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Format OM Observation Data for TMB Assessment Model #' Format data and observations from an `afscOM` operating model and update the model data and parameters required by the `SpatialSablefishAssessment` TMB assessment model.

format_em_data.Rd

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.

Usage

format_em_data(
  nyears,
  dem_params,
  land_caa,
  survey_indices,
  fxfish_caa_obs,
  ll_ac_obs,
  model_options,
  added_years = 1
)

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

one year worth of landed catch-at-age data (dimensins [1, nages, nsexes, nregions, nfleets])

survey_indices

one year worth of survey indices (LL RPN, LL RPW, and TW RPW)

fxfish_caa_obs

one year worth of catch-at-age observation from the fixed gear fishery

ll_ac_obs

one year worth of age composition observations frmo the longline survey

model_options

list of model options provided to the OM

added_year

the number of new years of data being added (should usually be 1)