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Set up discard age and length composition inputs

Setup_Mod_Discard_Comps.Rd

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,
  FishAgeComps_discard_bins = NULL,
  FishLenComps_discard_bins = NULL,
  FishAgeComps_discard_pop_bins = NULL,
  FishLenComps_discard_pop_bins = NULL,
  ...
)

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","iid-Logistic-Normal-miss0","1d-Logistic-Normal-miss0","2d-Logistic-Normal-miss0")

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.

FishAgeComps_discard_bins

Which age bins each fishery fleet's discard age composition is fitted over. Supply a list with one element per fleet, each a vector of bin indices or NULL for all bins, or an [n_obs_ages x n_fish_fleets] array of 0/1 weights. Indices refer to observed bins, that is after any ageing error. Excluded bins are left out of the likelihood rather than being forced to be explained. Default NULL, which fits all bins for all fleets.

FishLenComps_discard_bins

Which length bins each fishery fleet's discard length composition is fitted over, in the same format.

FishAgeComps_discard_pop_bins

Which age bins each fishery fleet's population-specific discard age composition is fitted over, in the same format.

FishLenComps_discard_pop_bins

Which length bins each fishery fleet's population-specific discard length composition is fitted over, in the same format.

...

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()