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-phylo@r-project.org/
