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Set up discards, fishery index, age composition, and length composition inputs

Setup_Mod_FishIdx_and_Comps.Rd

Populates input_list with observed fishery indices, age compositions, and length compositions (both pooled and population-specific) along with their usage indicators, likelihood types, composition structure types, input sample sizes, and overdispersion and correlation parameter starting values and mappings. Must be called after Setup_Mod_Catch_and_F.

Usage

Setup_Mod_FishIdx_and_Comps(
  input_list,
  ObsFishIdx,
  ObsFishIdx_SE,
  ObsFishIdx_pop = NULL,
  ObsFishIdx_pop_SE = NULL,
  UseFishIdx_pop = array(0, dim = c(input_list$data$n_pop, input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  fish_idx_type,
  UseFishIdx,
  ObsFishAgeComps,
  UseFishAgeComps,
  ISS_FishAgeComps = NULL,
  ObsFishLenComps,
  UseFishLenComps,
  ISS_FishLenComps = NULL,
  FishAgeComps_LikeType,
  FishLenComps_LikeType,
  FishAgeComps_Type,
  FishLenComps_Type,
  ObsFishAgeComps_pop = NULL,
  UseFishAgeComps_pop = array(0, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  ISS_FishAgeComps_pop = NULL,
  ObsFishLenComps_pop = NULL,
  UseFishLenComps_pop = array(0, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  ISS_FishLenComps_pop = NULL,
  FishAgeComps_pop_LikeType = rep("none", input_list$data$n_fish_fleets),
  FishLenComps_pop_LikeType = rep("none", input_list$data$n_fish_fleets),
  FishAgeComps_pop_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_fish_fleets, sep = ""),
  FishLenComps_pop_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_fish_fleets, sep = ""),
  ObsFishAgeComps_discard = array(0, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, length(input_list$data$ages),
    input_list$data$n_sexes, input_list$data$n_fish_fleets)),
  UseFishAgeComps_discard = array(0, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  ISS_FishAgeComps_discard = NULL,
  ObsFishLenComps_discard = array(0, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, length(input_list$data$lens),
    input_list$data$n_sexes, input_list$data$n_fish_fleets)),
  UseFishLenComps_discard = array(0, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  ISS_FishLenComps_discard = NULL,
  FishAgeComps_discard_LikeType = rep("none", input_list$data$n_fish_fleets),
  FishLenComps_discard_LikeType = rep("none", input_list$data$n_fish_fleets),
  FishAgeComps_discard_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_fish_fleets, sep = ""),
  FishLenComps_discard_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_fish_fleets, sep = ""),
  ObsFishAgeComps_discard_pop = NULL,
  UseFishAgeComps_discard_pop = array(0, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  ISS_FishAgeComps_discard_pop = NULL,
  ObsFishLenComps_discard_pop = NULL,
  UseFishLenComps_discard_pop = array(0, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  ISS_FishLenComps_discard_pop = NULL,
  FishAgeComps_discard_pop_LikeType = rep("none", input_list$data$n_fish_fleets),
  FishLenComps_discard_pop_LikeType = rep("none", input_list$data$n_fish_fleets),
  FishAgeComps_discard_pop_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_fish_fleets, sep = ""),
  FishLenComps_discard_pop_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_fish_fleets, sep = ""),
  ...
)

Arguments

input_list

Named list with $data, $par, $map, and $verbose sublists, as returned by upstream setup functions.

ObsFishIdx

Observed fishery CPUE or biomass index array [n_regions × n_years × n_seas × n_fish_fleets].

ObsFishIdx_SE

Standard errors of ObsFishIdx on the log scale, same dimensions as ObsFishIdx.

ObsFishIdx_pop

Observed population-specific fishery index array [n_pop × n_regions × n_years × n_seas × n_fish_fleets].

ObsFishIdx_pop_SE

Lognormal standard errors for ObsFishIdx_pop, same dimensions [n_pop × n_regions × n_years × n_seas × n_fish_fleets].

