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]]
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