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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_Type,
  UseCatch,
  Use_F_pen = 1,
  est_all_regional_F = 1,
  Catch_Constant = NULL,
  sigmaC_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_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.

Catch_Constant

Numeric vector of length n_fish_fleets specifying constants to add to catch observations.

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 and fleets. Other options include:

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

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

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

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

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

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.