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Hi Klaus and Emmanuel,
I am very grateful for your help.
All the best
Juan Antonio
El 23/01/2017 a las 14:48, Emmanuel
Paradis escribió:
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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street address:
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Spain.
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--
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
46071 Valencia,
Spain
e-mail: j.a.balbu...@uv.es
tel.
+34 963 543 658 fax +34 963 543 733
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
NOTE! For shipments by EXPRESS COURIER use
the following street
address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia),
Spain.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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