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
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" or "OU".