Check sample_struct_list — check_sample

Check that list object sample_struct_list has the expected form, including the correct names, correct column names (as in r4ss), and that all values in the dataframes are integer or numeric. This does not check for if numeric or interger values make sense given the model used.

Usage

check_sample_struct(
  sample_struct,
  valid_names = list(catch = c("Yr", "Seas", "FltSvy", "SE"), CPUE = c("Yr", "Seas",
    "FltSvy", "SE"), lencomp = c("Yr", "Seas", "FltSvy", "Sex", "Part", "Nsamp"), agecomp
    = c("Yr", "Seas", "FltSvy", "Sex", "Part", "Ageerr", "Lbin_lo", "Lbin_hi", "Nsamp"),
    meanbodywt = c("Yr", "Seas", "FltSvy", "Part", "Type", "Std_in"), MeanSize_at_Age_obs
    = c("Yr", "Seas", "FltSvy", "Sex", "Part", "Ageerr", "N_"))
)

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.
valid_names: The list to compare sample_struct to.

Author

Kathryn Doering