compute_tree_correlations_matrix.scOU

times of shared ancestry of all nodes and tips, result of function
<code>compute_times_ca</code>

times_shared

(matrix) : phylogenetic distance, result of function 
<code>compute_dist_phy</code>

distances_phylo

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

params_old

<code>compute_tree_correlations_matrix.scOU</code> 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.

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>.

compute_tree_correlations_matrix.scOU: Matrix of tree-induced correlations for the scOU

Description

Usage

Arguments

Value