rbi (version 0.6.0)

libbi_run: Using the LibBi wrapper to launch LibBi

Description

The method run of an instance of libbi allows to launch libbi with a particular set of command line arguments.

Arguments

options

list of additional arguments to pass to the call to libbi

add_options

deprecated, replaced by options

log_file_name

path to a file to text file to report the output of libbi

init

initialisation of the model, either supplied as a list of values and/or data frames, or a (netcdf) file name, or a libbi object which has been run (in which case the output of that run is used as input)

input

input of the model, either supplied as a list of values and/or data frames, or a (netcdf) file name, or a libbi object which has been run (in which case the output of that run is used as input)

obs

observations of the model, either supplied as a list of values and/or data frames, or a (netcdf) file name, or a libbi object which has been run (in which case the output of that run is used as observations)

time_dim

The time dimension in any R objects that have been passed (init, input) and obs); if not given, will be guessed

...

any unrecognised options will be added to options

See Also

libbi

Examples

bi_object <- libbi$new(client = "sample",
                       model = system.file(package="rbi", "PZ.bi"),
                       options = list(sampler = "smc2"))
## Not run: bi_object$run(options=list(nthreads = 1), verbose = TRUE)
if (bi_object$run_flag) {
  bi_file_summary(bi_object$output_file_name)
}