PCMTreeSetLabels: Set tip and internal node labels in a tree

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

Set tip and internal node labels in a tree

Description

Set tip and internal node labels in a tree

Usage

PCMTreeSetLabels(
  tree,
  labels = as.character(1:PCMTreeNumNodes(tree)),
  inplace = TRUE
)

Arguments

tree	a phylo object or a PCMTree object. If this is a PCMTree object, the internal edge.part and part.regime members will be updated accordingly.
labels	a character vector in the order 1:PCMTreeNumNodes(tree) as denoted in the tree$edge matrix.
inplace	a logical indicating if the change should be done in place on the object in the calling environment (in this case tree must not be a temporary object, e.g. returned by another function call). Default is TRUE.

Value

if inplace is FALSE, a copy of tree with set or modified tree$tip.label and tree$node.label. If the original tree has a member edge.part, the returned tree has tree$edge.part and tree$part.regime updated. If inplace is TRUE (the default), nothing is returned and the above changes are made directly on the input tree.

See Also

PCMTree

Examples

tree <- ape::rtree(5)
tree$tip.label
# the following three are NULLs
tree$node.label
tree$edge.part
tree$part.regime


tree <- PCMTree(tree)
PCMTreeSetPartition(tree, c(6, 8))
tree$tip.label
tree$node.label
tree$edge.part
tree$part.regime

PCMTreeSetLabels(
  tree, labels = paste0(c(rep("t", 5), rep("n", 4)), PCMTreeGetLabels(tree)))
PCMTreeGetLabels(tree)
tree$tip.label
tree$node.label
tree$edge.part
tree$part.regime

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