Run the annual cycle for a single simulation year

Orchestrates the complete annual sequence of operating model processes for year y and simulation replicate sim: initialises age structure and generates first-year recruitment at y = 1; applies population dynamics (movement, mortality, biomass); generates fishery catches, indices, and compositions; generates survey indices and compositions; releases conventional tags; generates fishery tag recaptures (when any use_conv_fish_tagging = 1); and generates recruitment for the following year (y + 1) when y < n_yrs.

Usage

run_annual_cycle(y, sim, sim_env)

Arguments

y

Integer. Year index.

sim

Integer. Simulation replicate index.

sim_env

Simulation environment created by Setup_sim_env and passed by reference. All annual-cycle helper functions modify this environment in place.

Value

invisible(NULL).

Details

The two standalone generate_recruitment() calls described above (at y = 1 and for y + 1) only run when rec_lag != 0. For rec_lag = 0 (age-0 recruitment), recruitment for year y depends on year y's own SSB, which isn't known until apply_pop_dy reaches spawn_seas within that year - generate_recruitment() is called from inside apply_pop_dy() instead, once that SSB is available.

See also

Other Simulation Setup: Setup_Sim_Biologicals(), Setup_Sim_Containers(), Setup_Sim_Dim(), Setup_Sim_Fishing(), Setup_Sim_Rec(), Setup_Sim_Survey(), Setup_Sim_Tagging(), Setup_sim_env(), Simulate_Pop_Static(), simulation_self_test()