Set up observed survey indices and composition data

Ingests observed survey index, age composition, and length composition data (both pooled and population-specific) into input_list$data, initialises overdispersion and correlation starting values in input_list$par, and constructs parameter maps via do_SrvAge_theta_mapping, do_SrvLen_theta_mapping, do_SrvAge_corr_pars_mapping, and do_SrvLen_corr_pars_mapping. When ISS_SrvAgeComps, ISS_SrvLenComps, ISS_SrvAgeComps_pop, or ISS_SrvLenComps_pop is NULL, input sample sizes are derived automatically by summing observed composition counts across the appropriate dimensions each year. Must be called after Setup_Mod_Dim and before model compilation.

Usage

Setup_Mod_SrvIdx_and_Comps(
  input_list,
  ObsSrvIdx,
  ObsSrvIdx_SE,
  UseSrvIdx,
  ObsSrvIdx_pop = NULL,
  ObsSrvIdx_pop_SE = NULL,
  UseSrvIdx_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_srv_fleets)),
  srv_idx_type,
  ObsSrvAgeComps,
  UseSrvAgeComps,
  ObsSrvLenComps,
  UseSrvLenComps,
  ISS_SrvAgeComps = NULL,
  ISS_SrvLenComps = NULL,
  SrvAgeComps_LikeType,
  SrvLenComps_LikeType,
  SrvAgeComps_Type,
  SrvLenComps_Type,
  ObsSrvAgeComps_pop = NULL,
  UseSrvAgeComps_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_srv_fleets)),
  ISS_SrvAgeComps_pop = NULL,
  ObsSrvLenComps_pop = NULL,
  UseSrvLenComps_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_srv_fleets)),
  ISS_SrvLenComps_pop = NULL,
  SrvAgeComps_pop_LikeType = rep("none", input_list$data$n_srv_fleets),
  SrvLenComps_pop_LikeType = rep("none", input_list$data$n_srv_fleets),
  SrvAgeComps_pop_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_srv_fleets, sep = ""),
  SrvLenComps_pop_Type = paste("none_Year_1-terminal_Fleet_",
    1:input_list$data$n_srv_fleets, sep = ""),
  ...
)

Arguments

input_list

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

ObsSrvIdx

Observed survey index array [n_regions × n_years × n_seas × n_srv_fleets].

ObsSrvIdx_SE

Lognormal standard errors for ObsSrvIdx, same dimensions [n_regions × n_years × n_seas × n_srv_fleets].

UseSrvIdx

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

ObsSrvIdx_pop

Observed population-specific survey index array [n_pop × n_regions × n_years × n_seas × n_srv_fleets].

ObsSrvIdx_pop_SE

Lognormal standard errors for ObsSrvIdx_pop, same dimensions [n_pop × n_regions × n_years × n_seas × n_srv_fleets].

UseSrvIdx_pop

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

srv_idx_type

Character vector [n_srv_fleets] specifying the index type per fleet. One of "biom" (biomass), "abd" (abundance), or "none" (no index for that fleet). Converted to integer codes (1, 0, 999) before storage.

ObsSrvAgeComps

Observed survey age compositions, array [n_regions × n_years × n_seas × n_ages × n_sexes × n_srv_fleets]. Values may be counts or proportions on a comparable scale.

UseSrvAgeComps

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

ObsSrvLenComps

Observed survey length compositions, array [n_regions × n_years × n_seas × n_lens × n_sexes × n_srv_fleets]. Only validated when fit_lengths = 1 in $data.

UseSrvLenComps

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

ISS_SrvAgeComps

Input sample sizes for survey age compositions, array [n_regions × n_years × n_seas × n_sexes × n_srv_fleets], or NULL to derive automatically by summing ObsSrvAgeComps across the age dimension each year, respecting SrvAgeComps_Type.

ISS_SrvLenComps

Input sample sizes for survey length compositions, same structure as ISS_SrvAgeComps, or NULL for automatic derivation from ObsSrvLenComps.

SrvAgeComps_LikeType

Character vector [n_srv_fleets] specifying the likelihood for survey age compositions. One of "none", "Multinomial", "Dirichlet-Multinomial", "iid-Logistic-Normal", "1d-Logistic-Normal", "2d-Logistic-Normal". Converted to integer codes (999, 0–4) before storage.

SrvLenComps_LikeType

Character vector [n_srv_fleets] specifying the likelihood for survey length compositions. Same options as SrvAgeComps_LikeType.

SrvAgeComps_Type

Character vector defining the survey age composition structure per fleet and year range. Each element follows the format "<type>_Year_<start>-<end>_Fleet_<fleet>". Use "terminal" in place of the end year to extend to the final model year. Valid types:

"agg": Aggregated across regions and sexes. Not compatible with "2d-Logistic-Normal".
"spltRspltS": Split by region and sex.
"spltRjntS": Split by region, joint across sexes.
"none": No composition data used.

Parsed into a [n_years × n_srv_fleets] integer matrix before storage. An error is raised if any cell remains NA after parsing, indicating an incomplete year range specification.

SrvLenComps_Type

Character vector defining the survey length composition structure. Same format and options as SrvAgeComps_Type.

ObsSrvAgeComps_pop

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

UseSrvAgeComps_pop

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

ISS_SrvAgeComps_pop

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

ObsSrvLenComps_pop

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

UseSrvLenComps_pop

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

ISS_SrvLenComps_pop

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

SrvAgeComps_pop_LikeType

Character vector of length n_srv_fleets specifying the likelihood for population-specific survey age compositions. Same options as SrvAgeComps_LikeType. Default: "none" for all fleets.

SrvLenComps_pop_LikeType

Character vector of length n_srv_fleets specifying the likelihood for population-specific survey length compositions. Same options as SrvLenComps_LikeType. Default: "none" for all fleets.

SrvAgeComps_pop_Type

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

SrvLenComps_pop_Type

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

...

Optional named starting values for overdispersion and correlation parameters.

Value

The input input_list with survey data stored in $data (ObsSrvIdx, ObsSrvIdx_SE, UseSrvIdx, ObsSrvIdx_pop, ObsSrvIdx_pop_SE, UseSrvIdx_pop, ObsSrvAgeComps, UseSrvAgeComps, ISS_SrvAgeComps, ObsSrvLenComps, UseSrvLenComps, ISS_SrvLenComps, ObsSrvAgeComps_pop, UseSrvAgeComps_pop, ISS_SrvAgeComps_pop, ObsSrvLenComps_pop, UseSrvLenComps_pop, ISS_SrvLenComps_pop, SrvAgeComps_LikeType, SrvLenComps_LikeType, SrvAgeComps_pop_LikeType, SrvLenComps_pop_LikeType, SrvAgeComps_Type, SrvLenComps_Type, SrvAgeComps_pop_Type, SrvLenComps_pop_Type, srv_idx_type); overdispersion and correlation starting values in $par; and factor maps in $map for all pooled and population-specific overdispersion and correlation parameter arrays.

Usage

Arguments

Value

See also