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

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

Usage

Setup_Mod_SrvIdx_and_Comps(
  input_list,
  ObsSrvIdx,
  ObsSrvIdx_SE,
  UseSrvIdx,
  srv_idx_type,
  ObsSrvAgeComps,
  UseSrvAgeComps,
  ObsSrvLenComps,
  UseSrvLenComps,
  ISS_SrvAgeComps = NULL,
  ISS_SrvLenComps = NULL,
  SrvAgeComps_LikeType,
  SrvLenComps_LikeType,
  SrvAgeComps_Type,
  SrvLenComps_Type,
  SrvAge_comp_agg_type = NULL,
  SrvLen_comp_agg_type = NULL,
  ...
)

Arguments

input_list

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

ObsSrvIdx

Observed survey index data as a numeric array with dimensions [n_regions, n_years, n_srv_fleets].

ObsSrvIdx_SE

Standard errors associated with ObsSrvIdx, also dimensioned [n_regions, n_years, n_srv_fleets].

UseSrvIdx

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

srv_idx_type

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

ObsSrvAgeComps

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

UseSrvAgeComps

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

ObsSrvLenComps

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

UseSrvLenComps

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

ISS_SrvAgeComps

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

ISS_SrvLenComps

Same as ISS_SrvAgeComps, but for length compositions.

SrvAgeComps_LikeType

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

SrvLenComps_LikeType

Same as SrvAgeComps_LikeType, but for survey length composition data.

SrvAgeComps_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").

SrvLenComps_Type

Same as SrvAgeComps_Type, but for length compositions.

SrvAge_comp_agg_type

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

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

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

Default is NULL.

SrvLen_comp_agg_type

Optional integer vector of length n_srv_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_SrvAge_theta, ln_SrvLen_theta, ln_SrvAge_theta_agg, ln_SrvLen_theta_agg).