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
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