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 -- View this message in context: http://r.789695.n4.nabble.com/Convert-filogenetic-tree-to-binary-matrix-tp3478961p3478961.html Sent from the R help mailing list archive at Nabble.com.
vanderlei52 <vanderleidebastianimach <at> yahoo.com.br> writes:> > I need to create a binary matrix with all node of a phylogenetic tree and the > presence of each taxo in their respective node. >I would suggest that you try this question on the r-sig-phylo mailing list instead. The phylobase package has an ancestors() functions that could help you put together a solution, but there may well be a quicker, easier way. Ben Bolker
Hi Ben, Thank you for your help. I did the same question in the r-sig-phylo mailing list. Liam Revell gave the following solution: 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 Vanderlei -- View this message in context: http://r.789695.n4.nabble.com/Convert-filogenetic-tree-to-binary-matrix-tp3478961p3484371.html Sent from the R help mailing list archive at Nabble.com.