R: Compute and Set Branching Times

compute.brtime {ape} | R Documentation

## Compute and Set Branching Times

### Description

This function computes the branch lengths of a tree giving its branching times (aka node ages or heights).

### Usage

    compute.brtime(phy, method = "coalescent", force.positive = NULL)

### Arguments

`phy` | an object of class `"phylo"`.
`method` | either `"coalescent"` (the default), or a numeric vector giving the branching times.
`force.positive` | a logical value (see details).

### Details

By default, a set of random branching times is generated from a simple coalescent, and the option `force.positive` is set to `TRUE` so that no branch length is negative.

If a numeric vector is passed to `method`, it is taken as the branching times of the nodes with respect to their numbers (i.e., the first element of `method` is the branching time of the node numbered n + 1 [= the root], the second element of the node numbered n + 2, and so on), so `force.positive` is set to `FALSE`. This may result in negative branch lengths. To avoid this, one should use `force.positive = TRUE` in which case the branching times are eventually reordered.

### Value

An object of class `"phylo"` with branch lengths and ultrametric.

### Author(s)

Emmanuel Paradis

### See Also

`compute.brlen`, `branching.times`

### Examples

    tr <- rtree(10)
    layout(matrix(1:4, 2))
    plot(compute.brtime(tr)); axisPhylo()
    plot(compute.brtime(tr, force.positive = FALSE)); axisPhylo()
    plot(compute.brtime(tr, 1:9)); axisPhylo() # a bit nonsense
    plot(compute.brtime(tr, 1:9, TRUE)); axisPhylo()
    layout(1)

[Package ape version 5.0 Index]