Hi Fran�ois,
Thanks again for your response. Wouldn't that lose the information of how many species were in each clade? And how would I specify that 'clades' to keep consist of those sharing either state? My original tree consists of almost 3000 species so going through such clades manually would be difficult at best, hence the need to automate it somehow. (I apologise, my R coding skills are improving but still leave a lot to be desired in many cases). I completely agree that BiSSE is far more appropriate for my aims, and indeed this was the approach I used. However, reviewers have asked if I get the same basic result using other methods, which is the only reason I am attempting such analyses now. Thank you kindly once again for your time, Kev ________________________________ From: Fran�ois Michonneau [francois.michonn...@gmail.com] Sent: 23 October 2014 16:05 To: Arbuckle, Kevin Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Extracting sister groups HI Kevin, If I understand correctly what you're trying to do, you'll first need to collapse some of your tips to create clades, a proportion of which will have the trait. You'll then be able to use this new tree to generate the data.frame needed by the functions you mentioned in your original post. Depending on what you're trying to do, you may not want to lose this phylogenetic information. Maybe a different approach, such as using BiSSE in the diversitree package might be more appropriate? Cheers, -- Fran�ois On Thu, Oct 23, 2014 at 10:27 AM, Arbuckle, Kevin <k.arbuc...@liverpool.ac.uk<mailto:k.arbuc...@liverpool.ac.uk>> wrote: Hi Fran�ois, Thank you kindly for your offer of help. The code below will simulate a phylogeny ("tree") and a dataframe ("trait") with one binary trait for 100 species. The format is representative of the data I am using for my analyses so should serve as a test case. Hopefully this helps, let me know if there's any other information I can provide. library(ape) library(phytools) tree<-rtree(100) tran<-matrix(c(-1,1,1,-1),2,2) rownames(tran)<-c("0","1") colnames(tran)<-c("0","1") phy<-sim.history(tree,tran) trait<-data.frame(sp=tree$tip.label,bt=getStates(phy,type="tips")) rownames(trait)<-tree$tip.label Cheers, Kev ________________________________ From: Fran�ois Michonneau [francois.michonn...@gmail.com<mailto:francois.michonn...@gmail.com>] Sent: 23 October 2014 14:54 To: Arbuckle, Kevin Subject: Re: [R-sig-phylo] Extracting sister groups Hi Kevin, We should be able to help you but it would be much easier if you provided us with a small data set that illustrate the format of your current dataset. How is your trait currently stored? and how is it associated with the tips in your tree? Cheers, -- Fran�ois On Thu, Oct 23, 2014 at 6:23 AM, Arbuckle, Kevin <k.arbuc...@liverpool.ac.uk<mailto:k.arbuc...@liverpool.ac.uk>> wrote: Hi everyone, I am attempting to run sister group analyses as one way to look at the effect of a binary trait on diversification. Two of the functions from ape that I'm looking at are diversity.contrast.test and richness.yule.test, but both have the same limitation. They require the data to be input as a dataframe of two columns, one with the number of species in clades that have the trait of interest, and the other with the number of species in the respective sister clades that don't have the trait. The issue is that I am working with a very large tree, and so extracting and entering such information by hand is not really feasible. I am therefore looking for a function which extracts all sister clades that differ in the presence vs absence of the trait, and ideally is capable of generating a dataframe of the appropriate format for the above functions automatically. It seems that a function to do this should exist already, but as I can't seem to find anything I would appreciate some help (hopefully someone will know of such a function that already exists). Thanks, Kevin Arbuckle [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto: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/