Thanks very much! Again, unfortunately, it's not working for me. I tried the read.beast command, and while it had no trouble reading the tree, there were no posterior support values.
Please forgive me if my questions are basic. I'm pretty new to phylogenetics in R, and I'm trying to get up to speed. Thanks for your time and help. ----- Original Message ----- From: Brian O'Meara To: Tom Diggs Cc: Jombart, Thibaut ; mailman, r-sig-phylo Sent: Wednesday, June 19, 2013 10:38 PM Subject: Re: [R-sig-phylo] Difficulty getting posterior probabilities into ape? Phyloch has never been on CRAN as far as I know, but you can get it from http://www.christophheibl.de/Rpackages.html . Best, Brian _______________________________________ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Wed, Jun 19, 2013 at 11:14 PM, Tom Diggs <jtdi...@mail.ad.uab.edu> wrote: Thank you very much for the answer. Unfortunately, that command is not working for me. It apparently reads the file just like the read.nexus command does in my case. The tree comes in fine, with the branch lengths, but no posterior values. So I guess that the read.nexus command ignores anything inside square brackets? I imagine that's what the read.annotated.nexus was designed to deal with, but unless I'm doing something incredibly wrong, it's not working. I also read that phyloch was a way to get around this problem, but it's not in CRAN anymore either. Otherwise, should I go through and just eliminate the square brackets manually? Replace them with regular parentheses? Leave them out altogether? The phylogeny I'm currently dealing with isn't THAT big, and while it'd be a pain to do it manually, it wouldn't be prohibitive. Has anyone done that before? Thanks, Tom ----- Original Message ----- From: "Jombart, Thibaut" <t.jomb...@imperial.ac.uk> To: "Tom Diggs" <jtdi...@mail.ad.uab.edu>; <r-sig-phylo@r-project.org> Sent: Wednesday, June 19, 2013 12:39 PM Subject: RE: [R-sig-phylo] Difficulty getting posterior probabilities into ape? Hello, Marc Suchard has recently implemented this in the package epibase - check the function read.annotated.nexus. All the best Thibaut. ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Tom Diggs [jtdi...@mail.ad.uab.edu] Sent: 19 June 2013 18:33 To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Difficulty getting posterior probabilities into ape? Hi all, I was wondering if anyone else has had this problem, and how they addressed it. I've been using BEAST to generate trees, and TreeAnnotator to summarize them. In the output nexus file, the tree plainly has posterior probabilities for each node listed, but when I try to import the trees into R, my tree has no node labels (mytree$node.labels = NULL). I searched the archives for this listserve, and found one instance of this problem cropping up with MrBayes output. http://www.mail-archive.com/r-sig-phylo@r-project.org/msg02227.html Unfortunately, the package "phybase", listed as a potential solution to the problem, is no longer in CRAN. Am I missing something obvious? Is ape having trouble reading the node labels for some reason? Any help would be much appreciated. Thanks so much. Tom [[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/ [[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/
