Dear Liam and Leandro, Thanks for your replies but think that i have not explained correctly. For example, i have a phylogeny with all branch lengths egual to 1:
library(ape) tree.1<-read.tree(text="(((A:1.0,B:1.0):1.0,(C:1.0,(D:1.0,E:1.0):1.0):1.0):1.0,F:1.0);") plot(tree.1) See that the branch length of taxon "F" is igual to 1 but it is proportionally equivalent to four smaller branchs. Therefore, i would like to rescale all branch lengths of the phylogeny like this: tree.2<-read.tree(text="(((A:1.0,B:1.0):2.0,(C:2.0,(D:1.0,E:1.0):1.0):1.0):1.0,F:4.0);") plot(tree.2) Today i make this transformation in the "Fig Tree" software using the options: >Trees>Transform branches>cladogram. However, i still could not get make this in the R. All the best, Fernando L. Sobral 2012/8/28 Liam J. Revell <liam.rev...@umb.edu> > Hi Fernando. > > I'm not entirely sure what you're going for, but let me try to be of some > help. > > The tree is stored in memory as what is called a "list" - basically, a set > of objects that can be of different types. The branch lengths of the tree > are stored in the list element "edge.length". So, for a "phylo" object with > the variable name tree, you can access the branch lengths of the tree using > tree$edge.length. (If your tree does not have branch lengths, this will be > NULL.) > > Consequently, you can assign any arbitrary values to the branch lengths of > the tree by assigning values to tree$edge.length. For instance, to set all > branch lengths to 1.0, you would just do: > > tree$edge.length<-rep(1,nrow(**tree$edge)) > > The order of tree$edge.length corresponds to the row order of tree$edge, > so if you want to see which branches in tree$edge.length correspond to > which branches on the tree, you can do something like the following (here, > I use a simple random tree for illustration): > > set.seed(1) > tree<-rtree(10); tree$edge.length<-rep(1,nrow(**tree$edge)) > X<-tree$edge > X[X[,2]%in%1:length(tree$tip),**2]<- > tree$tip[X[X[,2]%in%1:length(**tree$tip),2]] > names(tree$edge.length)<-**paste(X[,1],X[,2],sep=",") > plot(tree); nodelabels() > tree$edge.length > > Now if, for instance, I want to make the branch length leading from node > 13 to tip taxon "t6" to (for instance) 3.0, I could just do: > > tree$edge.length["13,t6"]<-3 > plot(tree); nodelabels() > > Of course, if we have some simple criterion on which we want to change our > branch lengths, we can do that to. For instance, if we wanted to set all > branch lengths with length <1 to 1.0 and all branch lengths with length >1 > to 2.0, we could do it as follows: > > tree$edge.length<-runif(n=**nrow(tree$edge),min=0,max=2) > tree$edge.length > tree$edge.length[tree$edge.**length<1]<-1 > tree$edge.length[tree$edge.**length>1]<-2 > tree$edge.length > plot(tree) > > I hope this is of some help. > > All the best, Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: > http://faculty.umb.edu/liam.**revell/<http://faculty.umb.edu/liam.revell/> > email: liam.rev...@umb.edu > blog: http://phytools.blogspot.com > > > On 8/28/2012 4:15 PM, Fernando Sobral wrote: > >> Hi, >> >> I am trying to alter the branch lengths of a phylogeny so that the smaller >> branch has size igual 1 and the larger branch is the proportional sum of >> the smaller branchs. For example, if the larger branch is equivalent to >> ten >> smaller branchs, it should have size igual to 10. I already tryed use some >> functions like compute.brlen(), compute.brtime() and rescaleTree(), but >> did >> not work. >> >> Any help would be greatly appreciated. >> >> Thanks, >> >> Fernando L. Sobral >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/r-sig-phylo<https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> >> [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
