Klaus and Others-
I tried reorder(), cladewise and pruningwise, and both methods
produced a new error message when I tried bind.tree().
> chosen_tree<-bind.tree(ct2,clade,where=tip)
Error in if (where == 0 || where == "root") where <- ROOTx :
missing value where TRUE/FALSE needed
-Dave
On Tue, Mar 8, 2011 at 5:28 PM, Klaus Schliep <klaus.schl...@gmail.com> wrote:
> Hi David,
>
> have you checked the ordering of the trees? allTrees returns trees in
> ''pruningwise" ordering. Different functions assume different things
> how this should look like, but often don't say it explicitely. Things
> like reorder from ape or phangorn:::reorderPruning (a bit faster) are
> generally a much faster alternative for read.tree(write.tree(...)),
> even this got also faster recently.
>
> Cheers,
> Klaus
>
> On 3/8/11, David Bapst <dwba...@uchicago.edu> wrote:
>> Hello all,
>>
>> Apologies for sending another post this week, but I've run into a
>> strange error with bind.tree(), as below. I'm binding one tree
>> ("clade") to a tip (4, in this case) on another tree ("chosen_tree").
>> "chosen_tree" is a tree from an allTrees() output.
>>
>>> bind.tree(chosen_tree,clade,where=tip)
>> Error in x$edge[sndcol, 2] <- newNb[-x$edge[sndcol, 2]] <- (n + 2):(n + :
>> number of items to replace is not a multiple of replacement length
>> In addition: Warning message:
>> In newNb[-x$edge[sndcol, 2]] <- (n + 2):(n + x$Nnode) :
>> number of items to replace is not a multiple of replacement length
>>
>> Bizarrely, while trying to create sample files for you to test, I
>> found that write.tree() and read.tree() actually get rid of the
>> problem, and furthermore, that the problem is with "chosen_tree" and
>> not "clade". So, as of the moment, I'm unfortunately unable to make
>> the error reproducible. Not all trees from an allTrees output do this,
>> either.
>>
>>> bind.tree(chosen_tree,read.tree(text=write.tree(clade,file="")),where=tip)
>> Error in x$edge[sndcol, 2] <- newNb[-x$edge[sndcol, 2]] <- (n + 2):(n + :
>> number of items to replace is not a multiple of replacement length
>> In addition: Warning message:
>> In newNb[-x$edge[sndcol, 2]] <- (n + 2):(n + x$Nnode) :
>> number of items to replace is not a multiple of replacement length
>>> bind.tree(read.tree(text=write.tree(chosen_tree,file="")),clade,where=tip)
>> Phylogenetic tree with 5 tips and 4 internal nodes.
>> Tip labels:
>> [1] "1781" "23" "24" "GR1210" "GR3799"
>> Rooted; no branch lengths.
>>
>> Anyone have any idea what's going on? For now, I'll solve it by using
>> the read.tree(write.tree()) kludge.
>> -Dave
>>
>>
>> --
>> David Bapst
>> Dept of Geophysical Sciences
>> University of Chicago
>> 5734 S. Ellis
>> Chicago, IL 60637
>> http://home.uchicago.edu/~dwbapst/
>>
>> _______________________________________________
>> R-sig-phylo mailing list
>> R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>
>
>
> --
> Klaus Schliep
> Université Paris 6 (Pierre et Marie Curie)
> 9, Quai Saint-Bernard, 75005 Paris
>
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
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