[R-sig-phylo] bind.tree() error

David Bapst dwbapst at uchicago.edu
Tue Mar 8 23:55:40 CET 2011


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/



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