equivalent_shifts_values

<code>equivalent_shifts_values</code> computes the values of the shifts given all
the possible allocations computed by function
<code>equivalent_shifts_edges</code>.

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

equivalent_shifts_values function

<dl><dt>phylo</dt>
<dd>a phylogenetic tree, class <code>phylo</code>.</dd>
<dt>eq_shifts_edges</dt>
<dd>matrix (optional) result of function
<code>equivalent_shifts_edges</code>.</dd>
<dt>T_tree_ac</dt>
<dd>matrix of incidence of the tree, result of function 
<code>incidence.matrix</code>, actualized with coefficients computed by
function <code>incidence_matrix_actualization_factors</code>.</dd></dl>

Arguments

Find values given edges. OU stationary case. Ultrametric tree. — equivalent_shifts_values

<dl>

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


<dt>eq_shifts_edges</dt>
<dd>matrix (optional) result of function
<code>equivalent_shifts_edges</code>.</dd>


<dt>T_tree_ac</dt>
<dd>matrix of incidence of the tree, result of function 
<code>incidence.matrix</code>, actualized with coefficients computed by
function <code>incidence_matrix_actualization_factors</code>.</dd>

</dl>

equivalent_shifts_values: Find values given edges. OU stationary case. Ultrametric tree.

Description

Usage

Value

Arguments

Details