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>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> *NOTE!* For shipments by EXPRESS COURIER use the following street address:
> C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), 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-ph...@r-project.org/
>
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
[[alternative HTML version deleted]]
_______________________________________________
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/
