Look at reorder.phylo() in ape and reorder() in phylo4: your desired tip order may be there.
Best, Brian _______________________________________ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars/omeara On Wed, Oct 8, 2014 at 4:45 AM, Juan Antonio Balbuena <[email protected]> wrote: > Hello > I am working on a simulation that requires adding a number of random tips > to multiple phylogenies: > > treeP <- read.nexus(file= "my file.tre") # 5K trees used to build a > consensus tree (treeP is thus a multiPhylo object) > NT = 30 # number of taxa in phylogeny > N.dup = 3 # number of tips (duplications) I want to add to the trees > sites <- sort(sample(1:NT, N.dup), decreasing=TRUE) # Random tips to > duplicate > dup.labels <- treeP[[1]]$tip.label[sites] > treeP <- .uncompressTipLabel(treeP) > # > # Add duplicates to branches following a Liam Revell recipe published in > his blog: > # > for (n in 1:length(treeP)) { > for (i in 1:N.dup ) { > pos <- runif(n=1)* > treeP[[n]]$edge.length[which(treeP[[n]]$edge[,2]==sites[i])] > edl <- runif(n=1)* > treeP[[n]]$edge.length[which(treeP[[n]]$edge[,2]==sites[i])] > treeP[[n]] <- bind.tip(treeP[[n]], tip.label=paste(dup.labels[i], 1, > sep="."), > edge.length=edl, where=sites[i], position=pos) > } > } > # > treeP<- .compressTipLabel(treeP) > # Check tip labels: > treeP$tip.label > $tip.label > [1] "S24" "S25" "S9" "S15" "S3" "S21" "S12" "S17" > "S19" "S30" "S22" "S4" "S16" "S27" "S10" "S23" "S1" > "S2" "S14" > [20] "S6" "S8" "S26" "S29" "S13" "S20" "S7" "S28" > "S18" "S5" "S11" "S18.1" "S20.1" "S16.1" > > When I plot any tree in treeP, S18.1, S20.1 and S16.1 appear together with > S18, S20 and S16, as intended. So why are they at the end of the array > above? This behaviour makes makes my life difficult because it forces me to > rearrange a number of matrices to make them match this tip label order. I > would appreciate if a kind soul can explain why it is that way and whether > is possible to reorder the tip labels, placing each added tip together with > its respective counterpart? > > Thanks in advance for your help. > > Juan Antonio > -- > > 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: [email protected] 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. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
