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 1 for the standard DAISIE model, for a relaxed-rate model a list with the following 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. relaxed_par: the parameter to relax (integrate over). Options are "cladogenesis", "extinction", "carrying_capacity", "immigration", or "anagenesis".
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, deSolve{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 Oct. 22, 2023, 1:06 a.m.