KeptPaths: Paths present in reduced tree

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Paths present in reduced tree

Description

Lists which paths present in a master tree are present when leaves are dropped.

Usage

KeptPaths(paths, keptVerts, all = TRUE)

## S3 method for class 'data.frame'
KeptPaths(paths, keptVerts, all = TRUE)

## S3 method for class 'matrix'
KeptPaths(paths, keptVerts, all = TRUE)

Arguments

paths	data.frame of paths in master tree, perhaps generated using PathLengths().
keptVerts	Logical specifying whether each entry is retained in the reduced tree, perhaps generated using KeptVerts().
all	Logical: if TRUE, return all paths that occur in the reduced tree; if FALSE, return only those paths that correspond to a single edge. that correspond to edges in the reduced tree. Ignored if paths is a matrix.

Value

KeptPaths() returns a logical vector specifying whether each path in paths occurs when keptVerts vertices are retained.

Author(s)

Martin R. Smith ([e-mail])

See Also

Other tree manipulation: AddTip(), CollapseNode(), ConsensusWithout(), DropTip(), EnforceOutgroup(), ImposeConstraint(), KeptVerts(), LeafLabelInterchange(), MakeTreeBinary(), Renumber(), RenumberTips(), RenumberTree(), RootTree(), SortTree(), Subtree(), TipTimedTree(), TrivialTree

Examples

master <- BalancedTree(9)
paths <- PathLengths(master)
keptTips <- c(1, 5, 7, 9)
keptVerts <- KeptVerts(master, keptTips)
KeptPaths(paths, keptVerts)
paths[KeptPaths(paths, keptVerts, all = FALSE), ]

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.