R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Fit Density Dependent Speciation Model to Branching Times

DensityDependent

R Documentation

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)

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 drabosky@umich.edu

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.

Examples

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