PCMTreeMatrixNodesInSamePart: Which couples from a given set of nodes in a tree belong to...

In PCMBase: Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Which couples from a given set of nodes in a tree belong to the same part?

Description

Which couples from a given set of nodes in a tree belong to the same part?

Which couples from a given set of nodes in a tree belong to the same regime?

Usage

PCMTreeMatrixNodesInSamePart(
  tree,
  nodes = seq_len(PCMTreeNumNodes(tree)),
  upperTriangle = TRUE,
  returnVector = TRUE
)

PCMTreeMatrixNodesInSameRegime(
  tree,
  nodes = seq_len(PCMTreeNumNodes(tree)),
  upperTriangle = TRUE,
  returnVector = TRUE
)

Arguments

tree	a PCMTree object or a phylo object.
nodes	an integer vector of length L >= 2 denoting a set of nodes in the tree.
upperTriangle	logical indicating if all duplicated entries and diagonal entries should be set to NA (by default TRUE).
returnVector	logical indicating if a vector instead of a matrix should be returned (corresponding to calling as.vector on the resulting matrix and removing NAs). Default: TRUE

Value

a L x L logical matrix with TRUE on the diagonal and for each couple of tips that belong to the same part or regime. If returnVector is TRUE (default) only a vector of the non-NA entries will be returned.

a L x L logical matrix with TRUE on the diagonal and for each couple of tips that belong to the same part or regime. If returnVector is TRUE (default) only a vector of the non-NA entries will be returned.

Examples

set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(8))
PCMTreeMatrixNodesInSamePart(tree, returnVector = FALSE)

PCMTreeSetPartition(tree, c(10, 12))
PCMTreeMatrixNodesInSamePart(tree, returnVector = FALSE)

PCMTreeMatrixNodesInSamePart(tree)
PCMTreeMatrixNodesInSamePart(tree, seq_len(PCMTreeNumTips(tree)))
PCMTreeMatrixNodesInSamePart(
  tree, seq_len(PCMTreeNumTips(tree)), returnVector = FALSE)

set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(8))
PCMTreeMatrixNodesInSamePart(tree, returnVector = FALSE)

PCMTreeSetPartition(tree, c(10, 12))
PCMTreeMatrixNodesInSamePart(tree, returnVector = FALSE)

PCMTreeMatrixNodesInSamePart(tree)
PCMTreeMatrixNodesInSamePart(tree, seq_len(PCMTreeNumTips(tree)))
PCMTreeMatrixNodesInSamePart(
  tree, seq_len(PCMTreeNumTips(tree)), returnVector = FALSE)

PCMBase documentation built on Nov. 18, 2022, 9:06 a.m.