Hi John,
It seems a problem occurs within write.tree and not with the pruning.
So try prune the trees first and then write them out.
tr2=vector(list, 1000)
for(i in 1:1000){
tr2[[i]] - drop.tip(tr[[i]],tr[[i]]$tip.label[-match(taxa,
tr[[i]]$tip.label)])
}
class(tr2) = multiPhylo
plot(tr2)
for(i in 1:1000){print(i);write.tree(tr2[[i]])} # may helps find you
the trees which fail
write.tree(tr2, file=result.tre)
Cheers,
Klaus
On 2/28/13, Klaus Schliep klaus.schl...@gmail.com wrote:
Dear John,
can you please be a bit more specific with your error message. It is
always good to have a reproducible example, e.g. adding a tree which
where drop.tip fails, and to run traceback() just after the error to
get more information where the error occurred. It is also useful to
add information of the version of ape and your operating system.
Regards,
Klaus
On 2/28/13, john d dobzhan...@gmail.com wrote:
Dear all,
I'm trying to prune a set of 1000 post-burnin trees to include only a
subset of taxa. Unfortunately the tree is too big to send to the list,
but if it is really necessary I'll figure out a way to do it.
tr is my tree and taxa is my list of selected terminals.
for(i in 1:1000){
write.tree(drop.tip(tr[[i]],tr[[i]]$tip.label[-match(taxa,
tr[[i]]$tip.label)]), file=result.tre, append=TRUE)
}
If I run that code, it works for some trees, but not for others, for
which I got the message Error in kids[[parent[i]]] : subscript out of
bounds.
Any suggestions?
John
___
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/
--
Klaus Schliep
Phylogenomics Lab at the University of Vigo, Spain
--
Klaus Schliep
Phylogenomics Lab at the University of Vigo, Spain
___
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/
