Hi Vanderlei,
Try this which uses ape function prop.part():
temp<-prop.part(tree)
X<-matrix(0,nrow=length(tree$tip),ncol=length(temp),dimnames=list(tree$tip.label,tree$node.label))
for(i in 1:ncol(X)) X[temp[[i]],i]<-1
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 4/28/2011 2:21 PM, Vanderlei Debastiani wrote:
Good morning!
I need to create a binary matrix with all node of a phylogenetic tree and the
presence of each taxo in their respective node.
Example:
require(ape)
y<-read.tree(text="(E,((H,I)D,(F,G)C)B)A;")
y
plot(y, show.node=TRUE)
I need to create a binary matrix as follows:
A B C D
G 1 1 1 0
F 1 1 1 0
I 1 1 0 1
H 1 1 0 1
E 1 0 0 0
Somebody could help me to solve this problem.
Thanks,
Vanderlei Debastiani
Laboratório de Ecologia Filogenética e Funcional
Programa de Pós-Graduação em Ecologia
Universidade Federal do Rio Grande do Sul
www.ufrgs.br/leff
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