| bd_loglik | Loglikelihood for diversity-independent diversification model |
| bd_ML | Maximization of the loglikelihood under the... |
| brts2phylo | Function to convert a set of branching times into a phylogeny... |
| conv | Function to do convolution of two vectors |
| DDD-package | DDD: Diversity-Dependent Diversification |
| dd_KI_loglik | Loglikelihood for diversity-dependent diversification models... |
| dd_KI_ML | Maximization of the loglikelihood under a diversity-dependent... |
| dd_KI_sim | Function to simulate a key innovation in macro-evolution with... |
| dd_loglik | Loglikelihood for diversity-dependent diversification models |
| dd_LR | Bootstrap likelihood ratio test of diversity-dependent... |
| dd_ML | Maximization of the loglikelihood under a diversity-dependent... |
| dd_MS_loglik | Loglikelihood for macro-evolutionary succession under... |
| dd_MS_ML | Maximization of the loglikelihood under a diversity-dependent... |
| dd_MS_sim | Function to simulate the macro-evolutionary succession... |
| dd_multiple_KI_loglik | Loglikelihood for diversity-dependent diversification models... |
| dd_sim | Function to simulate the diversity-dependent diversification... |
| dd_SR_loglik | Loglikelihood for diversity-dependent diversification models... |
| dd_SR_ML | Maximization of the loglikelihood under a diversity-dependent... |
| dd_SR_sim | Function to simulate the diversity-dependent diversification... |
| L2brts | Function to convert a table with speciation and extinction... |
| L2phylo | Function to convert a table with speciation and extinction... |
| optimizer | Carries out optimization (finding a minimum) |
| phylo2L | Function to convert phylogeny to a table with speciation and... |
| 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... |
| td_sim | Simulation of a diversity-dependent-like time-dependent... |
| transform_pars | Transforming parameters from -Inf to Inf into parameters from... |
| untransform_pars | Untransforming parameters from -1 to 1 into parameters from... |
