Skip to contents

Apply population dynamics within a simulation year

Source: R/sim_population.R
apply_pop_dy.Rd

Runs the within-year loop for year y: seasonal recruitment apportionment from season two on, movement, Baranov mortality, age advancement into the following year, and the spawning-season biomass quantities (total biomass, SSB, dynamic \(B_0\) and effective SSB under natal homing). The fished and unfished trajectories are tracked together, with the snapshots before and after movement stored in NAA_bef and NAA_aft. Movement runs only when n_regions > 1, and recruits are left out of it when do_recruits_move = 0. With one season and several populations, sgl_seas_spawning_movement is applied to both trajectories before the biomass quantities; with one sex, SSB and \(B_0\) are halved to give female-only spawning biomass.

Usage

apply_pop_dy(y, sim, sim_env)

Arguments

y

Integer. Year index.

sim

Integer. Simulation replicate index.

sim_env

Simulation environment from Setup_sim_env, modified in place: $ZAA, $NAA, $NAA0, $NAA_bef, $NAA_aft, $Total_Biom, $SSB, $Dynamic_SSB0 and $eff_SSB.

Value

invisible(NULL); everything is modified by reference within sim_env.

Details

Under rec_lag == 0 this year's recruitment is not knowable until spawn_seas, since it depends on this year's own SSB, so generate_recruitment is called from inside this function at seas == spawn_seas, mirroring the estimation model.