vcvPhylo {phytools}

Calculates cophenetic (i.e., phylogenetic VCV) matrix

Description

Computes a phylogenetic variance-covariance matrix.

Usage

vcvPhylo(tree, anc.nodes=TRUE, ...)

Arguments

tree

object of class "phylo".

anc.nodes

logical value indicating whether or not to include ancestral nodes.

...

optional arguments including internal (synonym of anc.nodes) and model (can be "BM", "OU", or "lambda".

Details

This function returns a so-called phylogenetic variance covariance matrix (e.g., see vcv.phylo), but (optionally) including ancestral nodes, as well as under multiple evolutionary models.

vcvPhylo is designed primarily for internal use by other phytools functions.

Value

A matrix.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.