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
bd_ML                   Maximization of the loglikelihood under the
                        diversity-independent, possibly time-dependent
                        diversification model
bd_loglik               Loglikelihood for diversity-independent
                        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_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_loglik            Loglikelihood for diversity-dependent
                        diversification models with decoupling of a
                        subclade from a main clade 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_LR                   Bootstrap likelihood ratio test of
                        diversity-dependent diversification model
dd_ML                   Maximization of the loglikelihood under a
                        diversity-dependent diversification model
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_loglik            Loglikelihood for macro-evolutionary succession
                        under diversity-dependent diversification with
                        the key innovation at time t = t_d
dd_MS_sim               Function to simulate the macro-evolutionary
                        succession process assuming diversity-dependent
                        diversification
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_SR_sim               Function to simulate the diversity-dependent
                        diversification process with a shift in one or
                        more of the parameters
dd_loglik               Loglikelihood for diversity-dependent
                        diversification models
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
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.
