Well, since 1000 are a sample, 100 sampled from those is a somewhat more manageable sample.
As to using, say, an 80% cutoff is a valid procedure, one question is what you're doing this for. I'd be tempted to just show or report the distribution of K, lambda, and p values and talk about what they mean in terms of your biological question: "We don't know the tree exactly, but it's clear that for most feasible trees, related things are similar" or something like that. If it's a question of scaling trees for later analyses, you can just (using a script, or built in functions) choose the particular scaling to be appropriate for each tree, and so the distribution across them doesn't matter in that case. Best, Brian _______________________________________________________________________ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teaching/feedback/> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Director for Postdoctoral Activities, National Institute for Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS) Communication Director, Society of Systematic Biologists On Thu, Dec 8, 2016 at 11:26 AM, Carturan, Bruno <bruno.cartu...@ubc.ca> wrote: > Hello R-sig-phylo community, > > I am trying to measure the phylogenetic signal of functional traits with > the Blomberg’s K and Pagel’s λ methods. My problem is that I don’t have one > phylogenetic tree but 1000 (the trees were created by first combining > different molecular, morphologic and taxonomic trees, then by conducting a > MCMC analysis and finally by selecting the 1000 trees – work made by Huang > and Roy 2015). > > Is there a way to proceed to test the significance of the K and λ values > for each trait with these 1000 trees? > > An idea I have is to run the test and obtain a p value for each of the > 1000 trees, which would give me a distribution of p values, and then > consider that if 80% (for instance) of the p values are significant, the K > or λ value is significant. This is computationally very demanding (I have > 735 species) and I don’t know if this could be considered as a valid > procedure. > > I am looking forward for you answer. > > Bruno Carturan > PhD Candidate > Complex Environmental Systems Lab > University of British Columbia > Okanagan Campus > > > ________________________________________ > From: Liam J. Revell [liam.rev...@umb.edu] > Sent: Wednesday, December 07, 2016 6:54 AM > To: Carturan, Bruno > Subject: Re: A question about phylogenetic signal significance with 1000 > trees > > Bruno. > > This is an interesting question. Since this doesn't pertain specifically > to phytools, perhaps you should pose it to the R-sig-phylo email > list-serve. You may get a good answer there. > > All the best, > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 12/6/2016 6:16 PM, Carturan, Bruno wrote: > > Hello Dr. Revell, > > > > > > > > I am a PhD student from the Complex Environmental Systems Lab, from the > > University of British Columbia and I would like to ask you question. > > > > > > > > I am trying to measure the phylogenetic signal of functional traits with > > the Blomberg’s K and Pagel’s λ methods. My problem is that I don’t have > > one phylogenetic tree but 1000 (the trees were created by first > > combining different molecular, morphologic and taxonomic trees, then by > > conducting a MCMC analysis and finally by selecting the 1000 trees – > > work made by Huang and Roy 2015). > > > > > > > > Is there a way to proceed to test the significance of the K and λ values > > for each trait with these 1000 trees? > > > > > > > > An idea I have is to run the test and obtain a p value for each of the > > 1000 trees, which would give me a distribution of p values, and then > > consider that if 80% (for instance) of the p values are significant, the > > K or λ value is significant. This is computationally very demanding (I > > have 735 species) and I don’t know if this could be considered as a > > valid procedure. > > > > > > > > I am looking forward for you answer. > > > > > > > > Best regards, > > > > > > Bruno Carturan > > PhD Candidate > > Complex Environmental Systems Lab > > University of British Columbia > > Okanagan Campus > > <http://www.ubc.ca/okanagan/> > > _______________________________________________ > 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-ph...@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/
