Re: [R-sig-phylo] Phylogenetic Logistic Regression

2011-11-21 Thread Anthony R Ives
Matt, Sorry about only having a matlab implementation. If there is a lot of interest, I could translate things into R. There are two other possibilities that I know about. As you mention, MCMCglmm should work, although it could not be used for standard frequentist model selection. Matt

[R-sig-phylo] covriance matrix internal nodes

2011-11-21 Thread ppiras
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

Re: [R-sig-phylo] Phylogenetic Logistic Regression

2011-11-21 Thread Matt Pennell
Tony, Emmanuel and others, Thank you very much for your thorough reply, Tony. I will try do what you propose. While that certaintly does sound a like heresy, it seems a fairly reasonable heresy. Also, i was curious how the properties of the GEE approach from Paradis and Claude 2002 (and