Helper to set map for Selectivity parameters

Maps base selectivity parameters (log_sel_slp, sel_inf, sel_coff) and time-varying deviations, based on Selectivity and Time_varying_sel settings in fleet_control.

Usage

build_map_selectivity(map_list, data_list, nyrs_hind, random_sel)

Arguments

map_list

The current TMB map list.

data_list

The data list containing model settings.

nyrs_hind

Number of historical years.

random_sel

Logical indicating if selectivity deviations are random effects.

Value

Updated map_list.

Details

Selectivity sets the curve's shape and Time_varying_sel whether it varies over time; for the allowed values of both, see "3. Selectivity (per fleet)" in vignette("model-options-and-functionality"), or rceattle_switch_maps for the code-to-name maps themselves. N_sel_bins is how many age or length bins the non-parametric and AR1 forms estimate (Selectivity 2, 5, 6, 7, 9 or 13); it is unused otherwise. random_sel in fit_mod() treats the deviations as random effects and estimates their variance.

The double-normal forms blend Gaussian ascending and descending limbs at the peak. DoubleNormal reads its four parameters from the shared arrays: sel_inf[1] = peak, sel_inf[2] = logit(right_floor) (the right-tail floor, SS3 P6/end_logit), log_sel_slp[1] = log(sigma_asc) and log_sel_slp[2] = log(sigma_desc). right_floor -> 0 is dome-shaped; right_floor -> 1 is logistic ascending only. DoubleNormalSS3 instead carries its own six-parameter array (sel_dn6).