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

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,
  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 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.

sigmaFishIdx_spec

Character string controlling the estimated component of the aggregated fishery index observation error, one value per fleet. One of:

"fix": The reported standard errors are used as they are and ln_sigmaFishIdx is not estimated. The default.
"est_additive": Total standard deviation is the reported standard error plus an estimated component, the additive extra standard deviation convention.
"est_quadrature": Total standard deviation is the reported standard error and the estimated component added in quadrature, treating them as independent variances.
"est_replace": An estimated standard deviation replaces the reported standard errors entirely.

An estimated component is confounded with a likelihood weight, since a weight on a normal likelihood is the same statement as dividing the variance by that weight. Setup_Mod_Weighting warns when both are used. Fleets with a multivariate normal index likelihood take their scale from the supplied covariance and cannot have one, which is an error rather than a silently unidentified parameter.

sigmaFishIdx_map

Optional integer vector of length n_fish_fleets giving the estimation groups for ln_sigmaFishIdx. Fleets sharing a value share a parameter and NA holds a fleet at its starting value. Defaults to one free parameter per fleet. Use it when a reference assessment estimated some fleets and pinned others at a bound.

sigmaFishIdx_pop_spec

Character string controlling the estimated component of the population-specific fishery index observation error, one value per fleet. One of:

"fix": The reported standard errors are used as they are and ln_sigmaFishIdx_pop is not estimated. The default.
"est_additive": Total standard deviation is the reported standard error plus an estimated component, the additive extra standard deviation convention.
"est_quadrature": Total standard deviation is the reported standard error and the estimated component added in quadrature, treating them as independent variances.
"est_replace": An estimated standard deviation replaces the reported standard errors entirely.

sigmaFishIdx_pop_map

Optional integer vector of length n_fish_fleets giving the estimation groups for 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. Use it when a reference assessment estimated some fleets and pinned others at a bound.

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.

t_fish

Array [n_regions x n_seas x n_fish_fleets] giving the fishery index timing: 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, the same convention t_srv uses for surveys. Defaults to 0 (start of season), which is what the model did before this argument existed; set 0.5 for a mid-season index.

FishLenComps_sel

Character vector [n_fish_fleets], whether a length-based selectivity is applied before or after the fish are spread over lengths. "age" (default) selects at age and spreads the catch afterwards, so every fish of an age is equally catchable and the length composition within an age is just the key's. "length" spreads the fish at each age over the key first and selects them length by length, so the long fish of an age are taken more often. The key is the fleet's own, at t_fish. Requires length-based fishery selectivity. Use "length" when selectivity is length based and the length compositions are what inform it. The two give different expected compositions, not two roundings of the same one.

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, $\sum_l P(l \mid a) s(l) w(l) / \sum_l P(l \mid a) s(l)$, instead of the population mean weight at that age. Use it when the gear selects strongly within an age. With flat or age-based selectivity the two are the same.

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

fish_idx_ages

Per-fleet selection of which ages contribute to the index total. Either a list with one element per fishery fleet, where each element is a vector of ages or NULL for all ages, or an array [n_ages x n_fish_fleets] of 0/1 weights. Default NULL uses every age for every fleet. The fleet's compositions are unaffected.

FishAgeComps_bins

Which age bins each fishery fleet's 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. Both observed and expected compositions are restricted to the named bins and renormalized within them, so excluded bins are left out of the likelihood rather than being forced to be explained; this is how a fleet that only ages part of its age range is fitted. Indices refer to observed bins, that is after any ageing error has mapped model ages onto observed ones. The restriction applies whatever the composition type: for sex-joint comps the named bins are dropped from each sex's block, so the sex ratio the joint comps have becomes the ratio within the fitted bins. Every fleet must retain at least two bins, since the proportion in a lone bin is one whatever the model predicts. Default NULL, which fits all bins for all fleets.

FishLenComps_bins

Which length bins each fishery fleet's length composition is fitted over, in the same format as FishAgeComps_bins. Indices refer to observed length bins, that is after any LenBinMap has mapped model bins onto observed ones.

Fish_caal_bins

Which age bins each fishery fleet's conditional age-at-length data are fitted over, in the same format as FishAgeComps_bins. Applied to every length bin's row of ages alike.

FishAgeComps_pop_bins

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

FishLenComps_pop_bins

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

FishIdx_LikeType

Character vector [n_fish_fleets] giving the error structure of each fishery index. Options are "lognormal" (default, the observation standard errors are on the log scale), "normal" (arithmetic scale), and "mvn" (multivariate normal on the arithmetic scale using a fixed covariance supplied through FishIdx_Cov). One-step-ahead residuals are available only for lognormal fleets. A fleet's population-specific index data source follows the same choice for "lognormal" and "normal", but stays lognormal under "mvn", whose covariance describes the regional series only.

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": Fit the observation against the prediction for the season it sits in. This is the default and what every data source did before this setting existed.
"aggSeas": Sum the prediction over every season of the year and fit it against a single observation.

Under "aggSeas" the observation still lives in whichever season it was placed in, and exactly one season per region and year may be turned on in the matching Use array. The likelihood and the reported negative log likelihood land in that season. An index measured at a point in time belongs in its own season rather than aggregated; this setting is for a data source that accumulates across the year.

FishIdx_Cov

List with one element per fishery fleet holding the fixed covariance matrix for fleets using "mvn", and NULL otherwise. Each matrix must be square with one row per observation the fleet fits, ordered as the observations 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]. A CAAL observation is the age composition of the fish aged from one length bin, so the age dim of each length row is what gets fit. NULL (default) for a model with 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 have 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 of length n_fish_fleets. One of "none", "Multinomial" or "Dirichlet-Multinomial". The logistic-normal families are not available for CAAL, since a single length bin's age sample is small and mostly zeros, which the additive log-ratio transform cannot handle.

Fish_caal_Type

Composition type specification, using the same "CompType_Year_x-y_Fleet_z" convention as the marginal compositions.

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
"iid-Logistic-Normal-miss0": Logistic-normal with the empty bins dropped and the standard deviation scaled by the input sample size
"1d-Logistic-Normal-miss0": The same, correlated across bins
"2d-Logistic-Normal-miss0": The same, correlated across bins and sexes
"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.

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

Usage

Arguments

Value

Details

See also