init.parsimonyCost

<code>init.parsimonyCost</code> initialize a (ntaxa + Nnode) x (nclus) matrix with
NAs everywhere, except for the tips.

internal

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

init.parsimonyCost function

<dl><dt>clusters</dt>
<dd>the vector of the clusters of the tips.</dd>
<dt>phylo</dt>
<dd>a phylogenetic tree, class <code>phylo</code>.</dd></dl>

Arguments

Initialization for parsimonyCost. — init.parsimonyCost

<dl>

<dt>clusters</dt>
<dd>the vector of the clusters of the tips.</dd>


<dt>phylo</dt>
<dd>a phylogenetic tree, class <code>phylo</code>.</dd>

</dl>

init.parsimonyCost: Initialization for parsimonyCost.

Description

Usage

Value

Arguments

Details