Monday, November 21, 2011

vcv.phylo() with ancestral nodes

An R-sig-phylo user just posted a request for a function to compute the so-called phylogenetic variance-covariance matrix. That is, the N×N matrix (for N species) containing in position i,j the height above the root of the MRCA of species i and j (as done in the ape function vcv.phylo) - but including ancestral nodes. As it turns out, I have a code fragment to do this in my function anc.trend() (link here). I pasted the fragment into a function vcvPhylo() as follows:

    C<-D; C[,]<-0
    for(i in 1:nrow(D)) for(j in 1:ncol(D)) 
  } else return(vcv.phylo(phy))

and it seems to do the trick.

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