Hi everyone, I have a time-calibrated phylogeny with ~100 species and a list of ~1000 observed species assemblages which vary from 2-20 species in size. I'd like to get the mean phylogenetic distance among species in each assemblage, but I'm having difficulty finding a way to do this. The comm.phylo.cor command in picante throws an error in as.hclust.default(x), that x cannot be coerced to class hclust, and I've hit a dead end finding a solution to that error. I'm not sure whether comm.phylo.cor will do what I want even if it works.
I wrote a loop to prune the phylogeny separately for each group of species, which can then theoretically be used to get the distances with cophenetic.phylo. However, as soon as I start to run cophenetic.phylo across my list of trees, R starts to hang up and freeze my entire computer even though my code is set to skip trees for which distance can't be measured. One time it managed run a few and gave a memory error (e.g., 6050235 Tb of memory is not available). But R freezes even when I try to run this on an 12 core mac. Does anyone have any other suggestions for how to get the mean phylogenetic distance for subsets of species on a tree? Thanks for any ideas! Zach -- Zachary W. Culumber Postdoctoral Research Associate Kansas State University Division of Biology [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/