Extract simulation outputs into SPoRC estimation model format

Subsets and reshapes biological, tagging, fishery, and survey arrays from a simulation environment or output list to cover years 1:y and simulation replicate sim, producing a named list ready for direct use in Setup_Mod_Biologicals, Setup_Mod_Catch_and_F, Setup_Mod_SrvIdx_and_Comps, and Setup_Mod_Tagging. Binary Use* indicator arrays are derived automatically from the extracted observation arrays (non-NA, positive values set to 1).

Usage

simulation_data_to_SPoRC(sim_env, y, sim)

Arguments

sim_env

Simulation environment or list (e.g., output from Simulate_Pop_Static or a Setup_sim_env environment) containing all operating model arrays.

y

Integer. Last year to include; years 1:y are retained.

sim

Integer. Simulation replicate index to extract.

Value

Named list with the following elements (all arrays have y in the year dimension unless noted): WAA [n_pop x n_regions x y x n_seas x n_ages x n_sexes], WAA_fish [... x n_fish_fleets], WAA_srv [... x n_srv_fleets], MatAA, SizeAgeTrans (or NULL), AgeingError [y x n_obs_ages x n_ages], use_conv_fish_tagging, conv_tag_release_indicator, obs_conv_tag_fish_recap, conv_tagged_fish, conv_tagged_fish_attr, n_tag_cohorts (all NULL when tagging inactive), ObsCatch, ln_sigmaC, UseCatch, ObsCatch_pop, ln_sigmaC_pop, UseCatch_pop, ObsDiscard, ln_sigmaD, UseDiscard, ObsDiscard_pop, ln_sigmaD_pop, UseDiscard_pop, ObsFishIdx, ObsFishIdx_SE, UseFishIdx, ObsFishIdx_pop, ObsFishIdx_pop_SE, UseFishIdx_pop, ObsFishAgeComps, ISS_FishAgeComps, UseFishAgeComps, ObsFishAgeComps_pop, ISS_FishAgeComps_pop, UseFishAgeComps_pop, ObsFishLenComps (or NULL), ISS_FishLenComps (or NULL), UseFishLenComps, ObsFishLenComps_pop (or NULL), ISS_FishLenComps_pop (or NULL), UseFishLenComps_pop, ObsFishAgeComps_discard, ISS_FishAgeComps_discard, UseFishAgeComps_discard, ObsFishAgeComps_discard_pop, ISS_FishAgeComps_discard_pop, UseFishAgeComps_discard_pop, ObsFishLenComps_discard (or NULL), ISS_FishLenComps_discard (or NULL), UseFishLenComps_discard, ObsFishLenComps_discard_pop (or NULL), ISS_FishLenComps_discard_pop (or NULL), UseFishLenComps_discard_pop, ObsSrvIdx, ObsSrvIdx_SE, UseSrvIdx, ObsSrvIdx_pop, ObsSrvIdx_pop_SE, UseSrvIdx_pop, ObsSrvAgeComps, ISS_SrvAgeComps, UseSrvAgeComps, ObsSrvAgeComps_pop, ISS_SrvAgeComps_pop, UseSrvAgeComps_pop, ObsSrvLenComps (or NULL), ISS_SrvLenComps (or NULL), UseSrvLenComps, ObsSrvLenComps_pop (or NULL), ISS_SrvLenComps_pop (or NULL), UseSrvLenComps_pop.

Details

Population-specific arrays (ObsCatch_pop, ObsFishIdx_pop, ObsFishAgeComps_pop, ObsFishLenComps_pop, ObsSrvIdx_pop, ObsSrvAgeComps_pop, ObsSrvLenComps_pop) are extracted when present in sim_env; corresponding Use*_PopSpec flags are derived automatically.

Input sample sizes for age and length compositions are extracted for both aggregate and population-specific data streams, including retained (ISS_FishAgeComps, ISS_FishLenComps, ISS_FishAgeComps_pop, ISS_FishLenComps_pop, ISS_SrvAgeComps, ISS_SrvLenComps, ISS_SrvAgeComps_pop, ISS_SrvLenComps_pop) and discard (ISS_FishAgeComps_discard, ISS_FishLenComps_discard, ISS_FishAgeComps_discard_pop, ISS_FishLenComps_discard_pop) data streams.

Length composition outputs (ObsFishLenComps, ObsSrvLenComps, and their population-specific and discard variants) and SizeAgeTrans are NULL when no size-age transition matrix is present in sim_env. Tagging outputs are NULL when use_conv_fish_tagging = 0; otherwise, only cohorts with release years in 1:y are retained.

See also

Setup_Mod_Biologicals, Setup_Mod_Catch_and_F, Setup_Mod_SrvIdx_and_Comps, Setup_Mod_Tagging, Simulate_Pop_Static, Setup_sim_env