UseFishIdx_pop

Binary indicator array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. 1 = include population-specific index in likelihood; 0 = exclude. Default: all zeros.

fish_idx_type

Character vector of length n_fish_fleets specifying the index type for each fleet. "biom" = biomass; "abd" = abundance; "none" = no index for this fleet.

UseFishIdx

Binary indicator array [n_regions × n_years × n_seas × n_fish_fleets]. 1 = include index in the likelihood; 0 = exclude.

ObsFishAgeComps

Observed fishery age composition array [n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets]. Values may be raw counts or proportions; if proportions, supply ISS_FishAgeComps explicitly.

UseFishAgeComps

Binary indicator array [n_regions × n_years × n_seas × n_fish_fleets]. 1 = fit age compositions; 0 = exclude.

ISS_FishAgeComps

Input sample size array [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL (default), computed automatically by summing ObsFishAgeComps within each year–fleet–season–region cell according to FishAgeComps_Type.

ObsFishLenComps

Observed fishery length composition array [n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets]. Only required when input_list$data$fit_lengths == 1.

UseFishLenComps

Binary indicator array [n_regions × n_years × n_seas × n_fish_fleets]. 1 = fit length compositions; 0 = exclude.

ISS_FishLenComps

Input sample size array for length compositions [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL (default), derived automatically from ObsFishLenComps.

FishAgeComps_LikeType

Character vector of length n_fish_fleets specifying the likelihood for fishery age compositions. Options: "Multinomial", "Dirichlet-Multinomial", "iid-Logistic-Normal", "1d-Logistic-Normal", "2d-Logistic-Normal", "none".

FishLenComps_LikeType

Same as FishAgeComps_LikeType but for length compositions.

FishAgeComps_Type

Character vector defining the age composition structure (aggregation level) for each fleet and time period. Each element must follow the format "<type>_Year_<start>-<end>_Fleet_<f>" or "<type>_Year_<start>-terminal_Fleet_<f>". Valid types:

"agg"

Aggregated across regions and sexes (incompatible with "2d-Logistic-Normal").

"spltRspltS"

Split by region and sex.

"spltRjntS"

Split by region, summed jointly across sexes.

"none"

No composition data for this fleet and period.

Example: c("spltRjntS_Year_1-10_Fleet_1", "agg_Year_11-terminal_Fleet_1").

FishLenComps_Type

Same format and options as FishAgeComps_Type but applied to length compositions.

ObsFishAgeComps_pop

Observed population-specific fishery age composition array [n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets]. Required when any element of UseFishAgeComps_pop is 1.

UseFishAgeComps_pop

Binary indicator array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. 1 = fit population-specific age compositions; 0 = exclude. Default: all zeros.

ISS_FishAgeComps_pop

Input sample size array for population-specific age compositions [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL (default), computed automatically by summing ObsFishAgeComps_pop within each population–year–fleet–season–region cell according to FishAgeComps_pop_Type.

ObsFishLenComps_pop

Observed population-specific fishery length composition array [n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets]. Required when input_list$data$fit_lengths == 1 and any element of UseFishLenComps_pop is 1.

UseFishLenComps_pop

Binary indicator array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. 1 = fit population-specific length compositions; 0 = exclude. Default: all zeros.

ISS_FishLenComps_pop

Input sample size array for population-specific length compositions [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL (default), derived automatically from ObsFishLenComps_pop.

FishAgeComps_pop_LikeType

Character vector of length n_fish_fleets specifying the likelihood for population-specific fishery age compositions. Same options as FishAgeComps_LikeType. Default: "none" for all fleets.

FishLenComps_pop_LikeType

Character vector of length n_fish_fleets specifying the likelihood for population-specific fishery length compositions. Same options as FishLenComps_LikeType. Default: "none" for all fleets.

FishAgeComps_pop_Type

Character vector defining the composition structure for population-specific age compositions. Same format and options as FishAgeComps_Type. Default: "none" for all fleets across all years.

FishLenComps_pop_Type

Character vector defining the composition structure for population-specific length compositions. Same format and options as FishLenComps_Type. Default: "none" for all fleets across all years.

ObsFishAgeComps_discard

Observed fishery age composition from discards [n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets]. Structure must match ObsFishAgeComps.

