Use EM as the management strategy option.

Usage

EM(
  EM_out_dir = NULL,
  init_loop = TRUE,
  OM_dat,
  verbose = FALSE,
  nyrs_assess,
  dat_yrs,
  sample_struct = NULL,
  seed = NULL,
  OM_out_dir,
  ...
)

Arguments

EM_out_dir: Relative or absolute path to the estimation model, if using a model outside of the SSMSE package.
init_loop: Logical. If this is the first initialization loop of the MSE, init_loop should be TRUE. If it is in further loops, it should be FALSE.
OM_dat: An valid SS data file read in using r4ss. In particular, this should be sampled data.
verbose: Want verbose output? Defaults to FALSE.
nyrs_assess: The number of years between assessments. E.g., if an assessment is conducted every 3 years, put 3 here. A single integer value.
dat_yrs: Which years should be added to the new model? Ignored if init_loop is TRUE.
sample_struct: A optional list including which years, seasons, and fleets should be added from the OM into the EM for different types of data. If NULL, the data structure will try to be inferred from the pattern found for each of the datatypes within the EM datafiles. Include this structure for the number of years to extend the model out. Note that the data should be specified using the list component names and column names as in would be used in r4ss::SS_readdat(). The run_SSMSE_iter function examples give an example of what this structure should be. Running the function create_sample_struct() will also produce a sample_struct object in the correct form. Can be NULL only when MS is not EM.
seed: A random seed so that reproducible results are possible.
OM_out_dir: The full path to the directory in which the OM is run.
...: Any additional parameters

Author

Kathryn Doering