Just to clarify for future users who stumble on Liam's solution for Lilian, the second block of code attaches the new tips to non-ultrametric trees at the same distance as the current tips at maximum distance from the root.
If this is a time-scaled phylogeny and the tree's root depth is equal to its age, these new tips then are at time=0, i.e. they are now extant tip taxa. If no tips actually extend to the present (i.e. the root depth isn't equal to the age of the root, as often occurs if the phylogeny is entirely composed of extinct taxa), or the tips are actually older then the present day, then further modification is necessary of the new branch length. (Also, if the tree isn't time-scaled but branches are instead scaled to some other measure, this may be undesirable because there may be no special meaning to being maximally far from the root, especially if its actually an unrooted tree.) If you're tree has a $root.time element indicating the root's age because it was time-scaled with packages strap or paleotree (or because you manually gave it a $root.time), then you can do, where tipAge is the tip's age before-present in the same time-units as the branches are scaled: newLength<-tree$root.time-tipAge-nodeheight(tree,node) tree1<-bind.tip(tree,"tip.label",where=node,edge.length=newLength) Cheers, -Dave On Sat, Jul 4, 2015 at 12:50 PM, Lilian Sayuri Ouchi de Melo <sayuriou...@gmail.com> wrote: > Hello Liam, > > Thank you very much for help me! My tree is not ultrametric and your second > suggestion works perfectly! > > All the best and have a good time in Brazil! > > Em sáb, 4 de jul de 2015 às 12:31, Liam J. Revell <liam.rev...@umb.edu> > escreveu: > >> Hi Lilian. >> >> If your tree is ultrametric, which you can check using: >> >> is.ultrametric(tree) >> >> then when you attach a tip to a node or edge using bind.tip the length >> of the terminal edge leading to that tip will automatically be specified >> so that the tree remains ultrametric. >> >> If this is not the case you could try the following, in which "node" is >> the node number you want to attach the tip to: >> >> depth<-max(nodeHeights(tree))-nodeheight(tree,node) >> tree<-bind.tip(tree,"tip.label",where=node,edge.length=depth) >> >> Let us know if this works. >> >> All the best, Lia >> >> 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 7/3/2015 5:33 PM, Lilian Sayuri Ouchi de Melo wrote: >> > Dear all, >> > >> > I have a time calibrated phylogeny and I need to insert some species on >> it. >> > When I added those species with bind.tip function (phytools) the new >> > phylogenetic tree doesn't have the calibration time. I tried to solve >> this >> > problem in other packages such as APE and other programs like Mesquite >> and >> > online platforms, but I did not get the solution. >> > >> > Is there any method that enable the insertion of additional species in a >> > time calibrated phylogeny without losing branch length information? >> > >> > Thank you all in advance >> > >> > -- > Lilian Sayuri Ouchi de Melo > (PhD student of São Paulo State University) > > [[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/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ 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/
