birthdeath: Estimation of Speciation and Extinction Rates With Birth-Death Models
Description
This function fits by maximum likelihood a birth-death model to the
branching times computed from a phylogenetic tree using the method of
Nee et al. (1994).
Usage
birthdeath(phy)
Arguments
phy
an object of class "phylo".
Value
A NULL value is returned, the results are simply printed.
Details
Nee et al. (1994) used 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. This is the approach used by the present function.
By contrast to Nee et al. (1994), this function computes the
standard-errors of the estimated parameters using a normal
approximations of the maximum likelihood estimates, though this is
likely to be inaccurate because of asymmetries of the likelihood
function (Nee et al. 1995).
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
Kendall, D. G. (1948) On the generalized ``birth-and-death''
process. Annals of Mathematical Statistics, 19, 1--15.
Nee, S., May, R. M. and Harvey, P. H. (1994) The reconstructed
evolutionary process. Philosophical Transactions of the Royal
Society of London. Series B. Biological Sciences, 344, 305--311.
Nee, S., Holmes, E. C., May, R. M. and Harvey, P. H. (1995) Estimating
extinctions from molecular phylogenies. in Extinction Rates,
eds. Lawton, J. H. and May, R. M., pp. 164--182, Oxford University Press.