compute_tree_correlations_matrix.scOU {PhylogeneticEM}R Documentation

Matrix of tree-induced correlations for the scOU

Description

compute_tree_correlations_matrix.scOU computes the (n+m)x(m+n) matrix of correlations induced by the tree. It takes two cases in consideration: root fixed, or root in stationary state.

Usage

compute_tree_correlations_matrix.scOU(times_shared, distances_phylo, params_old,
  ...)

Arguments

times_shared

times of shared ancestry of all nodes and tips, result of function compute_times_ca

distances_phylo

(matrix) : phylogenetic distance, result of function compute_dist_phy

params_old

(list) : old parameters to be used in the E step

Value

matrix of variance covariance for the scOU

[Package PhylogeneticEM version 1.1.0 Index]