# compute.brtime

##### Compute and Set Branching Times

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

- Keywords
- manip

##### 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.

##### See Also

##### 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)
```

*Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)*