Hi Anna.
Your attached file with extension .nwk is also a Nexus style file so it
cannot be read with read.tree or read.newick. read.tree and read.newick
read a simple Newick style text string, or a set of such strings on
separate lines in a file.
It looks like the problem with your Nexus file, extension .nex, is that
there are line breaks or spaces within the Newick string. The problem
with your Nexus file of extension .nwk is probably the figtree block
(although this is just a guess).
Try this:
obj<-readLines("IndTree.nwk")
ii<-grep("tree_1",obj)
x<-strsplit(obj[ii]," ")[[1]]
tree<-read.tree(text=x[length(x)])
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org
On 8/15/2014 9:56 AM, Anna Bastian wrote:
Dear list members,
I am trying to read a tree into R (‘ape’ package). I downloaded the
latest versions.
The tree has many polytomies and that might be the problem.
It contains ten species and each species contains of a different number
of individuals (those are the polytomies).
I attached it here.
I tried read.nexus
…and get:Error in trees[[i]] : subscript out of bounds
I tried read.tree #using a newick format for the tree)
…and get:Error in if (tp[3] != "") obj$node.label <- tp[3] :
missing value where TRUE/FALSE needed
I came across a “Robust Newick tree reader” by Liam Revell and tied the
code he provides
(http://www.phytools.org/read.newick/v0.5/read.newick.R) but I can’t
make it work.
Can somebody get the tree into R?
Please let me know if you know what’s wrong
Thanks a lot
Anna
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Department of Biological Sciences
Room 3.32
Tel: +27 (0)21 6502405
Fax: +27 (0)21 6502718
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