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Initialize output containers for the operating model simulation

Source: R/setup_sim_containers.R
Setup_Sim_Containers.Rd

Allocates the zero-filled arrays the simulation writes into, sized off the dimensions in sim_list. Call after Setup_Sim_Dim and before any operating model dynamics.

Usage

Setup_Sim_Containers(sim_list)

Arguments

sim_list

A simulation list returned by Setup_Sim_Dim, whose n_pop, n_regions, n_yrs, n_seas, n_ages, n_sexes, n_sims, n_fish_fleets, n_srv_fleets, n_obs_ages, n_lens and n_obs_lens size every container.

Value

sim_list with the containers added.

Biological: $NAA [n_pop × n_regions × (n_yrs+1) × n_seas × n_ages × n_sexes × n_sims], whose extra year holds the initial conditions and advances the population through the final year; $NAA_bef and $NAA_aft, the numbers before and after fishing mortality; $NAA0, the unfished numbers, for dynamic \(B_0\); $ZAA, total mortality at age over n_yrs; and $Rec, $SSB, $Dynamic_SSB0 and $Total_Biom [n_pop × n_regions × n_yrs × n_sims], with $eff_SSB [n_pop × n_yrs × n_sims], $ln_RecDevs on the SSB dims and $ln_InitDevs [n_pop × n_regions × (n_ages - 1) × n_sexes × n_sims].

Fishery: $ObsCatch and $TrueCatch [n_regions × n_yrs × n_seas × n_fish_fleets × n_sims], with $ObsFishIdx, $TrueFishIdx, $ObsDiscard and $TrueDiscard on the same dims; $ObsFishAgeComps and $ObsFishAgeComps_discard with n_obs_ages × n_sexes before the fleet dim, and $ObsFishLenComps and $ObsFishLenComps_discard with n_obs_lens × n_sexes. Each has a _pop counterpart with a leading n_pop. The true catch and discards at age and length are $CAA, $DAA [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims] and $CAL, $DAL with n_lens in place of n_ages.

Survey: $ObsSrvIdx and $TrueSrvIdx [n_regions × n_yrs × n_seas × n_srv_fleets × n_sims], $ObsSrvAgeComps and $ObsSrvLenComps with the observed bin and sex dims before the fleet dim, each with a _pop counterpart, and the true $SrvIAA [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_srv_fleets × n_sims] and $SrvIAL with n_lens in place of n_ages.

See also

Other Simulation Setup: Setup_Sim_Biologicals(), 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(), run_annual_cycle(), simulation_self_test()