Generate the preparatory files required for simulation.
run_flfll(
facts_file,
output_path = tempfile(),
log_path = output_path,
n_burn = NULL,
n_mcmc = NULL,
n_weeks_files = 10000,
n_patients_files = 10000,
n_mcmc_files = 0,
n_mcmc_thin = NULL,
flfll_seed = NULL,
flfll_offset = NULL,
verbose = FALSE,
max_sims = 99999L
)Character, name of a FACTS file.
Usually has a *.facts file extension.
Character, directory path to the files to generate.
Character, path to the log file generated by FLFLL.
Number of burn-in iterations for the MCMC.
Number of MCMC iterations used in inference.
Number of weeks*.csv files to save in output_path.
Number of patients*.csv files to save in
output_path.
Number of mcmc*.csv files to save in
output_path.
Number of thinning iterations for the MCMC.
Positive integer, random number generator seed for FLFLL.
This seed is only used for stochastic preprocessing steps for generating
the *.param files. It is not the random number generator seed
for the actual trial simulations. To set the trial simulation seed,
use the seed argument of run_facts(), run_engine(), or
one of the specific run_engine*() functions.
Integer, offset for the random number generator.
Logical, whether to print progress information to the R console.
Positive integer of length 1, maximum number of simulations
that will be allowed to run for certain engines like CRM
in subsequent calls to the engine. If the n_sims argument
of the engine is larger than max_sims, only max_sims
simulations will be run. The max_sims argument
only applies to FLFLL >= 6.4.1
and only needs to be set manually if you are manually calling
run_flfll() and then the engine instead of just run_facts().
Character, the value of output_path.
output_path is the directory path to the files generated by
run_flfll().
For advanced control over trial simulations, you must first call
run_flfll() and then call one of the engine functions
such as run_engine_contin().
run_flfll() generates the preparatory *.param files that the
run_engine_*() functions understand.
You will pass these *.param files or their parent
directory to param_files argument of run_engine_contin() etc.
# Can only run if system dependencies are configured:
if (file.exists(Sys.getenv("RFACTS_PATHS"))) {
facts_file <- get_facts_file_example("contin.facts") # example FACTS file
out <- run_flfll(facts_file, verbose = FALSE) # Generate param files.
# Run the simulations.
run_engine(
facts_file,
param_files = out,
n_sims = 1,
verbose = FALSE
)
read_patients(out)
}