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DDD

Diversity-Dependent Diversification

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> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>. Also contains functions to simulate the diversity-dependent process.

Functions (29)

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