Diversity-Dependent Diversification
Loglikelihood for diversity-independent diversification model
Maximization of the loglikelihood under the diversity-independent, pos...
Function to convert a set of branching times into a phylogeny with ran...
Function to do convolution of two vectors
Loglikelihood for diversity-dependent diversification models with deco...
Maximization of the loglikelihood under a diversity-dependent diversif...
Function to simulate a key innovation in macro-evolution with the inno...
Loglikelihood for diversity-dependent diversification models
Bootstrap likelihood ratio test of diversity-dependent diversification...
Maximization of the loglikelihood under a diversity-dependent diversif...
Loglikelihood for macro-evolutionary succession under diversity-depend...
Maximization of the loglikelihood under a diversity-dependent diversif...
Function to simulate the macro-evolutionary succession process assumin...
Loglikelihood for diversity-dependent diversification models with mult...
Function to simulate the diversity-dependent diversification process
Loglikelihood for diversity-dependent diversification models with a sh...
Maximization of the loglikelihood under a diversity-dependent diversif...
Function to simulate the diversity-dependent diversification process w...
DDD: Diversity-Dependent Diversification
Function to convert a table with speciation and extinction events to a...
Function to convert a table with speciation and extinction events to a...
Carries out optimization (finding a minimum)
Function to convert phylogeny to a table with speciation and extinctio...
Sampling in which zero probabilities are removed
Rounds up in the usual manner
Takes samples in the usual manner
Carries out optimization using a simplex algorithm (finding a minimum)
Simulation of a diversity-dependent-like time-dependent process
Transforming parameters from -Inf to Inf into parameters from -1 to 1
Untransforming parameters from -1 to 1 into parameters from -Inf to In...
Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565> and Laudanno et al. 2021. Syst. Biol. 70: 389–407, <DOI:10.1093/sysbio/syaa048>. Also contains functions to simulate the diversity-dependent process.