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.
This function computes the standard-errors of the estimated parameters
using a normal approximations of the maximum likelihood estimates:
this is likely to be inaccurate because of asymmetries of the
likelihood function (Nee et al. 1995). In addition, 95 intervals of both parameters are computed using profile likelihood:
they are particularly useful if the estimate of d/b is at the
boundary of the parameter space (i.e. 0, which is often the case).
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.