Re: [R-sig-phylo] 3. partial correlation with gls residuals? (Tom Schoenemann)

Hi Alejandro, I agree with almost all your points. A few additional comments below. Correlation gives the correlation among the estimated regression parameters: it is computed from the variance-covariance matrix extracted from the fitted object, model.fit$varBeta or vcov(model.fit) -- the

Re: [R-sig-phylo] Tree Permutation

Hi Sean, Conceptually speaking it helps to think about tree permutations in terms of snapping a tree at a random edge, and then re-attaching that edge somewhere else on the tree. That saves the problems with picking two independent nodes. There are standard routines for this kind of thing,

Re: [R-sig-phylo] Alternative to rapply() for nested lists of phylo objects?

Hi Dave, I believe that this does what you want ('d'apply for Dave). dapply - function(obj, FUN, class=phylo, default=NULL) { ret - lapply(obj, function(x) if (inherits(x, class)) FUN(x) else if (is.atomic(x)) default else dapply(x, FUN, class))

Re: [R-sig-phylo] Testing for phylogenetic signal in proportions

It is really too few species to have a sufficiently powerful test for phylogenetic signal. See Blomberg et al. (2003), available on my website. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951)