Diversity-Dependent Diversification

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Documentation for package ‘DDD’ version 5.2.2

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bd_loglik Loglikelihood for diversity-independent diversification model
bd_ML Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification model
brts2phylo Function to convert a set of branching times into a phylogeny with random topology This code is taken from the package TESS by Sebastian Hoehna, where the function is called tess.create.phylo
conv Function to do convolution of two vectors
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_multiple_KI_loglik Loglikelihood for diversity-dependent diversification models with multiple decoupling (rate shift) events
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
dd_SR_sim Function to simulate the diversity-dependent diversification process with a shift in one or more of the parameters
L2brts Function to convert a table with speciation and extinction events to a set of branching times
L2phylo Function to convert a table with speciation and extinction events to a phylogeny
optimizer Carries out optimization (finding a minimum)
phylo2L Function to convert phylogeny to a table with speciation and extinction events
rng_respecting_sample Sampling in which zero probabilities are removed
roundn Rounds up in the usual manner
sample2 Takes samples in the usual manner
simplex Carries out optimization using a simplex algorithm (finding a minimum)
td_sim Simulation of a diversity-dependent-like time-dependent process
transform_pars Transforming parameters from -Inf to Inf into parameters from -1 to 1
untransform_pars Untransforming parameters from -1 to 1 into parameters from -Inf to Inf.