Dear Colleagues, Thank you very much for your help, it’s all clear now. (I got way more than I asked for, for example, my trees include only extant taxa). And yes, branching.times() and getBtimes() return exact same numbers of course, I just didn’t understand ow indexing works.
Next question, a very simple one again. I have two newick trees, identical topology. In one I have branch lengths, in the other I have node names. I would like a tree with both. How do I do this? Thanks in advance! -- Lev Yampolsky Professor Department of Biological Sciences East Tennessee State University Box 70703 Johnson City TN 37614-1710 Cell 423-676-7489 Office/lab 423-439-4359 Fax 423-439-5958 On 1/13/16, 4:20 AM, "Emmanuel Paradis" <emmanuel.para...@ird.fr> wrote: >To pile a little bit more after David's message, ape has the function >ltt.plot.coords which does the same thing than phytools::ltt but with >different options, including 'tol' which specifies the tolerance for >considering a tree as ultrametric or not. > >Best, > >Emmanuel > >Le 13/01/2016 03:29, Liam J. Revell a écrit : >> Hi Lev. >> >> You could also look at ltt in phytools. The object returned has the time >> of all the events on the tree - including the end of lineages that go >> extinct before the present. To access these, you can do: >> >> obj<-ltt(tree,plot=FALSE) >> obj$times >> obj$ltt >> >> & to see how these are associated with events, you can do: >> >> plot(obj,show.tree=TRUE) >> >> All the best, Liam >> >> Liam J. Revell, Associate 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 1/12/2016 10:22 PM, Dan Rabosky wrote: >>> >>> Dear Lev- >>> >>> I don't think branching.times can compute these for non-ultrametric >>> trees. >>> >>> You can do this with package BAMMtools, but you need a "hidden" >>> internal function. You can access it as >>> >>> "BAMMtools:::NU.branching.times" >>> >>> It returns branching times relative to the most recently-occurring tip >>> in the tree. It's a R-based recursion that is a little slower that the >>> ape function, so it's not recommended as a replacement for >>> branching.times if you have an ultrametric tree. >>> >>> I'm not actively maintaining laser, but getBtimes returns the output >>> of branching.times after sorting the times and stripping out the node >>> names (this was useful for something many years ago!). If you plot >>> sort(getBtimes(x)) and sort(branching.times(x)) they should be >>>identical. >>> >>> ~Dan Rabosky >>> >>> >>> >>> On Jan 12, 2016, at 7:37 PM, Yampolsky, Lev <yampo...@mail.etsu.edu> >>> wrote: >>> >>>> Dear Colleagues, >>>> >>>> Does anyone know what is the difference between ape�s >>>> branching.times() and laser�s getBtimes()? >>>> And why they may be giving rather different results, particularly for >>>> internal branches? (From an ultrametric tree created by >>>> chronotree <- chronos(tree, lambda = 1, model = "correlated", quiet = >>>> FALSE, calibration = makeChronosCalib(tree), control = >>>> chronos.control()) >>>> >>>> Thank you very much in advance for your help! >>>> >>>> PS. A related but less important question: I am curious how does >>>> branching.times() calculate branching times from a non-ultrametric >>>>tree? >>>> >>>> -- >>>> Lev Yampolsky >>>> >>>> Professor >>>> Department of Biological Sciences >>>> East Tennessee State University >>>> Box 70703 >>>> Johnson City TN 37614-1710 >>>> Cell 423-676-7489 >>>> Office/lab 423-439-4359 >>>> Fax 423-439-5958 >>>> >>>> _______________________________________________ >>>> 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/ >>> >>> _____________________ >>> Dan Rabosky >>> Assistant Professor & Curator of Herpetology >>> Museum of Zoology & >>> Department of Ecology and Evolutionary Biology >>> University of Michigan >>> Ann Arbor, MI 48109-1079 USA >>> >>> drabo...@umich.edu >>> http://www-personal.umich.edu/~drabosky >>> http://www.lsa.umich.edu/ummz/ >>> >>> >>> >>> [[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/ > _______________________________________________ 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/
