Set up discard age and length composition inputs

Sets the observed discard compositions, pooled and population-specific, with their use flags, input sample sizes, likelihood and composition types, and the overdispersion and correlation parameters and maps.

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 with data, parameter and mapping lists.

ObsFishAgeComps_discard

Observed discard age compositions [n_regions, n_years, n_seas, n_sexes, n_fish_fleets].

UseFishAgeComps_discard

Use flags [n_regions, n_years, n_seas, n_fish_fleets].

ISS_FishAgeComps_discard

Optional input sample sizes [n_regions, n_years, n_seas, n_sexes, n_fish_fleets].

ObsFishLenComps_discard

Observed discard length compositions [n_regions, n_years, n_seas, n_lens, n_sexes, n_fish_fleets].

UseFishLenComps_discard

Use flags [n_regions, n_years, n_seas, n_fish_fleets].

ISS_FishLenComps_discard

Optional input sample sizes [n_regions, n_years, n_seas, n_sexes, n_fish_fleets].

FishAgeComps_discard_LikeType, FishLenComps_discard_LikeType

Character vectors [n_fish_fleets], one of "none", "Multinomial", "Dirichlet-Multinomial", the three logistic-normal forms or their three -miss0 counterparts.

FishAgeComps_discard_Type, FishLenComps_discard_Type

Encoded composition structure by year and fleet.

ObsFishAgeComps_discard_pop

Observed population-specific discard age compositions [n_pop, n_regions, n_years, n_seas, n_sexes, n_fish_fleets].

UseFishAgeComps_discard_pop

Use flags [n_pop, n_regions, n_years, n_seas, n_fish_fleets].

ISS_FishAgeComps_discard_pop

Optional input sample sizes [n_pop, n_regions, n_years, n_seas, n_sexes, n_fish_fleets].

ObsFishLenComps_discard_pop

Observed population-specific discard length compositions [n_pop, n_regions, n_years, n_seas, n_lens, n_sexes, n_fish_fleets].

UseFishLenComps_discard_pop

Use flags [n_pop, n_regions, n_years, n_seas, n_fish_fleets].

ISS_FishLenComps_discard_pop

Optional input sample sizes [n_pop, n_regions, n_years, n_seas, n_sexes, n_fish_fleets].

FishAgeComps_discard_pop_LikeType, FishLenComps_discard_pop_LikeType

Character vectors [n_fish_fleets] for the population-specific discard compositions.

FishAgeComps_discard_pop_Type, FishLenComps_discard_pop_Type

Encoded composition structure for the population-specific discard compositions.

FishAgeComps_discard_bins

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

FishLenComps_discard_bins, FishAgeComps_discard_pop_bins, FishLenComps_discard_pop_bins

Which bins the discard length, population-specific discard age and population-specific discard length compositions are fitted over, in the same format as FishAgeComps_discard_bins.

...

Optional starting values for the overdispersion and correlation parameters.

Value

input_list with the discard composition arrays, the computed or supplied input sample sizes, the integer-coded likelihood types, the composition type matrices by year and fleet, the population-specific discard structures, and the overdispersion and correlation parameters with their maps.

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()