check_parsimony_clusters

<code>check_parsimony_clusters</code> takes a vector clusters of the tips, and
checks whether the number of groups of the tips induced by this allocation is
exactly the number of shifts plus one.

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

check_parsimony_clusters function

<dl><dt>tree</dt>
<dd>phylogenetic tree.</dd>
<dt>clusters</dt>
<dd>a vector of clusters of the tips of the tree (result of
function <code>clusters_from_shifts</code>).</dd></dl>

Arguments

Check whether an allocation of the shifts is parsimonious, 
in the "infinite site model". — check_parsimony_clusters

<dl>

<dt>tree</dt>
<dd>phylogenetic tree.</dd>


<dt>clusters</dt>
<dd>a vector of clusters of the tips of the tree (result of
function <code>clusters_from_shifts</code>).</dd>

</dl>

check_parsimony_clusters: Check whether an allocation of the shifts is parsimonious, in the "infinite site model".

Description

Usage

Value

Arguments

Details