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