Initialise output containers for the operating model simulation

Allocates and appends zero-initialised arrays to sim_list for all biological, fishery, and survey quantities tracked during simulation. This function should be called after Setup_Sim_Dim and before any operating model dynamics are run. All arrays are pre-allocated and populated in subsequent simulation steps.

Usage

Setup_Sim_Containers(sim_list)

Arguments

sim_list

A simulation list returned by Setup_Sim_Dim. Dimension elements (e.g., 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) are used to size all output containers.

Value

The input sim_list with the following zero-initialised arrays added:

**Biological containers**

$NAA

Numbers-at-age [n_pop × n_regions × (n_yrs+1) × n_seas × n_ages × n_sexes × n_sims]. The +1 year dimension stores initial conditions and propagates population state through the final year.

$NAA_bef, $NAA_aft

Numbers-at-age immediately before and after fishing mortality is applied; same dimensions as $NAA.

$NAA0

Unfished numbers-at-age; same dimensions as $NAA. Used to compute dynamic \(B_0\) reference quantities.

$ZAA

Total instantaneous mortality-at-age [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_sims].

$Rec

Recruitment [n_pop × n_regions × n_yrs × n_sims].

$SSB

Spawning stock biomass [n_pop × n_regions × n_yrs × n_sims].

$eff_SSB

Effective (population-aggregated) spawning stock biomass [n_pop × n_yrs × n_sims].

$Dynamic_SSB0

Dynamic unfished spawning stock biomass [n_pop × n_regions × n_yrs × n_sims].

$Total_Biom

Total biomass [n_pop × n_regions × n_yrs × n_sims].

$ln_RecDevs

Log-scale recruitment deviations [n_pop × n_regions × n_yrs × n_sims].

$ln_InitDevs

Log-scale initial age-structure deviations [n_pop × n_regions × (n_ages - 1) × n_sims].

**Fishery containers**

*Retained catch and indices (aggregated)*

$ObsCatch, $TrueCatch

Observed and true catch [n_regions × n_yrs × n_seas × n_fish_fleets × n_sims].

$ObsFishIdx, $TrueFishIdx

Observed and true fishery CPUE index; same dimensions as $ObsCatch.

$ObsFishAgeComps

Observed fishery age compositions [n_regions × n_yrs × n_seas × n_obs_ages × n_sexes × n_fish_fleets × n_sims].

$ObsFishLenComps

Observed fishery length compositions [n_regions × n_yrs × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims].

*Discards (aggregated)*

$ObsDiscard, $TrueDiscard

Observed and true discard [n_regions × n_yrs × n_seas × n_fish_fleets × n_sims].

$ObsFishAgeComps_discard

Observed discard age compositions; same dimensions as $ObsFishAgeComps.

$ObsFishLenComps_discard

Observed discard length compositions; same dimensions as $ObsFishLenComps.

*Population-specific quantities*

$ObsCatch_pop, $TrueCatch_pop

Observed and true catch [n_pop × n_regions × n_yrs × n_seas × n_fish_fleets × n_sims].

$ObsFishIdx_pop, $TrueFishIdx_pop

Observed and true fishery index; same dimensions as $ObsCatch_pop.

$ObsFishAgeComps_pop

Observed fishery age compositions [n_pop × n_regions × n_yrs × n_seas × n_obs_ages × n_sexes × n_fish_fleets × n_sims].

$ObsFishLenComps_pop

Observed fishery length compositions [n_pop × n_regions × n_yrs × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims].

*Discards (population-specific)*

$ObsDiscard_pop, $TrueDiscard_pop

Observed and true discard; same dimensions as $ObsCatch_pop.

$ObsFishAgeComps_discard_pop

Observed discard age compositions; same dimensions as $ObsFishAgeComps_pop.

$ObsFishLenComps_discard_pop

Observed discard length compositions; same dimensions as $ObsFishLenComps_pop.

*True catch/discard at age and length*

$CAA, $DAA

Catch- and discard-at-age (true) [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims].

$CAL, $DAL

Catch- and discard-at-length (true) [n_pop × n_regions × n_yrs × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims].

**Survey containers**

*Aggregated*

$ObsSrvIdx, $TrueSrvIdx

Observed and true survey index [n_regions × n_yrs × n_seas × n_srv_fleets × n_sims].

$ObsSrvAgeComps

Observed survey age compositions [n_regions × n_yrs × n_seas × n_obs_ages × n_sexes × n_srv_fleets × n_sims].

$ObsSrvLenComps

Observed survey length compositions [n_regions × n_yrs × n_seas × n_lens × n_sexes × n_srv_fleets × n_sims].

*Population-specific*

$ObsSrvIdx_pop, $TrueSrvIdx_pop

Observed and true survey index [n_pop × n_regions × n_yrs × n_seas × n_srv_fleets × n_sims].

$ObsSrvAgeComps_pop

Observed survey age compositions [n_pop × n_regions × n_yrs × n_seas × n_obs_ages × n_sexes × n_srv_fleets × n_sims].

$ObsSrvLenComps_pop

Observed survey length compositions [n_pop × n_regions × n_yrs × n_seas × n_lens × n_sexes × n_srv_fleets × n_sims].

*True index at age and length*

$SrvIAA

Survey index-at-age (true) [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_srv_fleets × n_sims].

$SrvIAL

Survey index-at-length (true), same structure as $SrvIAA with n_lens replacing n_ages.

See also

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