Dear Lev, I hope this little example explains it:
tree <- read.tree(text = "((t3:1,t2:1)b:1,t1:2)a;") par(mfrow = c(1,2)) plot(tree, show.node.label=TRUE) plot(tree, show.tip.label=FALSE) nodelabels() tiplabels() tree$tip.label tree$node.label The tree$tip.label correspond to 1 to the number of tip labels and tree$node.label to (number of tip labels +1) to (number of nodes) in the tree$edge matrix. Regards, Klaus On Tue, Jan 12, 2016 at 7:54 PM, Yampolsky, Lev <yampo...@mail.etsu.edu> wrote: > A very simple question: I have a tree with all tips and nodes labeled and > I want parent-child pairs from it. Looking at tree$edge does not quite > help, because these parent and child pairs are labeled by the internal > index, not IDs from the newick file. Looking at tree$tip.label and > tree$node.label does not help, because these two vectors index tips and > nodes separately, so these indexes do not correspond to those in tree$edge. > > Should be very very obvious how to do it! > > Thanks! > > -- > Lev Yampolsky > > Professor > Department of Biological Sciences > East Tennessee State University > Box 70703 > Johnson City TN 37614-1710 > Cell 423-676-7489 > Office/lab 423-439-4359 > Fax 423-439-5958 > > _______________________________________________ > 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/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[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/
