compute_residuals.simple

<code>compute_residuals.simple</code> computes the residuals after the fit of the
data in the simple case where the inverse of the variance matrix is given.

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_residuals.simple function

<dl><dt>phylo</dt>
<dd>Input tree.</dd>
<dt>Y_data_vec</dt>
<dd>: vector indicating the data at the tips.</dd>
<dt>sim</dt>
<dd>(list) : result of function <code>simulate</code>.</dd>
<dt>Sigma_YY_chol_inv</dt>
<dd>: invert of the Cholesky variance-covariance matrix of the data.</dd></dl>

Arguments

Residuals — compute_residuals.simple

<dl>

<dt>phylo</dt>
<dd>Input tree.</dd>


<dt>Y_data_vec</dt>
<dd>: vector indicating the data at the tips.</dd>


<dt>sim</dt>
<dd>(list) : result of function <code>simulate</code>.</dd>


<dt>Sigma_YY_chol_inv</dt>
<dd>: invert of the Cholesky variance-covariance matrix of the data.</dd>

</dl>

compute_residuals.simple: Residuals

Description

Usage

Arguments

Details