculated values of L,m,r
only for the root or for all nodes in the tree.</p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>logical indicating if some debug-messages should printed.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list with the members A,b,C,d,E,f,L,m,r for all nodes in the tree or
only for the root if root.only=TRUE.</p>
</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>
</ul>
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