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
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
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
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