Hi, with a little hack you can use the function cophenetic.phylo from ape. You just set all branch lengths to 1 :
require(ape) >tree <- rtree(5,rooted=F) >n <- length(tree$edge.length) >tree$edge.length <- rep(1,n) >cophenetic.phylo(tree) t3 t1 t2 t4 t5 t3 0 3 3 3 3 t1 3 0 2 4 4 t2 3 2 0 4 4 t4 3 4 4 0 2 t5 3 4 4 2 0 Cheers On Wed, Jun 2, 2010 at 2:47 PM, Arnau Mir Torres <arnau....@uib.es> wrote: > Hello. > > I'd like to compute the associate vector of distances between leaves in a > binary non-rooted tree. The definition of a distance between two leaves in a > binary non-rooted tree is the number of edges in the path joining the two > leaves. > I've tried the ape package but I'm unable to find this vector. > For example, using rtree(5,rooted=F) I've obtained the following tree: > > $edge > [,1] [,2] > [1,] 6 7 > [2,] 7 1 > [3,] 7 8 > [4,] 8 2 > [5,] 8 3 > [6,] 6 4 > [7,] 6 5 > > $tip.label > [1] "t4" "t3" "t2" "t1" "t5" > > $edge.length > [1] 0.9126727 0.2765674 0.4996832 0.7904400 0.8508797 0.8174133 0.9027958 > > $Nnode > [1] 3 > > > My question is: how to compute the vector of distances between the 5 > leaves. This vector is in this case: > > v=(d(t1,t2),d(t1,t3),d(t1,t4),d(t1,t5),d(t2,t3),d(t2,t4),d(t2,t5),d(t3,t4),d(t3,t5),d(t4,t5))=(4,4,3,2,2,3,4,3,4,3). > > > Thanks in advance, > > Arnau. > ------------------------------------------------------------ > Arnau Mir Torres > Edifici A. Turmeda > Campus UIB > Ctra. Valldemossa, km. 7,5 > 07122 Palma de Mca. > tel: (+34) 971172987 > fax: (+34) 971173003 > email: arnau....@uib.es > URL: http://dmi.uib.es/~arnau <http://dmi.uib.es/%7Earnau> > ------------------------------------------------------------ > > > > > > > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
