Hi Klaus,

Thanks for tracking this. It's fixed.

Best,

Emmanuel

Le 20/01/2017 à 18:41, Klaus Schliep a écrit :
Hi Juan,
it seems that you trim too many taxa.

I can replicate the error message if I trim for example 19 out of a 20 tips
of a tree.
drop.tip(tree, sample(20, 19))
Error in integer(max(oldnodes)) : vector size cannot be infinite
In addition: Warning message:
In max(oldnodes) : no non-missing arguments to max; returning -Inf
traceback()
3: integer(max(oldnodes))
2: collapse.singles(phy)
1: drop.tip(tree, sample(20, 19))

Maybe you include a check into your function z that the pruned trees have
at least two tips left
if( length( setdiff(treeP$tip.label, colnames(hp))) < ( length(
treeP$tip.label ) -2 ) )

Cheers,
Klaus



On Fri, Jan 20, 2017 at 7:26 AM, Juan Antonio Balbuena <j.a.balbu...@uv.es>
wrote:

Hello all

I am working with a cophylogenetic problem where I have a host tree, a
parasite tree and a binary matrix HP encapsulating the host-parasite
associations . After trimming the matrix according to a given criterion, I
require to prune the trees accordingly. Since I am getting errors at the
execution I devised the following control function to check the number of
tree nodes after pruning:
z <- function (hp, treeH,treeP) {
  treeh <- drop.tip(treeH, setdiff(treeH$tip.label, rownames(hp)))
  treep <- drop.tip(treeP, setdiff(treeP$tip.label, colnames(hp)))
  res <- c(treeh$Nnode,treep$Nnode)
 return(res)
 }

Then I try the following

x <- sapply (THP, z, treeH=TreeH[[7]], treeP= TreeP[[7]])

where THP is a list of trimmed HP matrices and TreeH and TreeP are
multiphylo objects and get the following error:

Error in integer(max(oldnodes)) : vector size cannot be infinite

The traceback is

6. integer(max(oldnodes))
5. collapse.singles(phy)
4. drop.tip(treeP, setdiff(treeP$tip.label, colnames(hp)))
3. FUN(X[[i]], ...)
2. lapply(X = X, FUN = FUN, ...)
1. sapply(THP, z, treeH = TreeH[[7]], treeP = TreeP[[7]])

This error appears only with this particular pair of host and parasite
trees (#7) and I cannot find a reason why this case should be different.

Any help will be very much appreciated.

Juan A. Balbuena

--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia
http://www.uv.es/~balbuena
P.O. Box 22085
http://www.uv.es/cophylpaco
<http://www.uv.es/cavanilles/zoomarin/index.htm>
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.es    tel. +34 963 543 658
<+34%20963%2054%2036%2058>    fax +34 963 543 733
<+34%20963%2054%2037%2033>
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