ape (version 1.2-7)

bd.ext: Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates

Description

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.

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 function computed using a normal approximations of the maximum likelihood estimates. 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

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)