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

Sets the observed fishery indices and compositions, pooled and population-specific, with their use flags, likelihood types, composition types, input sample sizes and the overdispersion and correlation starting values and maps. A NULL ISS_* argument is summed from the matching observed array within each year, fleet, season and region cell, following that data source's composition type. Call after Setup_Mod_Catch_and_F.

Usage

Setup_Mod_FishIdx_and_Comps(
  input_list,
  ObsFishIdx,
  ObsFishIdx_SE,
  sigmaFishIdx_spec = "fix",
  sigmaFishIdx_map = NULL,
  sigmaFishIdx_pop_spec = "fix",
  sigmaFishIdx_pop_map = NULL,
  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,
  t_fish = array(0, dim = c(input_list$data$n_regions, input_list$data$n_seas,
    input_list$data$n_fish_fleets)),
  FishLenComps_sel = rep("age", input_list$data$n_fish_fleets),
  fish_waa_selected = rep(0, input_list$data$n_fish_fleets),
  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 = ""),
  fish_idx_ages = NULL,
  FishAgeComps_bins = NULL,
  FishLenComps_bins = NULL,
  Fish_caal_bins = NULL,
  FishAgeComps_pop_bins = NULL,
  FishLenComps_pop_bins = NULL,
  FishIdx_LikeType = rep("lognormal", input_list$data$n_fish_fleets),
  FishIdx_seas_Type = NULL,
  FishIdx_pop_seas_Type = NULL,
  FishAgeComps_seas_Type = NULL,
  FishAgeComps_pop_seas_Type = NULL,
  FishLenComps_seas_Type = NULL,
  FishLenComps_pop_seas_Type = NULL,
  FishAgeComps_discard_seas_Type = NULL,
  FishAgeComps_discard_pop_seas_Type = NULL,
  FishLenComps_discard_seas_Type = NULL,
  FishLenComps_discard_pop_seas_Type = NULL,
  FishIdx_Cov = NULL,
  ObsFish_caal = NULL,
  UseFish_caal = NULL,
  ISS_Fish_caal = NULL,
  Fish_caal_LikeType = rep("none", input_list$data$n_fish_fleets),
  Fish_caal_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, obs_len_bins(input_list),
    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.
ObsFishIdx: Observed fishery CPUE or biomass index array [n_regions × n_years × n_seas × n_fish_fleets].
ObsFishIdx_SE: Log-scale standard errors of ObsFishIdx, same dims.
sigmaFishIdx_spec, sigmaFishIdx_pop_spec: The estimated component of the aggregated and population-specific fishery index observation error, one value per fleet. "fix" (default) uses the reported standard errors as they are. "est_additive" adds an estimated component to them, "est_quadrature" adds it in quadrature, and "est_replace" replaces them. An estimated component is confounded with a likelihood weight, since a weight on a normal likelihood is the same statement as dividing the variance, and Setup_Mod_Weighting warns when both are used. A fleet with a multivariate normal index takes its scale from the supplied covariance and cannot have one, which is an error.
sigmaFishIdx_map, sigmaFishIdx_pop_map: Optional integer vectors [n_fish_fleets] of estimation groups for ln_sigmaFishIdx and ln_sigmaFishIdx_pop. Fleets sharing a value share a parameter and NA holds a fleet at its starting value. Defaults to one free parameter per fleet.
ObsFishIdx_pop: Observed population-specific index array [n_pop × n_regions × n_years × n_seas × n_fish_fleets].
ObsFishIdx_pop_SE: Lognormal standard errors for ObsFishIdx_pop, same dims.
UseFishIdx_pop: Binary array dimensioned like ObsFishIdx_pop. Default all zeros.
fish_idx_type: Character vector [n_fish_fleets]: "biom", "abd", or "none".
t_fish: Array [n_regions x n_seas x n_fish_fleets] of the fraction of the season elapsed when each index is observed. Numbers at age are decayed by exp(-t_fish * ZAA) before the index is formed, as t_srv does for surveys. Default 0; use 0.5 for a mid-season index.
FishLenComps_sel: Character vector [n_fish_fleets], whether length-based selectivity applies before or after the fish are spread over lengths. "age" (default) selects at age and spreads afterwards, so the length composition within an age is the key's. "length" spreads first and selects length by length, so the long fish of an age are taken more often. The key is the fleet's own at t_fish, and length-based fishery selectivity is required. The two give different expected compositions.
fish_waa_selected: Integer vector [n_fish_fleets] (0/1). With weight at age derived from growth and length-based selectivity, 1 makes the fleet's catch biomass use the mean weight of the fish it takes at each age, $\sum_l P(l \mid a) s(l) w(l) / \sum_l P(l \mid a) s(l)$, rather than the population mean weight. With flat or age-based selectivity the two agree.
UseFishIdx: Binary array dimensioned like ObsFishIdx, 1 to include the index in the likelihood.