UseFishAgeComps_discard

Binary indicator array for discard age compositions [n_regions × n_years × n_seas × n_fish_fleets]. 1 = include discard age compositions in likelihood; 0 = exclude.

ISS_FishAgeComps_discard

Input sample size array for discard age compositions [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL, derived automatically from ObsFishAgeComps_discard using FishAgeComps_discard_Type.

ObsFishLenComps_discard

Observed fishery length composition from discards [n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets]. Required if input_list$data$fit_lengths == 1.

UseFishLenComps_discard

Binary indicator array for discard length compositions [n_regions × n_years × n_seas × n_fish_fleets]. 1 = include discard length compositions in likelihood; 0 = exclude.

ISS_FishLenComps_discard

Input sample size array for discard length compositions [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL, derived automatically from ObsFishLenComps_discard.

FishAgeComps_discard_LikeType

Character vector of length n_fish_fleets specifying likelihood type for discard age compositions. Options:

"Multinomial"

Standard multinomial likelihood

"Dirichlet-Multinomial"

Overdispersed multinomial

"iid-Logistic-Normal"

Independent logistic-normal

"1d-Logistic-Normal"

1D correlated logistic-normal

"2d-Logistic-Normal"

2D correlated logistic-normal

"none"

No discard age composition likelihood

FishLenComps_discard_LikeType

Same specification as FishAgeComps_discard_LikeType, but for discard length compositions.

FishAgeComps_discard_Type

Character vector defining discard age composition structure by fleet and year block. Format: "<type>_Year_<start>-<end>_Fleet_<f>" or "<type>_Year_<start>-terminal_Fleet_<f>". Valid types:

"agg"

Aggregated across regions and sexes

"spltRspltS"

Split by region and sex

"spltRjntS"

Split by region, joint across sexes

"none"

No discard age composition

FishLenComps_discard_Type

Same format and options as FishAgeComps_discard_Type, applied to discard length compositions.

ObsFishAgeComps_discard_pop

Observed population-specific discard age composition array [n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets].

UseFishAgeComps_discard_pop

Binary indicator array for population-specific discard age compositions [n_pop × n_regions × n_years × n_seas × n_fish_fleets].

ISS_FishAgeComps_discard_pop

Input sample size array for population-specific discard age compositions [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL, computed from ObsFishAgeComps_discard_pop.

ObsFishLenComps_discard_pop

Observed population-specific discard length composition array [n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets].

UseFishLenComps_discard_pop

Binary indicator array for population-specific discard length compositions [n_pop × n_regions × n_years × n_seas × n_fish_fleets].

ISS_FishLenComps_discard_pop

Input sample size array for population-specific discard length compositions [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. If NULL, derived from ObsFishLenComps_discard_pop.

FishAgeComps_discard_pop_LikeType

Character vector of length n_fish_fleets specifying likelihood type for population-specific discard age compositions. Same options as FishAgeComps_discard_LikeType.

FishLenComps_discard_pop_LikeType

Same as above but for discard length compositions.

FishAgeComps_discard_pop_Type

Character vector defining structure for population-specific discard age compositions. Same format as FishAgeComps_discard_Type.

FishLenComps_discard_pop_Type

Character vector defining structure for population-specific discard length compositions. Same format as FishLenComps_discard_Type.

...

Optional starting value overrides for overdispersion and correlation parameters.

Value

The input input_list with $data, $par, and $map updated with all fishery index and composition fields, including pooled and population-specific observed arrays, computed or supplied ISS arrays, integer-coded likelihood and composition type matrices, overdispersion parameters, and their factor maps.

Details

When ISS_FishAgeComps, ISS_FishLenComps, ISS_FishAgeComps_pop, or ISS_FishLenComps_pop are NULL, input sample sizes are derived automatically by summing the observed composition arrays within each year–fleet–season–region cell, consistent with the specified composition type.

See also

Other Model Setup: Setup_Mod_Biologicals(), Setup_Mod_Catch_and_F(), Setup_Mod_Dim(), Setup_Mod_Discard_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()