Extract simulation data into SPoRC format

This function subsets and reshapes biological, tagging, fishery, and survey data from a simulation environment for use in SPoRC analyses.

Usage

simulation_data_to_SPoRC(sim_env, y, sim)

Arguments

sim_env

A simulation environment / object (list or environment) containing arrays of biological quantities, tagging information, fishery data, and survey data.

y

Integer. Number of years to retain (subset from `1:y`).

sim

Integer. Simulation replicate index to extract.

Value

A named list with the following elements:

WAA

Weight-at-age array [region × year × age × sex].

MatAA

Maturity-at-age array [region × year × age × sex].

SizeAgeTrans

Size–age transition array [region × year × length × age × sex].

AgeingError

Ageing error matrix [year × age × error × sim].

tag_release_indicator

Tag release indicators (or `NULL` if tagging not used).

Obs_Tag_Recap

Observed tag recapture array (or `NULL`).

Tagged_Fish

Tagged fish counts (or `NULL`).

n_tag_cohorts

Number of tag release cohorts (or `NULL`).

ObsCatch

Observed fishery catch array [region × year × fleet].

ln_sigmaC

Log Fishery Catch SD [region × year × fleet].

UseCatch

Binary indicator array for catch data availability.

ObsFishIdx

Observed fishery index array [region × year × fleet].

ObsFishIdx_SE

Standard error for fishery index array.

UseFishIdx

Binary indicator array for fishery indices.

ObsFishAgeComps

Observed fishery age composition array.

ObsFishLenComps

Observed fishery length composition array.

ISS_FishAgeComps

Implied sample sizes for fishery age compositions.

ISS_FishLenComps

Implied sample sizes for fishery length compositions.

UseFishAgeComps

Binary indicator array for fishery age comps.

UseFishLenComps

Binary indicator array for fishery length comps.

ObsSrvIdx

Observed survey index array [region × year × fleet].

ObsSrvIdx_SE

Standard error for survey index array.

UseSrvIdx

Binary indicator array for survey indices.

ObsSrvAgeComps

Observed survey age composition array.

ObsSrvLenComps

Observed survey length composition array.

ISS_SrvAgeComps

Implied sample sizes for survey age compositions.

ISS_SrvLenComps

Implied sample sizes for survey length compositions.

UseSrvAgeComps

Binary indicator array for survey age comps.

UseSrvLenComps

Binary indicator array for survey length comps.

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(), run_annual_cycle(), simulation_self_test()