R: Paint sub-trees with a discrete character

paintSubTree {phytools}

R Documentation

Paint sub-trees with a discrete character

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

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

`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.

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.

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

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