Thanks for providing constructive feedback Nick.
Brian On Thu, Apr 14, 2016 at 7:30 PM, Nick Matzke <mat...@nimbios.org> wrote: > On Thu, Apr 14, 2016 at 7:09 AM, Brian A. Gill <gillbri...@gmail.com> > wrote: > >> Hi Everyone. >> >> I'm trying to look at the association between a discrete binary predictor >> (Latitude: Colorado/Ecuador) and a continuous response (species richness). >> >> My phylogeny is a 50% majority rule consensus tree made in MrBayes. The >> tree has polytomies and is not ultrametric. >> >> I've found the methods below for looking at the influence of a discrete >> binary trait on richness, but I'm not sure if my tree is suitable or if >> there is a better approach. >> >> 1) Diversitree package BiSSE >> 2) Caper package using MacroCAIC >> >> Any suggestions would be greatly appreciated. >> >> Thank You. >> >> Brian >> > > > It sounds like your tree is *not* suitable: > > - It's usually considered Officially Bad to use a consensus tree for these > kinds of things. Polytomies are one problem (fatal, as SSE models consider > speciation, and speciation=splitting one lineage into two, for the purposes > of these models), another possible problem is that the consensus tree can > be different from any of the trees that were actually sampled in the > Bayesian analysis. An MCC tree would be better, or running the analysis > over a series of trees. > > - It sounds like your tree isn't dated, and as far as I know SSE methods > all assume dated trees where all the tips come up to the present, because > they involve calculations of things like the probability of > extinction-before-the-present. > > I haven't used caper but I bet there are similar issues. > > So, you should probably estimate a dated tree using e.g. Beast2, then try > GeoSSE which is specifically for looking at diversification rates in > different biogeographical regions. This might not solve all your problems, > as you still probably need good dates and a large tree (hundreds of tips) > to get a decently robust result that would be publishable, but it would be > right direction at least. > > Cheers, Nick > > > > > > > > >> >> -- >> Brian A. Gill >> >> VISIT MY WEBSITE: >> http://gillbriana.wix.com/brian-gill >> >> FOLLOW ME ON TWITTER: >> @CSUBrianGill >> >> Colorado State University Biology >> 1878 Campus Delivery >> Fort Collins, CO 80523 >> United States of America >> >> 970-215-7037 >> >> [[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/ >> > > -- Brian A. Gill VISIT MY WEBSITE: http://gillbriana.wix.com/brian-gill FOLLOW ME ON TWITTER: @CSUBrianGill Colorado State University Biology 1878 Campus Delivery Fort Collins, CO 80523 United States of America 970-215-7037 [[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/
