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

1
2
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.

See Also

make.simmap, read.simmap, plotSimmap, sim.history

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.