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

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Compute the actualization factors to apply to the incidence matrix.

Description

incidence_matrix_actualization_factors 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.

Usage

incidence_matrix_actualization_factors(
  tree,
  selection.strength,
  relativeTimes_tree = 0,
  times_shared = compute_times_ca(tree)
)

Arguments

tree	a phylogenetic tree.
selection.strength	the selection strength of the process.
relativeTimes_tree	a Nedge vector of relative times associated with the branches.
times_shared	a matrix, result of function compute_times_ca.

Value

Matrix of size ntaxa x Nedge

PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.