Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/compute.brtime.R

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

1 | ```
compute.brtime(phy, method = "coalescent", force.positive = NULL)
``` |

`phy` |
an object of class |

`method` |
either |

`force.positive` |
a logical value (see 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.

An object of class `"phylo"`

with branch lengths and ultrametric.

Emmanuel Paradis

`compute.brlen`

, `branching.times`

1 2 3 4 5 6 7 | ```
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)
``` |

```
```

ape documentation built on Sept. 24, 2018, 9:03 a.m.

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