Initial run of the OM — run

This function is used to initialize the OM and get either expected values or bootstrap.

Usage

run_OM(
  OM_dir,
  boot = TRUE,
  nboot = 1,
  init_run = FALSE,
  verbose = FALSE,
  debug_par_run = TRUE,
  sample_catch = FALSE,
  seed = NULL
)

OM_dir: The full path to the OM directory.
boot: Return the bootstrap dataset? If TRUE, function returns the number bootstrapped dataset specified in nboot. If FALSE, it returns the expected values.
nboot: The number bootstrapped data set. This value is only used if boot = TRUE. Note that this numbering does NOT correspond with the numbering in section of r4ss::SS_readdat. E.g., specifying section = 3 in SS_readdat is equivalent to specifying nboot = 1.
init_run: Is this the initial iteration of the OM? Defaults to FALSE.
verbose: Want verbose output? Defaults to FALSE.
debug_par_run: If set to TRUE, and the run fails, a new folder called error_check will be created, and the model will be run from control start values instead of ss.par. The 2 par files are then compared to help debug the issue with the model run. Defaults to TRUE.
sample_catch: Should catch be sampled or fixed at the OM values? Defaults to FALSE.
seed: A random seed so that reproducible results are possible.

Kathryn Doering