Yes, it looks like it!  Thank you!  Guess I was making it more complicated
than it needed to be.


On Thu, Feb 2, 2017 at 2:36 PM, Liam J. Revell <> wrote:

> Hi Zach.
> Do you just mean the mean patristic distance among all pairwise
> combinations of species in each assemblage?
> If you have your assemblages in a list of vectors, each containing the
> species of the corresponding assemblage, I think you could do:
> library(ape)
> D<-cophenetic(tree)
> d<-sapply(assemblages,function(sp,D) mean(as.dist(D[sp,sp])),D=D)
> Does that work?
> All the best, Liam
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> web:
> email:
> blog:
> On 2/2/2017 3:22 PM, Zach Culumber wrote:
>> 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

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