R: Paint sub-trees with a discrete character

paintSubTree {phytools}

R Documentation

Paint sub-trees with a discrete character

Description

This function maps or "paints" an arbitrary, i.e., user-specified, discrete character history on the tree. paintSubTree paints the clade downstream of node with a particular state; whereas paintBranches paints only a specified branch.

Usage

paintSubTree(tree, node, state, anc.state="1", stem=FALSE)
paintBranches(tree, edge, state, anc.state="1")

Arguments

`tree`	a phylogenetic tree as an object of class `"phylo"` or a modified object with mapped character traits.
`node`	an integer specifying the node number tipward of which the function should paint the derived state.
`edge`	an integer or vector of integers specifying the node or tip numbers of the edges that should be painted in `paintBranches`.
`state`	a string (or numeric value) specifying the state to paint on the tree tipward of `node`.
`anc.state`	the ancestral state to use; will only be applied if there are presently no character values mapped on the tree.
`stem`	logical or numeric value indicating whether to use the derived state on the stem leading to `node` (or not, if `stem=FALSE`), or, alternatively, what fraction of the stem should be assigned to the derived clade. Note that for tip clades `stem=FALSE` is not allowed.

Value

A modified phylogenetic tree of class "phylo" with the following additional elements:

`maps`	a list of named vectors containing the times spent in each state on each branch, in the order in which they occur.
`mapped.edge`	a matrix containing the total time spent in each state along each edge of the tree.

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.