Setup observed fishery indices and composition data (age and length comps)

Setup observed fishery indices and composition data (age and length comps)

Usage

Setup_Mod_FishIdx_and_Comps(
  input_list,
  ObsFishIdx,
  ObsFishIdx_SE,
  fish_idx_type,
  UseFishIdx,
  ObsFishAgeComps,
  UseFishAgeComps,
  ISS_FishAgeComps = NULL,
  ObsFishLenComps,
  UseFishLenComps,
  ISS_FishLenComps = NULL,
  FishAgeComps_LikeType,
  FishLenComps_LikeType,
  FishAgeComps_Type,
  FishLenComps_Type,
  FishAge_comp_agg_type = NULL,
  FishLen_comp_agg_type = NULL,
  ...
)

Arguments

input_list

List containing a data list, parameter list, and map list

ObsFishIdx

Observed fishery index data as a numeric array with dimensions [n_regions, n_years, n_fish_fleets].

ObsFishIdx_SE

Standard errors associated with ObsFishIdx, also dimensioned [n_regions, n_years, n_fish_fleets].

fish_idx_type

Character vector of length n_fish_fleets specifying the type of index data. Options are "abd" for abundance, "biom" for biomass, and "none" if no index is available.

UseFishIdx

Logical or binary indicator array ([n_regions, n_years, n_fish_fleets]) specifying whether to include a fishery index in the likelihood (1) or ignore it (0).

ObsFishAgeComps

Observed fishery age composition data as a numeric array with dimensions [n_regions, n_years, n_ages, n_sexes, n_fish_fleets]. Values should reflect counts or proportions (not required to sum to 1, but should be on a comparable scale).

UseFishAgeComps

Indicator array ([n_regions, n_years, n_fish_fleets]) specifying whether to fit fishery age composition data (1) or ignore it (0).

ISS_FishAgeComps

Input sample size for age compositions, array dimensioned [n_regions, n_years, n_sexes, n_fish_fleets]. Required if observed age comps are normalized (i.e., sum to 1), to correctly scale the contribution to the likelihood.

ObsFishLenComps

Observed fishery length composition data as a numeric array with dimensions [n_regions, n_years, n_lens, n_sexes, n_fish_fleets]. Values should reflect counts or proportions.

UseFishLenComps

Indicator array ([n_regions, n_years, n_fish_fleets]) specifying whether to fit fishery length composition data (1) or ignore it (0).

ISS_FishLenComps

Same as ISS_FishAgeComps, but for length compositions.

FishAgeComps_LikeType

Character vector of length n_fish_fleets specifying the likelihood type used for fishery age composition data. Options include "Multinomial", "Dirichlet-Multinomial", and "iid-Logistic-Normal". Use "none" to omit the likelihood.

FishLenComps_LikeType

Same as FishAgeComps_LikeType, but for fishery length composition data.

FishAgeComps_Type

Character vector specifying how age compositions are structured by fleet and year range. Options include:

• "agg": Aggregated across regions and sexes.

• "spltRspltS": Split by region and by sex (compositions sum to 1 within region-sex group).

• "spltRjntS": Split by region but summed jointly across sexes.

• "none": No composition data used.

Format each element as "<type>_Year_<start>-<end>_Fleet_<fleet number>" (e.g., "agg_Year_1-10_Fleet_1").

FishLenComps_Type

Same as FishAgeComps_Type, but for length compositions.

FishAge_comp_agg_type

Optional integer vector of length n_fish_fleets specifying the order of operations for aggregating age compositions when FishAgeComps_Type == "agg".

• 0: Normalize, then aggregate, then apply ageing error, then normalize again.

• 1: Aggregate first, normalize, then apply ageing error.

Default is NULL.

FishLen_comp_agg_type

Optional integer vector of length n_fish_fleets specifying the order of operations for aggregating length compositions.

• 0: Do not normalize before applying size–age transition.

• 1: Normalize before applying size–age transition.

Default is NULL.

...

Additional arguments specifying starting values for overdispersion parameters (e.g., ln_FishAge_theta, ln_FishLen_theta, ln_FishAge_theta_agg, ln_FishLen_theta_agg).