R: Calculate length of paths between each pair of vertices...

PathLengths {TreeTools} | R Documentation

## Calculate length of paths between each pair of vertices within tree

### Description

Given a weighted rooted tree `tree`, `PathLengths()` returns the distance from each vertex to each of its descendant vertices.

### Usage

    PathLengths(tree, fullMatrix = FALSE)

### Arguments

`tree` | Original tree of class `phylo`, in `Preorder`.
`fullMatrix` | Logical specifying return format; see "value" section'.

### Value

If `fullMatrix = TRUE`, `PathLengths()` returns a square matrix in which entry `[i, j]` denotes the distance from internal node `i` to the descendant vertex `j`. Vertex pairs without a continuous directed path are denoted `NA`. If `fullMatrix = FALSE`, `PathLengths()` returns a `data.frame` with three columns: `start` lists the deepest node in each path (i.e. that closest to the root); `end` lists the shallowest node (i.e. that closest to a leaf); `length` lists the total length of that path.

### Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

### See Also

Other tree properties: `ConsensusWithout()`, `NSplits()`, `NTip()`, `SplitsInBinaryTree()`, `TipLabels()`, `TreeIsRooted()`

### Examples

    tree <- rtree(6)
    plot(tree)
    add.scale.bar()
    nodelabels()
    tiplabels()
    PathLengths(tree)

[Package TreeTools version 1.7.2 Index]