Generate recruitment for a simulation year

Computes total recruitment for year y by first obtaining deterministic expected recruitment from Get_Det_Recruitment and then multiplying by lognormal deviations (bias-corrected). Recruitment is apportioned across sexes and seasons and written into sim_env$NAA[p, r, y, 1, 1, s, sim] (first season, age-1 slot). Unfished NAA (NAA0) is synchronised to match fished NAA at recruitment. If Rec_input exists in the environment and covers year y, those values override the stochastic draw entirely.

Usage

generate_recruitment(y, sim, sim_env, seas = 1)

Arguments

y

Integer. Year index for which recruitment is generated.

sim

Integer. Simulation replicate index.

sim_env

Simulation environment created by Setup_sim_env. Modified in place: $ln_RecDevs[p, r, y, sim], $Rec[p, r, y, sim], $NAA[p, r, y, seas, 1, s, sim], and $NAA0[p, r, y, seas, 1, s, sim] are updated.

seas

Integer. Season this recruitment first enters the population in, using rec_seas_prop[p, seas, sim]. Default 1, matching the classic rec_lag >= 1 case where recruitment for the whole year is already known before season 1 starts. rec_lag = 0 (age-0 recruitment) instead calls this with seas = spawn_seas, since that is the earliest season this year's own SSB (and hence recruitment) is knowable – see apply_pop_dy.

Value

invisible(NULL). All modifications are made by reference within sim_env.

Details

Recruitment deviation sharing follows the same population/region logic as generate_initial_age_structure: deviations are drawn once per population (n_pop > 1) or once per region (n_pop = 1, local density-dependence). Populations with R0 = 0 receive zero deviations. sigma_idx selects the natal region's ln_sigmaR for the bias-correction term.