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DDD (version 1.9)

Diversity-dependent diversification

Description

DDD 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, doi: 10.1098/rspb.2011.1439. DDD also implements a maximum likelihood method to detect key innovations defined as decoupling of diversity-dependence. See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.

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Version

Install

install.packages('DDD')

Monthly Downloads

755

Version

1.9

License

GPL-2

Maintainer

Rampal Etienne

Last Published

November 29th, 2012

Functions in DDD (1.9)

dd_ML

Maximization of the loglikelihood under a diversity-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_SR_ML

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

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

Loglikelihood for diversity-dependent diversification models
DDD-internal

Internal DDD Functions
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