DAISIE_logp0: Computes the log probability of no species present under the...

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Computes the log probability of no species present under the DAISIE model with clade-specific diversity-dependence

Description

Computes the log probability of no species present under the DAISIE model with clade-specific diversity-dependence. The output is a log value.

Usage

DAISIE_logp0(
  pars1,
  pars2,
  island_age,
  methode = "odeint::runge_kutta_cash_karp54",
  CS_version = list(model = 1, function_to_optimize = "DAISIE"),
  abstolint = 1e-16,
  reltolint = 1e-10
)

Arguments

pars1	Vector of model parameters: pars1[1] corresponds to lambda^c (cladogenesis rate) pars1[2] corresponds to mu (extinction rate) pars1[3] corresponds to K (clade-level carrying capacity) pars1[4] corresponds to gamma (immigration rate) pars1[5] corresponds to lambda^a (anagenesis rate).
pars2	Contains the model settings pars2[1] corresponds to lx = length of ODE variable x pars2[2] corresponds to ddmodel = diversity-dependent model, model of diversity-dependence, which can be one of ddmodel = 0 : no diversity dependence ddmodel = 1 : linear dependence in speciation rate ddmodel = 11: linear dependence in speciation rate and in immigration rate ddmodel = 2 : exponential dependence in speciation rate ddmodel = 21: exponential dependence in speciation rate and in immigration rate
island_age	the island age
methode	Method of the ODE-solver. Supported Boost ODEINT solvers (steppers) are: "odeint::runge_kutta_cash_karp54" "odeint::runge_kutta_fehlberg78" "odeint::runge_kutta_dopri5" "odeint::bulirsch_stoer" without odeint::-prefix, ode method is assumed. The default method overall is "lsodes" for DAISIE_ML_CS() and "ode45" from ode() for DAISIE_ML_IW().
CS_version	a numeric or list. Default is CS_version = list(model = 1, function_to_optimize = 'DAISIE'), but for a relaxed-rate model the list can contain more elements: model: the CS model to run, options are 1 for single rate DAISIE model, 2 for multi-rate DAISIE, or 0 for IW test model function_to_optimize: the DAISIE loglikelihood function that will be optimized. Options are: "DAISIE", default, the full DAISIE loglikelihood "DAISIE_approx", an approximate loglikelihood "DAISIE_DE", an exact loglikelkhood for K = Inf based on the D-E approach integration_method: the method used to do integraion in the relaxed rate model. Options are: 'standard' the default numerical integration 'MC' Monte Carlo integration 'stratified' using quantiles of the gamma distribution relaxed_par: the parameter to relax (integrate over) in the relaxed rate model. Options are "cladogenesis", "extinction", "carrying_capacity", "immigration", or "anagenesis" par_sd: standard deviation of the parameter to relax par_upper_bound upper bound of the parameter to relax seed: seed of the random number generator in case of 'MC' sample_size: size of sample in case of 'MC' or 'stratified' parallel: use parallel computing or not in case of 'MC' or 'stratified' n_cores: number of cores to use when run in parallel
abstolint	Numeric absolute tolerance of the integration
reltolint	Numeric relative tolerance of the integration

Value

The logarithm of the probability

Author(s)

Rampal S. Etienne & Bart Haegeman

DAISIE documentation built on June 8, 2025, 11:28 a.m.