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Setup fishing mortality and catch observations

Setup_Mod_Catch_and_F.Rd

Setup fishing mortality and catch observations

Usage

Setup_Mod_Catch_and_F(
  input_list,
  ObsCatch,
  catch_units = array("biom", dim = c(input_list$data$n_regions,
    input_list$data$n_fish_fleets)),
  Catch_Type = array(1, dim = c(length(input_list$data$years),
    input_list$data$n_fish_fleets)),
  UseCatch,
  Use_F_pen = 1,
  est_all_regional_F = 1,
  sigmaC_spec = "fix",
  sigmaC_agg_spec = "fix",
  sigmaF_spec = "fix",
  sigmaF_agg_spec = "fix",
  ...
)

Arguments

input_list

A list containing data, parameters, and map lists used by the model.

ObsCatch

Numeric array of observed catches, dimensioned [n_regions, n_years, n_fish_fleets].

catch_units

Catch units - Array dimensioned by n_regions x n_fish_fleets

  • "abd": Catch units in abundance

  • "biom": Catch units in biomass (default)

Catch_Type

Integer matrix with dimensions [n_years, n_fish_fleets], specifying catch data types:

  • 0: Use aggregated catch data for the year.

  • 1: Use region-specific catch data for the year.

UseCatch

Indicator array [n_regions, n_years, n_fish_fleets] specifying whether to include catch data in the fit:

  • 0: Do not use catch data.

  • 1: Use catch data and fit.

Use_F_pen

Integer flag indicating whether to apply a fishing mortality penalty:

  • 0: Do not apply penalty.

  • 1: Apply penalty.

est_all_regional_F

Integer flag indicating whether all regional fishing mortality deviations are estimated:

  • 0: Some fishing mortality deviations are aggregated across regions.

  • 1: All fishing mortality deviations are regional.

sigmaC_spec

Character string specifying observation error structure for catch data. Default behavior fixes sigmaC at a starting value of 1e-3 (log-scale ln_sigmaC = log(1e-3)) for all regions, years, and fleets. Other options include:

  • "est_shared_f": Estimate sigmaC shared across fishery fleets, unique by region and year.

  • "est_shared_r": Estimate sigmaC shared across regions, unique by fleet and year.

  • "est_shared_y": Estimate sigmaC shared across years, unique by region and fleet.

  • "est_shared_r_f": Estimate sigmaC shared across regions and fleets, unique by year.

  • "est_shared_f_y": Estimate sigmaC shared across fleets and years, unique by region.

  • "est_shared_r_y": Estimate sigmaC shared across regions and years, unique by fleet.

  • "est_shared_r_y_f": Estimate single sigmaC shared across regions, years, and fleets.

  • "fix": Fix sigmaC at the starting value.

  • "est_all": Estimate separate sigmaC for each region, year, and fleet combination.

sigmaC_agg_spec

Character string specifying process error structure for aggregated catch observation error. Default fixes sigmaC_agg at the starting value (log-scale sigmaC_agg). Other options include:

  • "est_shared_f": Estimate sigmaC_agg shared across fishery fleets, unique by year.

  • "est_shared_y": Estimate sigmaC_agg shared across years, unique by fleet.

  • "est_shared_y_f": Estimate single sigmaC_agg shared across years and fleets.

  • "fix": Fix at the starting value.

  • "est_all": Estimate separate parameters for each year and fleet combination.

sigmaF_spec

Character string specifying process error structure for fishing mortality. Default fixes sigmaF at 1 on the log scale (i.e., ln_sigmaF = 0). Other options include:

  • "est_shared_f": Estimate sigmaF shared across fishery fleets.

  • "est_shared_r": Estimate sigmaF shared across regions but unique by fleet.

  • "est_shared_r_f": Estimate sigmaF shared across regions and fleets.

  • "fix": Fix sigmaF at the starting value.

  • "est_all": Estimate separate sigmaF for each region and fleet.

sigmaF_agg_spec

Character string specifying process error structure for aggregated fishing mortality. Default fixes sigmaF_agg at the starting value (log-scale ln_sigmaF_agg). Other options include:

  • "est_shared_f": Estimate sigmaF_agg shared across fishery fleets.

  • "fix": Fix at the starting value.

  • "est_all": Estimate separate parameters for each fishery fleet.

...

Additional arguments specifying starting values for ln_sigmaC, ln_sigmaF, and ln_sigmaF_agg.

See also

Other Model Setup: Setup_Mod_Biologicals(), Setup_Mod_Dim(), Setup_Mod_FishIdx_and_Comps(), Setup_Mod_Fishsel_and_Q(), Setup_Mod_Movement(), Setup_Mod_Rec(), Setup_Mod_SrvIdx_and_Comps(), Setup_Mod_Srvsel_and_Q(), Setup_Mod_Tagging(), Setup_Mod_Weighting()