log_likelihood

log_likelihood.params_process

log_likelihood.PhyloEM

<code>log_likelihood</code> computes the log likelihood of some parameters.

Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.

Paul Bastide

PhylogeneticEM

Automatic Shift Detection using a Phylogenetic EM

Mahendra Mariadassou

log_likelihood function

<dl><dt>x</dt>
<dd>an object of class <code>params_process</code> or <code>PhyloEM</code>.</dd>
<dt>...</dt>
<dd>for a <code>PhyloEM</code> object, further arguments to be passed on to
<code>params_process.PhyloEM</code> (to choose which parameters to extract from
the results, see documentation of this function).</dd>
<dt>Y_data</dt>
<dd>matrix of data at the tips, size p x ntaxa. Each line is a
trait, and each column is a tip. The column names are checked against the
tip names of the tree.</dd>
<dt>phylo</dt>
<dd>a phylogenetic tree, class <code>phylo</code>.
<code>incidence.matrix.full</code>. Can be specified to avoid extra computations.</dd></dl>

Arguments

<ul>
<li><code>log_likelihood(params_process)</code>: <code>params_process</code> object</li>
<li><code>log_likelihood(PhyloEM)</code>: <code>PhyloEM</code> object</li>
</ul>

Methods (by class)

Log Likelihood of a fitted object — log_likelihood

<dl>

<dt>x</dt>
<dd>an object of class <code>params_process</code> or <code>PhyloEM</code>.</dd>


<dt>...</dt>
<dd>for a <code>PhyloEM</code> object, further arguments to be passed on to
<code>params_process.PhyloEM</code> (to choose which parameters to extract from
the results, see documentation of this function).</dd>


<dt>Y_data</dt>
<dd>matrix of data at the tips, size p x ntaxa. Each line is a
trait, and each column is a tip. The column names are checked against the
tip names of the tree.</dd>


<dt>phylo</dt>
<dd>a phylogenetic tree, class <code>phylo</code>.
<code>incidence.matrix.full</code>. Can be specified to avoid extra computations.</dd>

</dl>

log_likelihood: Log Likelihood of a fitted object

Description

Usage

Value

Arguments

Methods (by class)

See Also