That got it. Thanks so much, Liam. This was amazingly helpful.
- Original Message -
From: "Liam J. Revell"
To: "Tom Diggs"
Cc: "Brian O'Meara" ; "mailman, r-sig-phylo"
Sent: Wednesday, June 19, 2013 11:50 PM
Subject: Re: [R-sig-phylo] Difficulty getting posterior probabilities int
I meant to say "not being stored in tree$node.label" - but what's the
difference. The instructions still work. All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blo
Hi Tom.
The posterior probabilities from a BEAST output tree are not being
stored in tree$tip.label by read.beast in phyloch.
Try:
tree<-read.beast("treefilename")
plot(tree,no.margin=TRUE)
nodelabels(round(tree$posterior,3))
To see the full structure of the modified "phylo" object created b
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 t
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.in
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 anyt
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.a
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
