Re: [R] compute the associate vector of distances between leaves in a binary non-rooted tree

From: Joris Meys <jorismeys_at_gmail.com>
Date: Wed, 02 Jun 2010 15:14:27 +0200

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.mir_at_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.mir_at_uib.es
> URL: http://dmi.uib.es/~arnau <http://dmi.uib.es/%7Earnau>
> ------------------------------------------------------------
>
>
>
>
>
>
>
>
> ______________________________________________
> R-help_at_r-project.org mailing list
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> 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.Meys_at_Ugent.be
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Received on Wed 02 Jun 2010 - 13:19:17 GMT

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