Runs a parameteric bootstrapping likelihood ratio test on two DAISIE models

Usage

bootstrap_lr(
  daisie_data,
  data_name,
  model_1,
  model_2,
  array_index,
  cond,
  methode = "lsodes",
  optimmethod = "subplex",
  results_dir = NULL,
  test = FALSE
)

Arguments

daisie_data: A list, conforming to the DAISIE object format. Usually preprocessed by DAISIE::DAISIE_dataprep(), see it's documentation for details. Otherwise it may be generated via simulations, using DAISIE::DAISIE_sim_cr() and friends.
data_name: String. Will be used for the name of the created output folder.
model_1: A string with model that should run. For a list of options see documentation for model parameter in run_daisie_ml().
model_2: A string with model that should run. For a list of options see documentation for model parameter in run_daisie_ml().
array_index: A single numeric with the array index. It is used for naming the output file.
cond: An integer specifying conditioning, as described in DAISIE::DAISIE_ML_CS().
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, \link{deSolve}{ode}() method is assumed. The default method overall is "lsodes" for \link{DAISIE_ML_CS}() and "ode45" from \link[deSolve]{ode}() for \link{DAISIE_ML_IW}().
optimmethod: Method used in likelihood optimization. Default is subplex (see \link[subplex]{subplex}() for full details). Alternative is "simplex" which was the method in previous versions.
results_dir: A string with the path to the directory where results are to be stored or can be found. For example, if the data in question is (to be) stored in folder_with_res/$data_name, then results_dir should be "folder_with_res". Defaults to NULL, which indicates the default directories are to be used. Default directories are: * $HOME/results/$data_name if on the cluster * getwd()/results/$data_name if called from another environment If is.na(results_dir), then the object is returned to the R session and not saved to file.
test: A boolean, defaults to FALSE. Set to TRUE for testing purposes, to fix the seed.

Value

Nothing. Writes bootstrapping results to a .rds file. This file is stored in file_path. The directory in of file_path is created if it doesn't exist.

Examples

if (FALSE) {
data(Galapagos_datalist, package = "DAISIE")
bootstrap_lr(
  daisie_data = Galapagos_datalist,
  model_1 = "cr_dd",
  model_2 = "cr_di",
  array_index = 1,
  cond = 1,
)
}