DAISIE_loglik_integrate: Integrates the loglikelihood of a single clade across a...

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

Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution

Description

Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution

Usage

DAISIE_loglik_integrate(
  pars1,
  pars2,
  brts,
  stac,
  missnumspec,
  CS_version,
  methode,
  abstolint,
  reltolint,
  verbose
)

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	Vector of settings: pars2[1] corresponds to res, the maximum number of endemics or non-endemics for which the ODE system is solved; this must be much larger than the actual number for which the probability needs to be calculated.) pars2[2] corresponds to M, size of the mainland pool, i.e the number of species that can potentially colonize the island.
brts	Numeric vector of branching times
stac	Numeric of Endemicity status
missnumspec	Numeric of missing species
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
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().
abstolint	Numeric absolute tolerance of the integration
reltolint	Numeric relative tolerance of the integration
verbose	A numeric vector of length 1, which in simulations and 'DAISIEdataprep()' can be '1' or '0', where '1' gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed. The default: '0' does not print, '1' prints the initial likelihood and the settings that were selected (which parameters are to be optimised, fixed or shifted), '2' prints the same as '1 and also the intermediate output of the parameters and loglikelihood, while '3' the same as '2' and prints intermediate progress during likelihood computation.

Value

A loglikelihood value

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