R: Paths present in reduced tree

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]