compute_betas_from_shifts

<code>compute_betas_from_shifts</code> computes the optimal values at the nodes and tips of the
tree, given the value at the root and the list of shifts occurring in the tree.
It assumes an OU 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

compute_betas_from_shifts function

<dl><dt>phylo</dt>
<dd>a phylogenetic tree, class <code>phylo</code>.</dd>
<dt>optimal.value</dt>
<dd>the optimal value at the root of the tree.</dd>
<dt>shifts</dt>
<dd>position and values of the shifts .</dd></dl>

Arguments

Computation of the optimal values at nodes and tips. — compute_betas_from_shifts

<dl>

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


<dt>optimal.value</dt>
<dd>the optimal value at the root of the tree.</dd>


<dt>shifts</dt>
<dd>position and values of the shifts .</dd>

</dl>

compute_betas_from_shifts: Computation of the optimal values at nodes and tips.

Description

Usage

Value

Arguments

Details