# Diversity-Dependent Diversification

## Documentation for package ‘DDD’ version 5.0

- DESCRIPTION file.

## Help Pages

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.