laser (version 2.1)

DensityDependent: Fit Density Dependent Speciation Model to Branching Times

Description

Functions that fit density-dependent speciation rate models to branching times derived from phylogenetic data. DDX and DDL fit exponential and logistic variants of the density-dependent speciation rate model.

Usage

DDX(x)
DDL(x)

Value

• a list with the following components:
• LH
  The log-likelihood at the maximum
• aic
  the Akaike Information Criterion
• r1
  the initial speciation rate
• kparam
  the K parameter in the logistic density dependent model
• xparam
  the x parameter in the density-dependent exponetial model

Details

DDX models the speciation rate as a function of the number of extant lineages at any point in time, r(t) = r0 * (Nt ^ (-x)), where r0 is the initial speciation rate, Nt is the number of lineages at some time t, and x is a parameter controlling the magnitude of the rate change. DDL models the speciation rate as r(t) = r0 * (1 - Nt / K), where r0 is the initial speciation rate, Nt is the number of extant lineages at some time t, and K is analogous to the 'carrying capacity' parameter of population ecology.

References

Nee, S., R. M. May, and P. H. Harvey. 1994b. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B 344:305-311.

Nee, S., A. Mooers, and P. H. Harvey. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl. Acad. Sci. USA 89:8322-8326.

See Also

yule-n-rate, rvbd, fitdAICrc

Examples

data(plethodon)
  resX <- DDX(plethodon)
  resL <- DDL(plethodon)