bootstrap_lr: Runs a parameteric bootstrapping likelihood ratio test on two...

In tece-lab/DAISIEutils: Utility Functions for the DAISIE Package

Runs a parameteric bootstrapping likelihood ratio test on two DAISIE models

Description

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

## Not run: 
data(Galapagos_datalist, package = "DAISIE")
bootstrap_lr(
  daisie_data = Galapagos_datalist,
  model_1 = "cr_dd",
  model_2 = "cr_di",
  array_index = 1,
  cond = 1,
)

## End(Not run)

tece-lab/DAISIEutils documentation built on Jan. 31, 2024, 12:09 p.m.