Here is an alternative version that is more than twice as fast (helpful
for large trees), and only a little bit slower than vcv.phylo():
vcvPhylo2-function(tree,anc.nodes=T){
n-length(tree$tip.label)
h-nodeHeights(tree)[order(tree$edge[,2]),2]
h-c(h[1:n],0,h[(n+1):length(h)])
Hi all,
Having a tree (NOT ultrametric in my case) I would
like to extract the phylogenetic covariance matrix
including both tips and nodes (like dist.nodes for
patristic distances).
vcv returns the cov matric just for tips.
Someone has a fast way?
Thankyou very much
Paolo
