incidence_matrix_actualization_factors

<code>incidence_matrix_actualization_factors</code> computes a ntaxa x Nedge matrix of the 
(1 - exp(-alpha * (t_i - t_pa(j) - nu_j * l_j)))_{i tip, j node}.
This matrix is to be multiplied to the incidence matrix with an outer product.

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

incidence_matrix_actualization_factors function

<dl><dt>tree</dt>
<dd>a phylogenetic tree.</dd>
<dt>selection.strength</dt>
<dd>the selection strength of the process.</dd>
<dt>relativeTimes_tree</dt>
<dd>a Nedge vector of relative times associated with the branches.</dd>
<dt>times_shared</dt>
<dd>a matrix, result of function <code>compute_times_ca</code>.</dd></dl>

Arguments

Compute the actualization factors to apply to the incidence matrix. — incidence_matrix_actualization_factors

<dl>

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


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


<dt>relativeTimes_tree</dt>
<dd>a Nedge vector of relative times associated with the branches.</dd>


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

</dl>

incidence_matrix_actualization_factors: Compute the actualization factors to apply to the incidence matrix.

Description

Usage

Value

Arguments