Run the annual cycle for a single simulation year

Runs the operating model's processes for year y and replicate sim in order: initial age structure and first-year recruitment at y = 1, population dynamics, fishery catches, indices and compositions, survey indices and compositions, tag releases, fishery tag recaptures when any use_conv_fish_tagging = 1, and next year's recruitment 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 from Setup_sim_env, passed by reference and modified in place by every annual-cycle helper.

Value

invisible(NULL).

Details

Those two standalone generate_recruitment() calls only run when rec_lag != 0. Under rec_lag = 0 recruitment depends on year y's own SSB, which is not known until apply_pop_dy reaches spawn_seas, so it is called from inside apply_pop_dy() instead. Its deviations are still drawn here at the end of the year before, through draw_sim_rec_devs, so a catch target for that year can be converted to F knowing its recruits.

See also

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