Set up discard age and length composition inputs

Set up discard age and length composition inputs

Usage

Setup_Mod_Discard_Comps(
  input_list,
  ObsFishAgeComps_discard,
  UseFishAgeComps_discard,
  ISS_FishAgeComps_discard,
  ObsFishLenComps_discard,
  UseFishLenComps_discard,
  ISS_FishLenComps_discard,
  FishAgeComps_discard_LikeType,
  FishLenComps_discard_LikeType,
  FishAgeComps_discard_Type,
  FishLenComps_discard_Type,
  ObsFishAgeComps_discard_pop,
  UseFishAgeComps_discard_pop,
  ISS_FishAgeComps_discard_pop,
  ObsFishLenComps_discard_pop,
  UseFishLenComps_discard_pop,
  ISS_FishLenComps_discard_pop,
  FishAgeComps_discard_pop_LikeType,
  FishLenComps_discard_pop_LikeType,
  FishAgeComps_discard_pop_Type,
  FishLenComps_discard_pop_Type,
  ...
)

Arguments

input_list

Main model input list containing data, parameters, and mapping structures.

ObsFishAgeComps_discard

5D array of observed discard age compositions: [n_regions, n_years, n_seas, n_sexes, n_fish_fleets]

UseFishAgeComps_discard

Matrix indicating whether discard age comps are used: [n_regions, n_years, n_seas, n_fish_fleets]

ISS_FishAgeComps_discard

Optional ISS (effective sample size) array for discard age comps: [n_regions, n_years, n_seas, n_sexes, n_fish_fleets]

ObsFishLenComps_discard

6D array of observed discard length compositions: [n_regions, n_years, n_seas, n_lens, n_sexes, n_fish_fleets]

UseFishLenComps_discard

Matrix indicating whether discard length comps are used: [n_regions, n_years, n_seas, n_fish_fleets]

ISS_FishLenComps_discard

Optional ISS array for discard length comps: [n_regions, n_years, n_seas, n_sexes, n_fish_fleets]

FishAgeComps_discard_LikeType

Character vector (length n_fish_fleets) specifying likelihood type: one of c("none","Multinomial","Dirichlet-Multinomial","iid-Logistic-Normal","1d-Logistic-Normal","2d-Logistic-Normal")

FishLenComps_discard_LikeType

Character vector (length n_fish_fleets) specifying likelihood type

FishAgeComps_discard_Type

List/encoded character strings defining composition structure by year and fleet.

FishLenComps_discard_Type

List/encoded character strings defining composition structure by year and fleet.

ObsFishAgeComps_discard_pop

6D array of population-specific discard age comps: [n_pop, n_regions, n_years, n_seas, n_sexes, n_fish_fleets]

UseFishAgeComps_discard_pop

5D array indicating use of population age comps: [n_pop, n_regions, n_years, n_seas, n_fish_fleets]

ISS_FishAgeComps_discard_pop

Optional ISS array for population discard age comps: [n_pop, n_regions, n_years, n_seas, n_sexes, n_fish_fleets]

ObsFishLenComps_discard_pop

7D array of population-specific discard length comps: [n_pop, n_regions, n_years, n_seas, n_lens, n_sexes, n_fish_fleets]

UseFishLenComps_discard_pop

5D array indicating use of population length comps: [n_pop, n_regions, n_years, n_seas, n_fish_fleets]

ISS_FishLenComps_discard_pop

Optional ISS array for population length comps: [n_pop, n_regions, n_years, n_seas, n_sexes, n_fish_fleets]

FishAgeComps_discard_pop_LikeType

Character vector (length n_fish_fleets) for population age likelihood types.

FishLenComps_discard_pop_LikeType

Character vector (length n_fish_fleets) for population length likelihood types.

FishAgeComps_discard_pop_Type

Encoded structure definitions for population age comps by year/fleet.

FishLenComps_discard_pop_Type

Encoded structure definitions for population length comps by year/fleet.

...

Optional starting values for parameters (e.g., dispersion, correlation)

Value

The input input_list updated with:

• discard age and length composition data structures

• ISS (effective sample size) arrays (computed or supplied)

• likelihood type mappings (integer-coded)

• composition type matrices by year and fleet

• population-specific discard composition structures

• parameter arrays for dispersion and correlation

• mapping configurations for estimation

Details

All composition arrays follow consistent indexing conventions:

• Age compositions: [region, year, season, sex, fleet]

• Length compositions: [region, year, season, length, sex, fleet]

• Population age comps: [pop, region, year, season, sex, fleet]

• Population length comps: [pop, region, year, season, length, sex, fleet]

See also

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