New version of treeSlice

The phytools function treeSlice cuts a phylogeny at a particular height above the root and returns all non-trivial subtrees (that is, subtrees with two or more taxa). A user requested that I add the capacity to return trivial as well as non-trivial subtrees. This is straightforward, but it cannot be done using the ape function extract.clade, because that only permits the extraction of trees with two or more tips. Instead, for subtrees with only one tip we create the "phylo" object directly. Here is how we do it:

for(i in 1:length(nodes)){
  if(nodes[i]>length(tree$tip)){
    trees[[i]]<-extract.clade(tree,node=nodes[i])
    trees[[i]]$root.edge<-H[which(tree$edge[,2]==nodes[i]),2] -slice
  } else {
    z<-list(edge=matrix(c(2,1),1,2), edge.length=H[which(tree$edge[,2]==nodes[i]),2]-slice, tip.label=tree$tip.label[nodes[i]],Nnode=1L)
    class(z)<-"phylo"; trees[[i]]<-z
  }
}

Seems to work fine. The default performance of treeSlice is to return only non-trivial subtrees. To return trivial subtrees, we set the new argument trivial=TRUE. So, for instance:

> set.seed(1)
> tree<-pbtree(n=10,scale=1)
> plot(tree); add.scale.bar(length=0.5)

> trees<-treeSlice(tree,0.5,trivial=T)
> str(trees)
Class "multiPhylo"
List of 6
 $ :List of 5
  ..$ edge       : num [1:2, 1:2] 3 3 1 2
  ..$ edge.length: num [1:2] 0.204 0.204
  ..$ tip.label  : chr [1:2] "t7" "t8"
  ..$ Nnode      : int 1
  ..$ root.edge  : num 0.296
  ..- attr(*, "class")= chr "phylo"
  ..- attr(*, "order")= chr "cladewise"
...
 $ :List of 4
  ..$ edge       : num [1, 1:2] 2 1
  ..$ edge.length: num 0.5
  ..$ tip.label  : chr "t2"
  ..$ Nnode      : int 1
  ..- attr(*, "class")= chr "phylo"
...

That's it.

I have posted a new version of phytools with this function. You can download it here and install from source.