compute_actualization_matrix_ultrametric

<code>compute_actualization_matrix_ultrametric</code> computes a squares p*Nedge bloc diagonal
matrix of the (I_p - exp(-A * (h - t_pa(j))))_{j node}.

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

compute_actualization_matrix_ultrametric function

<dl><dt>tree</dt>
<dd>a phylogenetic tree.</dd>
<dt>selection.strength</dt>
<dd>the selection strength of the process.</dd>
<dt>times_shared</dt>
<dd>a matrix, result of function <code>compute_times_ca</code>.</dd></dl>

Arguments

Compute Matrix W of actualization (Ultrametric case) — compute_actualization_matrix_ultrametric

<dl>

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


<dt>selection.strength</dt>
<dd>the selection strength of the process.</dd>


<dt>times_shared</dt>
<dd>a matrix, result of function <code>compute_times_ca</code>.</dd>

</dl>

compute_actualization_matrix_ultrametric: Compute Matrix W of actualization (Ultrametric case)

Description

Usage

Value

Arguments

Details