Just to clarify, off-list discussion with Graham reveals (after some confusion on my part) that if the simple format option is used in sumt in MrBayes, then ape's read.nexus will natively read the posterior probability values as node-labels. Which is interesting and I had not come across that information previously.
Graham's comment is not in reference to the functioning of read.annotated.nexus. Cheers, -Dave On Fri, Oct 3, 2014 at 8:49 AM, Slater, Graham <slat...@si.edu> wrote: > Dave, > > I’ve had the same trouble with shuffling. However, all of this can be > avoided if you specify the simple format for your .con file in the mrBayes > block. > > sumt conformat = simple; > > The resulting tree will correctly display posterior probabilities in a > phyloformat tree. > > Graham > > > > ------------------------------------------------------------ > Graham Slater > Peter Buck Post-Doctoral Fellow > Department of Paleobiology > National Museum of Natural History > The Smithsonian Institution [NHB, MRC 121] > P.O. Box 37012 > > > (202) 633-1316 > slat...@si.edu > www.fourdimensionalbiology.com > > > > > > On Oct 3, 2014, at 10:42 AM, David Bapst <dwba...@gmail.com> wrote: > > Hello all, > > Recently, I wanted to display posterior probabilities on a 50% > compatibility tree from a MrBayes run, created with the 'sumt' > command. I looked around for ways to do this and found this email > thread from last year: > > https://stat.ethz.ch/pipermail/r-sig-phylo/2013-June/002825.html > > ...which suggests using read.annotated.nexus() in package epibase, > which has been renamed OutbreakTools more recently. > > Unfortunately, it appears read.annotated.nexus in OutbreakTools > (v0.1-11, in R 3.1.1) improperly creates the new edge matrix, > resulting in an apparent shuffling of tip labels. As this function was > discussed on R-Sig-Phylo, I am sending this bug report to both the > list and to the package maintainer (Thibaut J.). > > I don't have any BEAST output files, so I cannot test if this occurs > with files that are not created by MrBayes. > > To show this phenomen, I have created an example .con.tre file using > an example matrix of standard characters for several elephants that I > stole off of Joe F.'s website. You can find the .con.tre file here on > gdrive: > > https://drive.google.com/file/d/0B_xvEcEvKno_LTFhSVJrdHMtNFU/view?usp=sharing > > And now in R, a comparison with a tree: > > library(OutbreakTools) > library(ape) > > tree1<-read.nexus("mat.nex.con.tre") > tree2<-read.annotated.nexus("mat.nex.con.tre") > > layout(1:2) > plot(tree1,no.margin=TRUE) > plot(tree2,no.margin=TRUE) > > identical(tree1$tip.label,tree2$tip.label) > identical(tree1$edge.length,tree2$edge.length) > identical(tree1$edge,tree2$edge) > > Inspection of the tree file with FigTree suggests that the ape > function is producing the correct tree and the OutbreakTools function > is not. We can see the why with last three lines in the console: > > identical(tree1$tip.label,tree2$tip.label) > > [1] TRUE > > identical(tree1$edge.length,tree2$edge.length) > > [1] TRUE > > identical(tree1$edge,tree2$edge) > > [1] FALSE > > Closer inspection suggests that the issue appears to be that some > terminal edges are inappropriately shuffled, thus shuffling the > terminal tip labels on those edges, while leaving the tip.label order > and the edge lengths the same. Also, larger trees seem to produce > larger inconsistencies in the tree produced. > > So... now for the list, are there any other methods on CRAN for > obtaining the posterior probabilities from a .con.tre file? Otherwise, > next I guess I'll be trying phyloch. > > Cheers, > -Dave > > -- > 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/ > > -- 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/
