mergeMappedStates2: Rename, merge, or split mapped states

In willgearty/pcmtools: Tools for Phylogenetic Comparative Methods

Description

This function renames, merges, or splits mapped states on a tree.

Usage

mergeMappedStates2(tree, old.states, new.state, node = NULL)

Arguments

tree	an object of class "simmap" or "multiSimmap" containing one or more phylogenetic trees with a mapped discrete character
old.states	state(s) to rename or merge
new.state	name for new state
node	a node index, used to specify a subclade of interest

Details

If node is specified, only mapped states of descendants edges of that node are modified. This function is based on the similarly named utility function by Liam Revell in phytools.

Value

An object of class "simmap" or "multiSimmap".

Examples

library(phytools)
# simulate a mapped tree
set.seed(4)
Q <- matrix(c(-2,1,1,1,-2,1,1,1,-2),3,3)
rownames(Q) <- colnames(Q) <- letters[1:3]
tree <- sim.history(pbtree(n=100,scale=1),Q)
cols <- setNames(c("blue","red","green","orange"),letters[1:4])

# plot the mapping
plot(tree, cols, ftype="i", fsize=0.7)

# split state c to state d within subclade
tree2 <- mergeMappedStates2(tree, "c", "d", 173)

# plot the new mapping
plot(tree2, cols, ftype="i", fsize=0.7)

willgearty/pcmtools documentation built on Nov. 5, 2019, 12:20 p.m.