allocate_shifts_from_regimes

<code>allocate_shifts_from_regimes</code> returns the position of the shifts induced
by the allocation of the regimes. Only works in an "infinite site" model.

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

allocate_shifts_from_regimes function

<dl><dt>phylo</dt>
<dd>a phylogenetic tree, class <code>phylo</code>.</dd>
<dt>regimes</dt>
<dd>: vector of size (ntaxa + Nnode) of the regimes of each node
and tip.</dd></dl>

Arguments

Allocation of shifts to edges — allocate_shifts_from_regimes

<dl>

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


<dt>regimes</dt>
<dd>: vector of size (ntaxa + Nnode) of the regimes of each node
and tip.</dd>

</dl>

allocate_shifts_from_regimes: Allocation of shifts to edges

Description

Usage

Value

Arguments