KeptPaths {TreeTools}R Documentation

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 (martin.smith@durham.ac.uk)

See Also

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

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), ]
[Package TreeTools version 1.7.2 Index]