https://github.com/cran/ape
Tip revision: 5b65bad8bfd199e9c9bbab99ffec36161994e8d8 authored by Emmanuel Paradis on 05 December 2014, 00:00:00 UTC
version 3.2
version 3.2
Tip revision: 5b65bad
subtrees.R
## subtrees.R (2008-04-14)
## All subtrees of a Phylogenetic Tree
## Copyright 2008 Damien de Vienne
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
subtrees<-function(tree, wait = FALSE)
{
N.tip<-Ntip (tree)
N.node<-Nnode(tree)
limit<-N.tip+N.node
sub<-list(N.node)
u<-0
for (k in (N.tip+1):limit)
{
u<-u+1
if (wait==TRUE) cat("wait... Node",u,"out of", N.node, "treated\n")
fils<-NULL
pere<-res <- k
repeat
{
for (i in 1: length(pere)) fils<-c(fils, tree$edge[,2][tree$edge[,1]==pere[i]])
res<-c(res, fils)
pere<-fils
fils<-NULL
if (length(pere)==0) break
}
len<-res[res>N.tip]
if (u==1) {
tree2<-tree
len<-(N.tip+1):limit
}
else {
len.tip<-res[res<N.tip+1]
vec<-1:length(tree$tip.label)
len.tip.stay<-setdiff(vec, len.tip)
tree2<-drop.tip(tree, len.tip.stay)
}
sub[[u]]<-tree2
sub[[u]]$name<-k
#sub[[u]]$name<-tree2$node.label[1]
sub[[u]]$Ntip<-Ntip(tree2)
sub[[u]]$Nnode<-Nnode(tree2)
if (is.null(tree$node.label))
sub[[u]]$node.label<-len
}
return(sub)
cat("\n")
}