Learn R Programming
⚠️There's a newer version (5.2.2) of this package.Take me there.

DDD (version 3.2)

Diversity-Dependent Diversification

Description

Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, . Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence. See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, . Finally, DDD contains a function to simulate the diversity-dependent process.

Copy Link

Version

Install

install.packages('DDD')

Monthly Downloads

693

Version

3.2

License

GPL-3

Maintainer

Rampal Etienne

Last Published

February 9th, 2016

Functions in DDD (3.2)

bd_ML

Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification model
dd_KI_ML

Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics
dd_MS_ML

Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics
dd_loglik

Loglikelihood for diversity-dependent diversification models
DDD-package

Diversity Dependent Diversification
dd_KI_loglik

Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_d
dd_SR_loglik

Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshift
dd_MS_loglik

Loglikelihood for macro-evolutionary succession under diversity-dependent diversification with the key innovation at time t = t_d
dd_KI_sim

Function to simulate a key innovation in macro-evolution with the innovative clade decoupling from the diversity-dependent diversification dynamics of the main clade
dd_sim

Function to simulate the diversity-dependent diversification process
dd_SR_ML

Maximization of the loglikelihood under a diversity-dependent diversification model with a shift in the parameters
DDD-internal

Internal DDD Functions
bd_loglik

Loglikelihood for diversity-independent diversification model
dd_ML

Maximization of the loglikelihood under a diversity-dependent diversification model
dd_LR

Bootstrap likelihood ratio test of diversity-dependent diversification model
dd_MS_sim

Function to simulate the macro-evolutionary succession process assuming diversity-dependent diversification