Simulate OM Observation Data for TMB Assessment Model — simulate_em

Format data and observations from an `afscOM` operating model and update the model data and parameters required by the `SpatialSablefishAssessment` TMB assessment model.

Usage

simulate_em_data(
  nyears,
  dem_params,
  land_caa,
  survey_indices,
  fxfish_caa_obs,
  twfish_caa_obs,
  ll_ac_obs,
  tw_ac_obs,
  ll_srv_indic,
  tw_srv_indic,
  model_options,
  added_years = 1,
  file_suffix = ""
)

Arguments

nyears: the number of years of data that will be passed to the model
dem_params: demographic parameter matrices subsetted to 1 year
land_caa: nyears worth of landed catch-at-age data (dimensins [1, nages, nsexes, nregions, nfleets])
survey_indices: nyears worth of survey indices (LL RPN, LL RPW, and TW RPW)
fxfish_caa_obs: nyears worth of catch-at-age observation from the fixed gear fishery
twfish_caa_obs: nyears worth of catch-at-age observation from the trawl gear fishery
ll_ac_obs: nyears worth of age composition observations frmo the longline survey
tw_ac_obs: nyears worth of age composition observations frmo the trawl survey
model_options: list of model options provided to the OM
file_suffix: suffix to append to saved outputs
added_year: the number of new years of data being added (should usually be 1)

Details

This function requires the existence of 'data/sablefish_em_data_2022.RDS', and 'data/sablefish_em_par_2022.RDS' files, which come packaged with the `SablefishMSE` codebase.