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!


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
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

Reply via email to