log_likelihood

log_likelihood.params_process

log_likelihood.PhyloEM

an object of class <code><a rd-options="" href="/link/params_process?package=PhylogeneticEM&version=1.2.1" data-mini-rdoc="PhylogeneticEM::params_process">params_process</a></code> or <code><a rd-options="" href="/link/PhyloEM?package=PhylogeneticEM&version=1.2.1" data-mini-rdoc="PhylogeneticEM::PhyloEM">PhyloEM</a></code>.

for a <code>PhyloEM</code> object, further arguments to be passed on to
<code><a rd-options="" href="/link/params_process.PhyloEM?package=PhylogeneticEM&version=1.2.1" data-mini-rdoc="PhylogeneticEM::params_process.PhyloEM">params_process.PhyloEM</a></code> (to choose which parameters to extract from
the results, see documentation of this function).

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.

Y_data

a phylogenetic tree, class <code><a rd-options="ape" href="/link/phylo?package=PhylogeneticEM&version=1.2.1&to=ape" data-mini-rdoc="ape::phylo">phylo</a></code>.
<code><a rd-options="" href="/link/incidence.matrix.full?package=PhylogeneticEM&version=1.2.1" data-mini-rdoc="PhylogeneticEM::incidence.matrix.full">incidence.matrix.full</a></code>. Can be specified to avoid extra computations.

phylo

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

Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein<e2><80><93>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

<ul>
<li><code>params_process</code>: <code><a rd-options="" href="/link/params_process?package=PhylogeneticEM&version=1.2.1" data-mini-rdoc="PhylogeneticEM::params_process">params_process</a></code> object</li>
<li><code>PhyloEM</code>: <code><a rd-options="" href="/link/PhyloEM?package=PhylogeneticEM&version=1.2.1" data-mini-rdoc="PhylogeneticEM::PhyloEM">PhyloEM</a></code> object</li>
</ul>

Methods (by class)

an object of class <code><a rd-options='' href='params_process'>params_process</a></code> or <code><a rd-options='' href='PhyloEM'>PhyloEM</a></code>.

for a <code>PhyloEM</code> object, further arguments to be passed on to
<code><a rd-options='' href='params_process.PhyloEM'>params_process.PhyloEM</a></code> (to choose which parameters to extract from
the results, see documentation of this function).

a phylogenetic tree, class <code><a rd-options='ape' href='phylo'>phylo</a></code>.
<code><a rd-options='' href='incidence.matrix.full'>incidence.matrix.full</a></code>. Can be specified to avoid extra computations.

Log Likelihood of a fitted object — log_likelihood

<ul>
<li><code>params_process</code>: <code><a rd-options='' href='params_process'>params_process</a></code> object</li>
<li><code>PhyloEM</code>: <code><a rd-options='' href='PhyloEM'>PhyloEM</a></code> object</li>
</ul>

log_likelihood: Log Likelihood of a fitted object

Description

Usage

Arguments

Value

Methods (by class)

See Also