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DDD (version 5.2.2)

Diversity-Dependent Diversification

Description

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, , Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, , Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, and Laudanno et al. 2021. Syst. Biol. 70: 389–407, . Also contains functions to simulate the diversity-dependent process.

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Version

Install

install.packages('DDD')

Monthly Downloads

627

Version

5.2.2

License

GPL-3

Maintainer

Rampal Etienne

Last Published

July 10th, 2023

Functions in DDD (5.2.2)

DDD: Diversity-Dependent Diversification

Function to convert a table with speciation and extinction events to a set of branching times

Function to simulate the diversity-dependent diversification process with a shift in one or more of the parameters

Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshift

Bootstrap likelihood ratio test of diversity-dependent diversification model

Maximization of the loglikelihood under a diversity-dependent diversification model

Simulation of a diversity-dependent-like time-dependent process

Carries out optimization using a simplex algorithm (finding a minimum)

Function to convert a table with speciation and extinction events to a phylogeny

Loglikelihood for diversity-independent diversification model

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

Function to simulate the macro-evolutionary succession process assuming diversity-dependent diversification

Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification model

Takes samples in the usual manner

rng_respecting_sample

Sampling in which zero probabilities are removed

Function to convert phylogeny to a table with speciation and extinction events

Maximization of the loglikelihood under a diversity-dependent diversification model with a shift in the parameters

Loglikelihood for diversity-dependent diversification models

Rounds up in the usual manner

dd_multiple_KI_loglik

Loglikelihood for diversity-dependent diversification models with multiple decoupling (rate shift) events

Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics

Loglikelihood for macro-evolutionary succession under diversity-dependent diversification with the key innovation at time t = t_d

Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_d

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.

Function to simulate the diversity-dependent diversification process

Function to simulate a key innovation in macro-evolution with the innovative clade decoupling from the diversity-dependent diversification dynamics of the main clade

Carries out optimization (finding a minimum)

Function to do convolution of two vectors

Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics