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| DDD-package | Diversity Dependent Diversification |
| bd_loglik | Loglikelihood for diversity-independent diversification model |
| bd_ML | Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification model |
| DDD | 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_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_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_loglik | Loglikelihood for diversity-dependent diversification models |
| dd_LR | Bootstrap likelihood ratio test of diversity-dependent diversification model |
| dd_ML | Maximization of the loglikelihood under a diversity-dependent diversification model |
| dd_MS_loglik | Loglikelihood for macro-evolutionary succession under diversity-dependent diversification with the key innovation at time t = t_d |
| 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_MS_sim | Function to simulate the macro-evolutionary succession process assuming diversity-dependent diversification |
| dd_sim | Function to simulate the diversity-dependent diversification process |
| dd_SR_loglik | Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshift |
| dd_SR_ML | Maximization of the loglikelihood under a diversity-dependent diversification model with a shift in the parameters |