Apply population dynamics within a simulation year

Executes the full within-year population dynamics loop for year y: seasonal recruitment apportionment (seasons 2+), movement, Baranov catch-equation mortality, age advancement into the following year, and spawning-season biomass calculations (total biomass, SSB, dynamic $B_0$, and effective SSB for multi-population natal homing). Both fished (NAA) and unfished (NAA0) trajectories are tracked in parallel. For single-season multi-population models, sgl_seas_spawning_movement is applied to NAA and NAA0 prior to computing spawning biomass quantities. Single-sex models have SSB and $B_0$ multiplied by 0.5 to obtain 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 created by Setup_sim_env. Modified in place: $ZAA, $NAA, $NAA0, $NAA_bef, $NAA_aft, $Total_Biom, $SSB, $Dynamic_SSB0, and $eff_SSB are updated.

Value

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

Details

Pre- and post-movement snapshots are stored in NAA_bef and NAA_aft respectively. Movement is only applied when n_regions > 1; recruits (a = 1) are excluded from movement when do_recruits_move = 0.

When rec_lag == 0 (age-0 recruitment), this year's recruitment can't be known until spawn_seas is reached (it depends on this year's own SSB), so generate_recruitment is called from inside this function at seas == spawn_seas instead of beforehand - see the "rec_lag == 0" block below, which mirrors the equivalent restructuring in the estimation model (SPoRC_rtmb.R).