Re: [R-sig-phylo] algorithm for maximum and minimum phylogenetic diversity
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 R� 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/
Re: [R-sig-phylo] algorithm for maximum and minimum phylogenetic diversity
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/
Re: [R-sig-phylo] algorithm for maximum and minimum phylogenetic diversity
Hi Leonardo, Minh et al. have two papers related to this. http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf http://sysbio.oxfordjournals.org/content/58/6/586.full.pdf Their software is available, which the manual says is GPL. I didn't see any source code, so you might have to ask if you want it. http://www.cibiv.at/software/pda/ -Graham On 14 November 2014 03:58, 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/ ___ 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/
Re: [R-sig-phylo] algorithm for maximum and minimum phylogenetic diversity
Thank you Graham! This is exactly what I was looking for. It does not solve the minimum PD issue, but possibly these algorithms can be adapted for that. On Thu, Nov 13, 2014 at 10:18 PM, Graham Gower graham.go...@gmail.com wrote: Hi Leonardo, Minh et al. have two papers related to this. http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf http://sysbio.oxfordjournals.org/content/58/6/586.full.pdf Their software is available, which the manual says is GPL. I didn't see any source code, so you might have to ask if you want it. http://www.cibiv.at/software/pda/ -Graham On 14 November 2014 03:58, 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/
Re: [R-sig-phylo] algorithm for maximum and minimum phylogenetic diversity
You may find the most recent paper from Minh others useful too, as it describes some (previously known) algorithms for selection quite well: http://onlinelibrary.wiley.com/doi/10./2041-210X.12299/abstract Regards, Rich Rich Grenyer Associate Professor of Biodiversity and Biogeography Academic Director: MSc in Biodiversity, Conservation Management School of Geography The Environment, University of Oxford South Parks Road, Oxford, OX1 3QY Fellow, and Tutor in Physical Geography, Jesus College Oxford http://www.geog.ox.ac.uk/staff/rgrenyer.html http://www.geog.ox.ac.uk/graduate/msc-bcm/ http://geography.jesus.ox.ac.ukhttp://geography.jesus.ox.ac.uk/ CPLEX There are no solutions. On 14 Nov 2014, at 00:19, Graham Gower graham.go...@gmail.commailto:graham.go...@gmail.com wrote: Hi Leonardo, Minh et al. have two papers related to this. http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf http://sysbio.oxfordjournals.org/content/58/6/586.full.pdf Their software is available, which the manual says is GPL. I didn't see any source code, so you might have to ask if you want it. http://www.cibiv.at/software/pda/ -Graham On 14 November 2014 03:58, Leonardo R� Jorge leonardorejo...@gmail.commailto: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.orgmailto: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/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.orgmailto: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/