ObsFishAgeComps: Observed fishery age composition array [n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets], raw counts or proportions; supply ISS_FishAgeComps for proportions.
UseFishAgeComps: Binary array [n_regions × n_years × n_seas × n_fish_fleets], 1 to fit the age compositions.
ISS_FishAgeComps: Input sample size array [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL (default) sums ObsFishAgeComps.
ObsFishLenComps: Observed fishery length composition array [n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets]. Only needed when input_list$data$fit_lengths == 1.
UseFishLenComps: Binary array [n_regions × n_years × n_seas × n_fish_fleets], 1 to fit the length compositions.
ISS_FishLenComps: Input sample size array [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL (default) sums ObsFishLenComps.
FishAgeComps_LikeType: Character vector [n_fish_fleets]: "Multinomial", "Dirichlet-Multinomial", "iid-Logistic-Normal", "1d-Logistic-Normal", "2d-Logistic-Normal", the three -miss0 forms, which drop the empty bins and scale the standard deviation by the input sample size, or "none".
FishLenComps_LikeType: As FishAgeComps_LikeType, for length compositions.
FishAgeComps_Type: Character vector of the composition structure per fleet and time period, each "<type>_Year_<start>-<end>_Fleet_<f>" with "terminal" allowed as the end year. Types are "agg" (aggregated across regions and sexes, not valid with "2d-Logistic-Normal"), "spltRspltS" (split by region and sex), "spltRjntS" (split by region, joint across sexes) and "none". For example c("spltRjntS_Year_1-10_Fleet_1", "agg_Year_11-terminal_Fleet_1").
FishLenComps_Type: As FishAgeComps_Type, for length compositions.
ObsFishAgeComps_pop: Observed population-specific age composition array [n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets]. Required when any UseFishAgeComps_pop is 1.
UseFishAgeComps_pop: Binary array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. Default all zeros.
ISS_FishAgeComps_pop: Input sample size array [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL (default) sums ObsFishAgeComps_pop.
ObsFishLenComps_pop: Observed population-specific length composition array [n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets]. Required when fit_lengths == 1 and any UseFishLenComps_pop is 1.
UseFishLenComps_pop: Binary array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. Default all zeros.
ISS_FishLenComps_pop: Input sample size array [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL (default) sums ObsFishLenComps_pop.
FishAgeComps_pop_LikeType, FishLenComps_pop_LikeType: Character vectors [n_fish_fleets] for the population-specific compositions, with the same options as FishAgeComps_LikeType. Default "none".
FishAgeComps_pop_Type, FishLenComps_pop_Type: Composition structure for the population-specific compositions, in the same format as FishAgeComps_Type. Default "none" for every fleet and year.
fish_idx_ages: Which ages contribute to each fleet's index total, either a list with one element per fleet (a vector of ages, or NULL for all) or an [n_ages x n_fish_fleets] array of 0/1 weights. NULL (default) uses every age. The compositions are unaffected.
FishAgeComps_bins: Which age bins each fleet's 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. Observed and expected are both restricted to the named bins and renormalized within them, so excluded bins leave the likelihood rather than being forced to be explained. Indices are observed bins, after any ageing error. For sex-joint comps the named bins are dropped from each sex's block, so the sex ratio becomes the ratio within the fitted bins. Every fleet must keep at least two bins. Default NULL, all bins.
FishLenComps_bins: Which length bins each fleet's length composition is fitted over, as FishAgeComps_bins. Indices are observed length bins, after any LenBinMap.
Fish_caal_bins: Which age bins each fleet's CAAL data are fitted over, as FishAgeComps_bins, applied to every length bin's row of ages alike.
FishAgeComps_pop_bins, FishLenComps_pop_bins: Which bins each fleet's population-specific age and length compositions are fitted over, as FishAgeComps_bins.
FishIdx_LikeType: Character vector [n_fish_fleets] of each index's error structure: "lognormal" (default, standard errors on the log scale), "normal" (arithmetic scale), or "mvn" (multivariate normal on the arithmetic scale with a fixed covariance from FishIdx_Cov). One-step-ahead residuals are available for lognormal fleets only. A fleet's population-specific index follows the same choice for the first two and stays lognormal under "mvn", whose covariance describes the regional series alone.
