Get the full sample structure from user input

Get the full sample structure from user input by looking at the OM data. If it cannot be unambiguously determined, this function will return an error describing what additional user input is required.

Usage

get_full_sample_struct(sample_struct, OM_out_dir)

Arguments

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.

OM_out_dir

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

Value

A list of the full sample structure, using names as input by the user input by the user (not r4ss names).