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

Description

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

Usage

1
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".

Value

A matrix.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

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