phytools: treeSlice – R documentation

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treeSlice

Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point

Description

This function slices a tree at a particular height above the root and returns all subtrees or all non-trivial subtrees (i.e., subtrees with more than 1 taxon). Uses extract.clade in the "ape" package.

It can also be used to crop the terminal fraction of a tree for orientation="rootwards".

Usage

treeSlice(tree, slice, trivial=FALSE, prompt=FALSE, ...)

Arguments

`tree`	is a phylogenetic tree in `"phylo"` format.
`slice`	a real number indicating the height above the root at which to slice the tree.
`trivial`	a logical value indicating whether or not to return subtrees with a number of tips less than two (default is `FALSE`).
`prompt`	logical value indicating whether or not the height of the slice should be given interactively.
`...`	for `prompt=TRUE`, other arguments to be passed to `plotTree`. In addition, the argument `orientation` can be used to specify whether the `"tipwards"` subtrees or the `"rootwards"` phylogeny are/is to be returned by the function call (using those two argument values, respectively).

Value

An object of class "phylo" or "multiPhylo".

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.