DensityDependent: Fit Density Dependent Speciation Model to Branching Times

In laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

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)

Arguments

x	a numeric vector of branching times

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.

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

Author(s)

Dan Rabosky [e-mail]

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, fitdAICrc

Examples

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

Example output

Loading required package: ape
Loading required package: geiger

laser documentation built on Jan. 15, 2017, 4:49 p.m.