compute_tree_correlations_matrix.scOU

<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–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

compute_tree_correlations_matrix.scOU function

<dl><dt>times_shared</dt>
<dd>times of shared ancestry of all nodes and tips, result of function
<code>compute_times_ca</code></dd>
<dt>distances_phylo</dt>
<dd>(matrix) : phylogenetic distance, result of function 
<code>compute_dist_phy</code></dd>
<dt>params_old</dt>
<dd>(list) : old parameters to be used in the E step</dd></dl>

Arguments

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

<dl>

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


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


<dt>params_old</dt>
<dd>(list) : old parameters to be used in the E step</dd>

</dl>

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

Description

Usage

Value

Arguments