R: Re-root a tree along an edge

reroot {phytools}

R Documentation

Re-root a tree along an edge

Description

This function re-roots a phylogenetic tree at an arbitrary position along an edge.

Usage

reroot(tree, node.number, position)

Arguments

`tree`	a phylogenetic tree in `"phylo"` format.
`node.number`	number of the node descending from the target branch in `tree$edge` - this can also be a tip in which case the node number is the index number of the tip in `tree$tip.label`.
`position`	position along the target edge at which to re-root the tree.

Details

This function had an error for rootings along edges descended from the root node for phytools<=0.2-47. This should be fixed in the present version. Now uses paste.tree, root, and splitTree internally. Earlier versions also had an error related to node labels. This should be fixed in phytools>=0.4-47.

Value

A phylogenetic tree in "phylo" format.

Author(s)

Liam Revell liam.revell@umb.edu

References

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.

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