Might also want to look at expected.pd in picante from: J.P. O’Dwyer, S.W. Kembel, and J.L. Green. 2012. Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8(12): e1002832.
Good luck! Matt On Thu, Nov 13, 2014 at 1:12 PM, Eliot Miller <em...@mail.umsl.edu> wrote: > Hello Leonardo, > > I'm I understand your question correctly, I believe that when using mean > pairwise phylogenetic distance (e.g., MPD from the picante package) the > maximum MPD will occur between the two most distantly related species in > the phylogeny, and the minimum will occur between the two most closely > related. With PD, the maximum will occur with the entire phylogeny, and the > minimum will again occur with the two most closely related species. If you > really want to calculate that (my guess is I misunderstood your question), > you could simply subset the pairwise genetic distance matrix from > cophenetic() to the relevant species and prune the tree accordingly. > > One can't calculate MPD with < 2 species. I suppose one could calculate PD > with < 2 species if you wanted to define it as going "through" the root, > but then PD would just equal the tree height, assuming an ultrametric tree, > and there would be no single tree with minimum PD. > > Best, > Eliot > > On Thu, Nov 13, 2014 at 9:28 AM, Leonardo Ré Jorge < > leonardorejo...@gmail.com> wrote: > > > Dear list members, > > > > I am studying the phylogenetic structure of interactions, and in order to > > build null models I need to calculate, for a given phylogeny with N > > species, what is the subset K (for K = 1 to N) of the species with > maximum > > (and minumum) phylogenetic diversity, measured as mean phylogenetic > > distance and/or PD. > > After looking up, it does not look like a trivial problem as it would > seem > > at first thought, and I am struggling to find some already written code, > or > > at least some algorithm or strategy to measure this. Do you have any > > advice? > > > > Best regards, > > Leonardo R. Jorge > > > > [[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/ > > > > [[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/ > -- Department of Animal Ecology Vrije Universiteit Amsterdam matthelmus.com [[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/
