incidence_matrix_actualization_factors

tree

the selection strength of the process.

selection.strength

a nedge vector of relative times associated with the branches.

relativeTimes_tree

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

times_shared

<code>incidence_matrix_actualization_factors</code> computes a ntaxa x nedges 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<e2><80><93>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>.

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

Description

Usage

Arguments

Value