FishIdx_seas_Type, FishIdx_pop_seas_Type, FishAgeComps_seas_Type, FishAgeComps_pop_seas_Type, FishLenComps_seas_Type, FishLenComps_pop_seas_Type, FishAgeComps_discard_seas_Type, FishAgeComps_discard_pop_seas_Type, FishLenComps_discard_seas_Type, FishLenComps_discard_pop_seas_Type: Whether a seasonal model reports this data source once a season or once a year, one value for every fleet or one per fleet. "spltSeas" (default) fits the observation against the prediction for the season it sits in; "aggSeas" sums the prediction over the year's seasons and fits one observation. Under "aggSeas" the observation stays in the season it was placed in, exactly one season per region and year may be on in the matching Use array, and the likelihood lands in that season. An index measured at a point in time belongs in its own season.
FishIdx_Cov: List with one element per fleet holding the fixed covariance for "mvn" fleets and NULL otherwise. Each matrix is square with one row per observation the fleet fits, ordered as they appear when scanning that fleet's UseFishIdx slice in array order.
ObsFish_caal: Observed conditional age-at-length array [n_regions x n_years x n_seas x n_lens x n_ages x n_sexes x n_fish_fleets]. An observation is the age composition of the fish aged from one length bin, so the age dim of each length row is what is fit. NULL (default) for no CAAL data.
UseFish_caal: Use flags [n_regions x n_years x n_seas x n_lens x n_fish_fleets]. Length bins with no aged fish take a zero and are skipped.
ISS_Fish_caal: Input sample sizes [n_regions x n_years x n_seas x n_lens x n_sexes x n_fish_fleets], the number aged within each length bin rather than the number measured. Summed from ObsFish_caal when NULL.
Fish_caal_LikeType: Character vector [n_fish_fleets]: "none", "Multinomial" or "Dirichlet-Multinomial". The logistic-normal families are not available for CAAL, since a length bin's age sample is small and mostly zeros.
Fish_caal_Type: Composition type, in the same "CompType_Year_x-y_Fleet_z" vocabulary as the marginal compositions.
ObsFishAgeComps_discard: Observed discard age composition [n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets], structured as ObsFishAgeComps.
UseFishAgeComps_discard: Binary array [n_regions × n_years × n_seas × n_fish_fleets].
ISS_FishAgeComps_discard: Input sample size array [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL sums ObsFishAgeComps_discard.
ObsFishLenComps_discard: Observed discard length composition [n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets]. Required when fit_lengths == 1.
UseFishLenComps_discard: Binary array [n_regions × n_years × n_seas × n_fish_fleets].
ISS_FishLenComps_discard: Input sample size array [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL sums ObsFishLenComps_discard.
FishAgeComps_discard_LikeType, FishLenComps_discard_LikeType: Character vectors [n_fish_fleets] for the discard compositions, with the same options as FishAgeComps_LikeType.
FishAgeComps_discard_Type, FishLenComps_discard_Type: Composition structure for the discard compositions, in the same format as FishAgeComps_Type.
ObsFishAgeComps_discard_pop: Observed population-specific discard age composition [n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets].
UseFishAgeComps_discard_pop: Binary array [n_pop × n_regions × n_years × n_seas × n_fish_fleets].
ISS_FishAgeComps_discard_pop: Input sample size array [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL sums ObsFishAgeComps_discard_pop.
ObsFishLenComps_discard_pop: Observed population-specific discard length composition [n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets].
UseFishLenComps_discard_pop: Binary array [n_pop × n_regions × n_years × n_seas × n_fish_fleets].
ISS_FishLenComps_discard_pop: Input sample size array [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. NULL sums ObsFishLenComps_discard_pop.
FishAgeComps_discard_pop_LikeType, FishLenComps_discard_pop_LikeType: Character vectors [n_fish_fleets] for the population-specific discard compositions, with the same options as FishAgeComps_LikeType.
FishAgeComps_discard_pop_Type, FishLenComps_discard_pop_Type: Composition structure for the population-specific discard compositions, in the same format as FishAgeComps_Type.
...: Optional starting values for the overdispersion and correlation parameters.

Value

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

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

Usage

Arguments

Value

See also