paintSubTree: Paint sub-trees with a discrete character

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Paint sub-trees with a discrete character

Description

Paints regimes on a tree to create an object of class "simmap" with mapped regimes.

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.

Details

These functions map or "paint" arbitrary (i.e., user-specified) discrete character histories on the tree.

paintSubTree paints the clade downstream of node with a particular state; whereas paintBranches paints only a specified branch.

Value

An object of class "simmap" that contains the specified paintings as a mapped discrete character.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

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

phytools documentation built on April 3, 2025, 10:43 p.m.