Slicing a tree to create all subtrees

Someone recently emailed me about slicing a tree at a particular height from the root and then keeping all the subtrees. This seemed pretty easy, so I thought I would implement it using the {ape} function extract.clade(). This is how I did it. First, I reordered the tree "cladewise", using reorder.phylo(); next, I computed the heights of all the internal and terminal nodes in the tree and put these values into a matrix to match the $edge matrix from my "phylo". Then, I found all the edges intersected by my slice and identified the tipward nodes on those edges, excluding all the nodes that were also tips. Finally, I extracted each subtree descended from the nodes using extract.clade() and added a $root.edge to each tree depending on where its root branch was sliced. I then returned all of these trees as a "multiPhylo" object.

The function is posted to my website, here. Please be warned that I'm not sure what will happen if the slice point is greater than the tree length or if it only intersects terminal edges.

First, let's create a random tree:

> require(geiger)
> tree<-birthdeath.tree(b=1,d=0,taxa.stop=20)



Now, let's slice it at slice=0.6, shown as the dotted line above (having verified, of course, that this will indeed produce some non-trivial subtrees):

> source("treeSlice.R")
> trees<-treeSlice(tree,0.6)
> plot(trees,root.edge=T)

which, in this case, produces the following set of three trees:



We're done!