Am 16.08.2016 um 15:20 schrieb Joseph W. Brown: > I agree that it is almost certainly numerical precision, as rescaling the > tree fixes things: > > > is.ultrametric(phy); > [1] FALSE > > fie <- phy; > > fie$edge.length <- fie$edge.length * 0.1; > > is.ultrametric(fie); > [1] TRUE > > I�ve also tested the ultrametricity(?) with a non-R program and the results > are the same. So can we assume this is not a PhyloBayes issue, and rather an > unavoidable problem with large, old trees? But the fact that MrBayes trees > are ultrametric is confusing; does MrBayes use less precise edge lengths?
Actually the MrBayes branch lengths appear to be MORE precise. Martin >> >> On 16 Aug, 2016, at 08:53, Liam J. Revell <liam.rev...@umb.edu> wrote: >> >> Hi Martin. >> >> Since you are writing & reading trees to file, my guess is that it has to do >> with numerical precision - that is, the rounding of your edge lengths when >> they are written to file. >> >> Does your tree look ultrametric when plotted in R? If so, this is probably >> the case. >> >> My recommendation is that you use phangorn to compute the non-negative >> least-squares edge lengths with the condition that the tree is ultrametric. >> This will give you the edge lengths that result in the distances between >> taxa with minimum sum of squared differences from the distances implied by >> your input tree, under the criterion that the resulting tree is ultrametric. >> >> To do this you need to merely run: >> >> library(phytools) >> library(phangorn) >> is.ultrametric(tree) ## fails >> plotTree(tree,ftype="off") ## does my tree look ultrametric? >> nnls<-nnls.tree(cophenetic(tree),tree,rooted=TRUE) >> is.ultrametric(tree) ## should pass >> >> Let us know if this works. 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 8/16/2016 6:41 AM, Martin Dohrmann wrote: >>> Hi, >>> I want to do some diversification pattern analyses with various R packages. >>> I'm using a time-calibrated tree produced by PhyloBayes. Branch lengths are >>> in millions of years and all taxa are extant, so the tree should be >>> ultrametric. However, when I call "is.ultrametric", it returns "FALSE". >>> >>> Has anybody encountered something like this? Any ideas about what's going >>> on/how to solve this? >>> >>> Some further information: >>> I also tried other PhyloBayes time trees, with the same result. In >>> contrast, MrBayes time trees I tried for comparison are recognized as >>> ultrametric. Regarding my diversification analyses, TESS would not run, >>> telling me "The likelihood function is only defined for ultrametric >>> trees!". On the other hand, BAMMtools doesn't seem to have a problem with >>> my tree. I haven't tried other packages yet, but I suspect RPANDA, TreePar >>> etc. might also have issues if they don't recognize my tree as ultrametric. >>> >>> I'd appreciate any help! >>> >>> Best wishes, >>> Martin >>> >>> Dr. Martin Dohrmann >>> Ludwig-Maximilians-University Munich >>> Dept. of Earth & Environmental Sciences >>> Palaeontology & Geobiology >>> Molecular Geo- & Palaeobiology Lab >>> Richard-Wagner-Str. 10 >>> 80333 Munich, Germany >>> Phone: +49-(0)89-2180-6593 >>> >>> >>> [[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/ > Dr. Martin Dohrmann Ludwig-Maximilians-University Munich Dept. of Earth & Environmental Sciences Palaeontology & Geobiology Molecular Geo- & Palaeobiology Lab Richard-Wagner-Str. 10 80333 Munich, Germany Phone: +49-(0)89-2180-6593 [[alternative HTML version deleted]]
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