Hi Karla,

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Here is a way to compare nested models in order to assess the significance of rate differences for a given tree and mapped regimes (in a similar fashion to what is proposing Liam). # Here a function to collapse the regimes mappedTrees <- function(tree, names){ combined <- rowSums(tree$mapped.edge[,names]) allnames <- colnames(tree$mapped.edge) to_remove <- allnames[!allnames%in%names] newmat <- cbind(tree$mapped.edge[,to_remove], combined) newnames <- c(to_remove,paste(names, collapse="_")) colnames(newmat) <- newnames tree$mapped.edge <- newmat return(tree) } ## A worked example library(mvMORPH) set.seed(1) tree<-pbtree(n=80) # Setting the regime states of tip species sta<-as.vector(c(rep("Forest",20),rep("Savannah",30),rep("Mountains",30))); names(sta)<-tree$tip.label # Making the simmap tree with mapped states tree<-make.simmap(tree,sta , model="ER", nsim=1) # Simulate the traits sigma<-list(1,3,6) theta<-c(0) data<-mvSIM(tree, param=list(sigma=sigma, theta=theta), model="BMM", nsim=1) # fit the models with common rate (fit_1), and different rates for each regimes (fit_2) fit_1 <- mvBM(tree, data, model="BM1") fit_2 <- mvBM(tree, data, model="BMM") # Here a scenario where we assume that both Forest and Mountains regimes are similar combined <- c("Forest", "Mountains") treeForestMount <- mappedTrees(tree, combined) fit_3 <- mvBM(treeForestMount, data, model="BMM") # Then compare the three models aicw(list(fit_1, fit_2, fit_3)) # Use LRT on the two multiple rates models LRT(fit_2, fit_3) All the best, Julien ________________________________ De : R-sig-phylo <r-sig-phylo-boun...@r-project.org> de la part de Liam J. Revell <liam.rev...@umb.edu> Envoy� : dimanche 23 juillet 2017 04:07 � : Karla Shikev Cc : R-sig-phylo@r-project.org Objet : Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades Hi Karla. This is not yet possible, but it would be straightforward to add. For instance, we could let the user specify different models such as A==B!=C vs. A!=B==C and so on, and then compare this models in a standard way. I will try to do this soon and then get back to you & the list. All the best, Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ Revell lab at UMass Boston - umb.edu<http://faculty.umb.edu/liam.revell/> faculty.umb.edu Welcome to the Revell lab webpages. This website contains information about research in the laboratory of Dr. Liam Revell. Research in the Revell lab takes place in ... email: liam.rev...@umb.edu blog: http://blog.phytools.org [http://2.bp.blogspot.com/-R--OyW00QOU/WB-UaQC7MLI/AAAAAAAADRQ/afyJAHnQfCAKtRW4l1KE6EhtQKbq0ZE6gCK4B/s80/14915472_10154224922482872_7349753094314809681_n.jpg%253Foh%253D6b28620478ddf91f645e47f84b91f818%2526oe%253D5898CE31%2526__gda__%253D1485369678_e7db5dad2c7aa5d03d967bc8ccac9fab]<http://blog.phytools.org/> Phylogenetic Tools for Comparative Biology<http://blog.phytools.org/> blog.phytools.org The following is a demo of the phytools functions & methods I used to create the graphics for my Evolution 2017 meeting talk entitled �Some additional new methods ... On 7/22/2017 8:51 PM, Karla Shikev wrote: > Thanks, Liam! > > Just a quick follow-up question: in the example I saw on your webpage (with > three clades, one of which with a higher rate), how would you go about a > sort of "post-hoc" test to determine which clades differ significantly from > one another in their rates? > > Karla > > On Sat, Jul 22, 2017 at 4:13 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > >> Hi Karla. >> >> phytools has a function called ratebytree for this. This essentially >> corresponds to the 'censored' model of O'Meara et al. 2006, but we also >> have a submitted manuscript describing it. I can send you that in a second >> email. >> >> For more information about using the function you can search for >> 'ratebytree' on my blog, blog.phytools.org. >> >> All the best, Liam >> >> Liam J. Revell, Associate Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ Revell lab at UMass Boston - umb.edu<http://faculty.umb.edu/liam.revell/> faculty.umb.edu Welcome to the Revell lab webpages. This website contains information about research in the laboratory of Dr. Liam Revell. Research in the Revell lab takes place in ... >> email: liam.rev...@umb.edu >> blog: http://blog.phytools.org [http://2.bp.blogspot.com/-R--OyW00QOU/WB-UaQC7MLI/AAAAAAAADRQ/afyJAHnQfCAKtRW4l1KE6EhtQKbq0ZE6gCK4B/s80/14915472_10154224922482872_7349753094314809681_n.jpg%253Foh%253D6b28620478ddf91f645e47f84b91f818%2526oe%253D5898CE31%2526__gda__%253D1485369678_e7db5dad2c7aa5d03d967bc8ccac9fab]<http://blog.phytools.org/> Phylogenetic Tools for Comparative Biology<http://blog.phytools.org/> blog.phytools.org The following is a demo of the phytools functions & methods I used to create the graphics for my Evolution 2017 meeting talk entitled �Some additional new methods ... >> >> >> On 7/22/2017 3:10 PM, Karla Shikev wrote: >> >>> Dear all, >>> >>> I'd like to test whether the rate of evolution of a phenotypic trait (e.g. >>> body size) is significantly different among distantly-related clades (e.g. >>> mammals vs birds). I got tip data and completely resolved and callibrated >>> trees. One possibility would be to estimate rates and their confidence >>> intervals for each clade and to compare them directly, but I'm sure >>> there's >>> a more elegant way to do this. >>> >>> Karla >>> >>> [[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-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/ r-sig-phylo - The Mail Archive<http://www.mail-archive.com/r-sig-phylo@r-project.org/> www.mail-archive.com Messages by Thread [R-sig-phylo] FW: error on finding the most distinctive clades Fernanda Coelho De Souza [R-sig-phylo] Is my subset of species random? > _______________________________________________ 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 - The Mail Archive<http://www.mail-archive.com/r-sig-phylo@r-project.org/> www.mail-archive.com Messages by Thread [R-sig-phylo] FW: error on finding the most distinctive clades Fernanda Coelho De Souza [R-sig-phylo] Is my subset of species random? 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