R: Fit Rate-Constant Birth-Death Model to Branching Times
bd
R Documentation
Fit Rate-Constant Birth-Death Model to Branching Times
Description
Finds maximum likelihood estimates of the net diversification rate r
(speciation rate S minus the extinction rate E) and the extinction
fraction a = E/S, using branching times derived from an
ultrametric phylogenetic tree.
Usage
bd(x, ai = c(0.1, 0.5, 0.9))
Arguments
x
a numeric vector of branching times
ai
a vector of initial a parameterizations for the optimization algorithm
Details
Non-linear optimization can be exceedingly difficult, and the algorithms used here can become trapped
on local (rather than global) optima. The default 'ai' parameters specified above fit the constant-rate
birth-death model to branching times using three initial a values. You should check your results
against those obtained using the pureBirth model. If the log-likelihood under bd is
less than pureBirth, you should explore alternative initial parameterizations. For example,
ai = seq(0.05, 0.99, length.out = 20) would attempt the optimization with 20 equally spaced a
values on the interval (0.05, 0.99).
I have found the default option to be satisfactory for all phylogenies I have examined.
Value
a list with the following components:
LH
the log-likelihood at the maximum
aic
the Akaike Information Criterion
r
the net diversification rate giving the maximum log-likelihood
a
the extinction fraction giving the maximum log-likelihood
Kendall, D. G. 1948. On the generalized "birth-and-death" process.
Ann. Math. Stat. 19:1-15.
Nee, S., E. C. Holmes, R. M. May, and P. H. Harvey. 1994a. Extinction rates
can be estimated from molecular phylogenies. Philos. Trans. R. Soc. Lond. B 344:77-82.
Nee, S., R. M. May, and P. H. Harvey. 1994b. The reconstructed evolutionary process.
Philos. Trans. R. Soc. Lond. B 344:305-311.