Actually I did play around with different tol values and I could get is.ultrametric to recognize my tree. But, exactly as Joseph says, this doesn't really help. Anyway, Liam's suggestion solved the problem.
Martin Am 16.08.2016 um 16:22 schrieb Joseph W. Brown: > That�s a good tip, but the issue here is that many packages use > is.ultrametric internally with a hard-coded (likely, default) value of tol. > In this case, Martin simply cannot perform the analyses he wants to run > because this option is inaccessible. > > JWB > ________________________________________ > Joseph W. Brown > Post-doctoral Researcher, Smith Laboratory > University of Michigan > Department of Ecology & Evolutionary Biology > Room 2071, Kraus Natural Sciences Building > Ann Arbor MI 48109-1079 > josep...@umich.edu > > > >> On 16 Aug, 2016, at 10:15, Klaus Schliep <klaus.schl...@gmail.com> wrote: >> >> Hello all, >> this may come be surprising to many, but consulting the manual >> ?is.ultrametric can be helpful. Why not simply try e.g. is.ultrametric(tree, >> tol=.01) ???? >> So in this sense RTFM >> Regards, >> Klaus >> >> >> On Aug 16, 2016 9:31 AM, "Martin Dohrmann" <m.dohrm...@lrz.uni-muenchen.de> >> wrote: >> >> 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]] >> >> >> _______________________________________________ >> 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]]
_______________________________________________ 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/
