Build the full selectivity array for one selectivity type (retention, fishery, survey)

Evaluates Get_Selex across regions, years, fleets, and sexes for a single selectivity type, and mean standardizes the result where the time-varying or non-parametric form calls for it. Total fishery, retention, and survey selectivity all share this code path and differ only in which data arrays are handed in.

Usage

Get_Selex_Array(
  selex_type,
  bins,
  sel_blocks,
  sel_model,
  fixed_sel_pars,
  cont_tv_sel,
  ln_seldevs,
  use_fixed_sel,
  sel_input,
  bicubic_Wbin,
  bicubic_Wyr,
  bicubic_binnodes,
  bicubic_yrnodes,
  n_pop,
  n_regions,
  n_yrs,
  n_proj_yrs_devs,
  n_seas,
  n_ages,
  n_lens,
  n_sexes,
  n_fleets,
  bin_devs = NULL,
  bin_dev_bins = NULL,
  sel_norm_bins = NULL,
  sex_par_offset = NULL,
  sex_scale_offset = NULL,
  sex_apical_offset = NULL,
  sex_scale = NULL,
  nselbins = NULL,
  dbnrml_raw = NULL,
  dbnrml_startbin = NULL
)

Arguments

selex_type: Integer switch (0 = age-based, 1 = length-based).
bins: Numeric vector of bins; ages when selex_type == 0 and lens when selex_type == 1.
sel_blocks: Integer array n_regions x n_yrs x n_fleets of selectivity block indices.
sel_model: Integer array n_regions x n_yrs x n_fleets of selectivity functional forms (see Get_Selex).
fixed_sel_pars: Array n_regions x n_pars x n_blocks x n_sexes x n_fleets of fixed-effect selectivity parameters.
cont_tv_sel: Integer matrix n_regions x n_fleets of continuous time-varying forms.
ln_seldevs: Array n_regions x n_yrs_total x n_bins x n_sexes x n_fleets of selectivity deviations; sliced per fleet internally.
use_fixed_sel: Integer vector of length n_fleets (0 = estimate, 1 = use sel_input).
sel_input: Array n_pop x n_regions x n_yrs x n_seas x n_bins x n_sexes x n_fleets of fixed selectivity values.
bicubic_Wbin, bicubic_Wyr: Bicubic spline bin-node and year-node weight arrays (Selex_Model == 8 only).
bicubic_binnodes, bicubic_yrnodes: Integer arrays n_regions x n_yrs x n_fleets giving each block's true node counts (Selex_Model == 8 only).
n_pop, n_regions, n_yrs, n_proj_yrs_devs, n_seas, n_ages, n_lens, n_sexes, n_fleets: Model dimensions.
sex_par_offset: Integer vector of length n_fleets (0/1), or NULL for all zero. For a fleet flagged 1, the stored fixed-effect selectivity parameters of every sex beyond the first are additive offsets on the first sex's stored parameters, evaluated as pars[sex 1] + pars[sex s] on the transformed (usually log) scale. Because most forms exponentiate their parameters, an offset of \(\delta\) makes the sex-\(s\) natural-scale parameter the first sex's value times \(e^{\delta}\), which is the male-offset convention several existing assessments use. An offset kept at zero reproduces sex-shared parameters.
sex_scale_offset: Integer vector of length n_fleets (0/1), or NULL for all zero. For a fleet flagged 1, the realized selectivity curve of every sex beyond the first is multiplied by exp(sex_scale[region, block, sex, fleet]), a constant log-scale offset on the whole curve. The scaled curve may exceed one, matching the convention of a male selectivity offset applied in log space. Not meaningful for forms whose scale is standardized away downstream (non-parametric forms and the semi-parametric time-varying structures); setup refuses those combinations.
sex_apical_offset: Integer vector of length n_fleets (0/1), or NULL. Where it is 1, every sex beyond the first builds its double normal up to exp(sex_scale[region, block, sex, fleet]) rather than to one, leaving the first and last bins where their own parameters put them. Mutually exclusive with a scale offset on the same fleet.
sex_scale: Array n_regions x n_blocks x n_sexes x n_fleets of log-scale curve offsets read when sex_scale_offset or sex_apical_offset flags a fleet, or NULL when no fleet is flagged.
nselbins: Integer array n_regions x n_yrs x n_fleets naming each cell's plateau bin (0 = none), or NULL. Bins beyond it are kept at its value for the parametric forms (see n_sel_bins in Get_Selex); the bicubic form's own setup-built plateau is unaffected.
dbnrml_startbin: Integer vector [n_fleets] or NULL, the bin each fleet's double normal anchors its ascending limb at; see Get_Selex.

Value

List with sel, the age-based array (n_pop x n_regions x n_yrs_total x n_seas x n_ages x n_sexes x n_fleets), and sel_l, the length-based array (n_regions x n_yrs_total x n_lens x n_sexes x n_fleets). Only the array matching selex_type is populated; when selex_type == 1, sel is filled downstream by multiplying sel_l through the size-age transition matrix.