R help - Jun 2010 - compute the associate vector of distances between leaves in a binary non-rooted tree

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
------------------------------------------------------------

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@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@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

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