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-bounces@r-project.**org<r-sig-phylo-boun...@r-project.org>[ > r-sig-phylo-bounces@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-ph...@r-project.org/**msg02227.html<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<https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > Searchable archive at http://www.mail-archive.com/r-** > sig-ph...@r-project.org/<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<https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > Searchable archive at http://www.mail-archive.com/r-** > sig-ph...@r-project.org/<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/
