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Create the OM

Source: R/initOM.R
create_OM.Rd

This function manipulates the OM as needed so that it can be used as an operating model.

Usage

create_OM(
  OM_out_dir,
  overwrite = TRUE,
  writedat = TRUE,
  verbose = FALSE,
  nyrs = NULL,
  nyrs_assess = NULL,
  nscen = 1,
  scen_name = NULL,
  niter = 1,
  future_om_dat = NULL,
  verify_OM = TRUE,
  sample_struct_hist = NULL,
  sample_struct = NULL,
  seed = NULL
)

Arguments

OM_out_dir

The full path to the directory in which the OM is run.

overwrite

Allow existing files to be overwritten?

writedat

Should a new datafile be written?

verbose

Want verbose output? Defaults to FALSE.

nyrs

Number of years beyond the years included in the OM to run the MSE. A single integer value.

nyrs_assess

The number of years between assessments. This is used to structure the forecast file for use in the OM.

nscen

The scenario number

scen_name

The scenario name

niter

the iteration number

future_om_dat

An optional data_frame including changes that should be made after the end year of the input model. Including parameter variations, recruitment deviations, and implementation errors.

verify_OM

Should the model be run without estimation and some basic checks done to verify that the OM can run? Defaults to TRUE.

sample_struct_hist

An optional list including which years should be sampled for the historical period for the data generated from the OM. If this is left as NULL, then the same sampling scheme will be used as in the OM's data file. If it is not NULL, then each year.

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.

Value

A modified datafile

Author

Kathryn Doering & Nathan Vaughan