# bd.ext

##### Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates

This function fits by maximum likelihood a birth-death model to the combined phylogenetic and taxonomic data of a given clade. The phylogenetic data are given by a tree, and the taxonomic data by the number of species for the its tips.

- Keywords
- models

##### Usage

`bd.ext(phy, S)`

##### Arguments

- phy
- an object of class
`"phylo"`

. - S
- a numeric vector giving the number of species for each tip.

##### Details

A re-parametrization of the birth-death model studied by Kendall
(1948) so that the likelihood has to be maximized over *d/b* and
*b - d*, where *b* is the birth rate, and *d* the death
rate.

The standard-errors of the estimated parameters are computed using a normal approximation of the maximum likelihood estimates.

If the argument `S`

has names, then they are matched to the tip
labels of `phy`

. The user must be careful here since the function
requires that both series of names perfectly match, so this operation
may fail if there is a typing or syntax error. If both series of names
do not match, the values `S`

are taken to be in the same order
than the tip labels of `phy`

, and a warning message is issued.

Note that the function does not check that the tree is effectively ultrametric, so if it is not, the returned result may not be meaningful.

##### References

Paradis, E. (2003) Analysis of diversification: combining phylogenetic
and taxonomic data. *Proceedings of the Royal Society of
London. Series B. Biological Sciences*, **270**, 2499--2505.

##### See Also

`birthdeath`

, `branching.times`

,
`diversi.gof`

, `diversi.time`

,
`ltt.plot`

, `yule`

, `yule.cov`

##### Examples

```
### An example from Paradis (2003) using the avian orders:
data(bird.orders)
### Number of species in each order from Sibley and Monroe (1990):
S <- c(10, 47, 69, 214, 161, 17, 355, 51, 56, 10, 39, 152,
6, 143, 358, 103, 319, 23, 291, 313, 196, 1027, 5712)
bd.ext(bird.orders, S)
```

*Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)*