Dear David and Santiago, Thank you very much! Indeed, tree3$node.label<-tree2$node.label is pretty obvious once one figures out the structure of tree!
-- Lev From: Santiago Sánchez <santiago.snc...@gmail.com<mailto:santiago.snc...@gmail.com>> Date: Thu, 14 Jan 2016 09:48:16 -0700 To: "r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>" <r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>>, LY <yampo...@mail.etsu.edu<mailto:yampo...@mail.etsu.edu>> Subject: Re: getBtimes vs. branching.times Dear Lev, I simple way to do what you request would be to follow this example with your data: > library(ape) # here I'm creating a random tree with branch lengths > treeBL <- rtree(10) > treeBL$edge.length [1] 0.59962263 0.76458987 0.48171189 0.26387301 0.76967429 0.42754456 [7] 0.30173612 0.10535179 0.01769042 0.49671428 0.61575421 0.91297819 [13] 0.52992782 0.68690369 0.35537999 0.56974770 0.97019530 0.49849792 # this would be the tree with the same topology but without branch lengths > treeNN <- treeBL > treeNN$edge.length <- NULL > treeNN Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: t1, t9, t4, t3, t7, t10, ... Rooted; no branch lengths. # create node labels > treeNN$Nnode [1] 9 > treeNN$node.label <- paste("n",1:treeNN$Nnode,sep='') > treeNN$node.label [1] "n1" "n2" "n3" "n4" "n5" "n6" "n7" "n8" "n9" > treeNN Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: t1, t9, t4, t3, t7, t10, ... Node labels: n1, n2, n3, n4, n5, n6, ... Rooted; no branch lengths. # check if the internal structure of both trees is identical > identical(treeNN$edge,treeBL$edge) [1] TRUE > if (identical(treeNN$edge,treeBL$edge)){ + newtree <- treeBL + newtree$node.label <- treeNN$node.label } > newtree Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: t1, t9, t4, t3, t7, t10, ... Node labels: n1, n2, n3, n4, n5, n6, ... Rooted; includes branch lengths. Hope this helps. Cheers, Santiago -- Santiago Sánchez-Ramírez Environmental Genomics Group Max Planck Institute for Evolutionary Biology August-Thienemann-Str. 2 24306 Plön Germany Website: https://sites.google.com/site/santiagosnchezrmirez/ Message: 1 Date: Wed, 13 Jan 2016 23:39:21 +0000 From: "Yampolsky, Lev" <yampo...@mail.etsu.edu<mailto:yampo...@mail.etsu.edu>> To: Emmanuel Paradis <emmanuel.para...@ird.fr<mailto:emmanuel.para...@ird.fr>>, "Liam J. Revell" <liam.rev...@umb.edu<mailto:liam.rev...@umb.edu>>, Dan Rabosky <drabo...@umich.edu<mailto:drabo...@umich.edu>> Cc: "r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>" <r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>> Subject: Re: [R-sig-phylo] getBtimes vs. branching.times Message-ID: <d2bc4988.7376e%yampo...@mail.etsu.edu<mailto:d2bc4988.7376e%25yampo...@mail.etsu.edu>> Content-Type: text/plain; charset="utf-8" Dear Colleagues, Thank you very much for your help, it?s all clear now. (I got way more than I asked for, for example, my trees include only extant taxa). And yes, branching.times() and getBtimes() return exact same numbers of course, I just didn?t understand ow indexing works. Next question, a very simple one again. I have two newick trees, identical topology. In one I have branch lengths, in the other I have node names. I would like a tree with both. How do I do this? Thanks in advance! -- Lev Yampolsky Professor Department of Biological Sciences East Tennessee State University Box 70703 Johnson City TN 37614-1710 Cell 423-676-7489<tel:423-676-7489> Office/lab 423-439-4359<tel:423-439-4359> Fax 423-439-5958<tel: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/
