[R-sig-phylo] Enigmatic error with drop.tip

[Juan Antonio Balbuena]

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 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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