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)
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
