PCMTreeGetTipsInRegime: Get the tips belonging to a regime in a tree

In venelin/PCMBase: Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Get the tips belonging to a regime in a tree

Description

Get the tips belonging to a regime in a tree

Usage

PCMTreeGetTipsInRegime(tree, regime)

Arguments

tree	a phylo object with an edge.regime member or a PCMTree object
regime	a character or integer denoting a regime in the tree.

Value

an integer vector with the ids of the tips belonging to regime.

See Also

PCMTreeGetTipsInPart, PCMTreeGetPartNames, PCMRegimes, PCMTreeGetPartRegimes, PCMTreeSetPartRegimes, PCMTreeGetPartition

Examples

set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- ape::rtree(10)
regimes <- sample(letters[1:3], nrow(tree$edge), replace = TRUE)
PCMTreeSetRegimesForEdges(tree, regimes)

if(requireNamespace("ggtree"))
PCMTreePlot(tree) + ggtree::geom_nodelab() + ggtree::geom_tiplab()

regime <- PCMRegimes(tree)[1]
PCMTreeGetTipsInRegime(tree, regime)
print(regime)

venelin/PCMBase documentation built on March 14, 2024, 8:24 p.m.