Sorry, forgot the most important part of R version [1] "R version 2.15.3 (2013-03-01)" On Aug 19, 2013, at 10:12 PM, "Liam J. Revell" <liam.rev...@umb.edu> wrote:
> Hi Kamila. > > 1) A tree stored in memory as an object of class "phylo" can have a root edge > - but no root label. One option (if your tree has edge lengths) that > approximates what it sounds like you want to do is to re-root the tree 0 > distance below the tip that is your root. You can do this using the function > reroot (which uses root internally) from the phytools package. E.g., to > re-root the (random, in this case) tree 'tree' at the tip "t10": > > library(phytools) > tree<-rtree(n=10) ## just for demonstration > nn<-which(tree$tip.label=="t10") ## get node number of tip > tt<-reroot(tree,nn,tree$edge.length[which(tree$edge[,2]==nn)]) > plotTree(tt) > > 2) To better help you with this, can you give us a reproducible error? (E.g., > your tree, the code that produces the error, your version of R and ape.) > > 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 8/19/2013 9:51 PM, Naxerova, Kamila wrote: >> Dear list, >> >> I have just started playing around with ape, and I have some naive newbie >> questions. Any help would be very much appreciated. >> >> 1) In my data set, the root is extant. Is there a way to directly designate >> one of the taxa as the root? >> 2) When I use the rotate function on what I think is a fairly small and >> simple tree, R always freezes and I have to kill it and start over. Any >> ideas what I might be doing wrong? >> >> Many thanks in advance. >> Kamila >> _______________________________________________ >> 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/
