compute_variance_covariance.scOU

<code>compute_variance_covariance.scOU</code> computes the (n+m)*p squared variance covariance
matrix of vec(X).

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_variance_covariance.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

Complete variance covariance matrix for scOU — compute_variance_covariance.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_variance_covariance.scOU: Complete variance covariance matrix for scOU

Description

Usage

Value

Arguments