Hello all,
I recently decided to manually edit a very large supertree (>1700
taxa) in Mesquite (I had to collapse a few nodes into polytomies,
something I can only seem to do in Mesquite). I read it out of R as a
Newick file, than into Mesquite, where I did my little edits and then
saved the tree as a Nexus file, which I then tried to read into ape.
But then I get this.
> spec_tree<-read.nexus(file.choose())
Error in if (sum(tr$edge[, 1] == ROOT) == 1 && dim(tr$edge)[1] > 1) { :
missing value where TRUE/FALSE needed
I also tried reading the Nexus file into TreeFig, which didn't work.
If I cut out a lot of the internal structure of the Nexus file (who
needs Mesquite and Taxon blocks anyway?), I can get TreeFig to read
it, export it into a Newick file or a new Nexus file and then try
opening it in R with read.nexus(). That works. But then i can't write
it in a new file in R with write.tree() nor write.nexus(), and also
plot(tree) causes R to freeze.
> write.tree(spec_id_tree,file.choose())
Error in kids[[parent[i]]] : attempt to select less than one element
> write.nexus(spec_id_tree,file.choose())
#NEXUS
[R-package APE, Mon Feb 28 10:03:59 2011]
Read 1756 items
Error in 1:(start - 1) : argument of length 0
After saving and opening the file in Mesquite a bunch of times, I
repeatedly found new un-collapsed double node branches on the tree. No
idea where they came from (maybe a by-product of my node collapsing?).
I removed the new ones that popped up, deassigned branch lengths to
the tree (it's a super-cladogram) and then saved and... finally, R
read the nexus file and write.tree() worked. write.nexus() didn't work
(same error as above), but I can read my tree and write it, at least,
so my issue is solved but I'd still like to know what was causing the
problems to begin with. I have no idea where the un-collapsed double
branches came from or why they were causing this issue.
I am using R v2.12.2 and ape v2.6-3. So that the error is completely
reproducible, I have placed two Nexus files on my website which
produce both the read.nexus() error (trash_a.nex) and the
write.nexus() and write.tree() errors (trash_b). These are small,
partially collapsed portions of my supertree with the species names
deleted. They can be found at:
http://home.uchicago.edu/~dwbapst/trash_a.nex
http://home.uchicago.edu/~dwbapst/trash_b.nex
-Dave
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
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