You could try something like the following: tips<-tree$tip.label genera<-unique(sapply(strsplit(tips,"_"),function(x) x[1])) ii<-sapply(genera,function(x,y) grep(x,y)[1],y=tips) tree<-drop.tip(tree,setdiff(tree$tip.label,tips[ii]))
Let us know if this works. All the best, Liam Liam J. Revell, Assistant 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 11/3/2014 11:56 AM, Susan Kapust wrote:
Dear colleagues, I have a large species-level phylogeny in which the tip labels are indicated as "Genus_species". All genera are monophyletic. I have two things I'm struggling with: (1) I'd like to drop all but one of the tips in each genus (i.e. to generate a genus-level phylogeny). Given that all genera are monophyletic, it shouldn't matter which species I pick. (2) I'd like to establish an era (e.g. 25 Mya) and leave only one representative of the clades there were present at that point in time. Given that I actually have a post-burnin set of trees, once I figure out how to do the steps above I could (hopefully) do that for all trees. thanks so much for your help. Susan. [[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 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/