Description of Simulation Dimensions • SPoRC

The following tables describes key elements generated from simulations conducted in SPoRC, for which can be input into an estimation framework and utilized for comparison.

Simulation Settings

Element	Dimension	Description
`n_sims`	`1`	Number of simulations
`n_regions`	`1`	Number of regions
`n_years`	`1`	Number of years
`n_ages`	`1`	Number of ages
`n_lens`	`1`	Number of length bins
`n_sexes`	`1`	Number of sexes
`n_fish_fleets`	`1`	Number of fishery fleets
`n_srv_fleets`	`1`	Number of survey fleets

Population, Recruitment, and Biological Processes

Element	Dimension	Description
`sexratio`	`n_regions, n_years, n_sexes, n_sims`	Sex ratio values
`R0`	`n_regions, n_years, n_sims`	Regional Unfished or mean recruitment
`Rec`	`n_regions, n_years, n_sims`	Realized recruitment
`Init_NAA`	`n_regions, n_ages, n_sexes, n_sims`	Equilibrium initial abundance-at-age
`NAA`	`n_regions, n_ages, n_years, n_sexes, n_sims`	Numbers-at-age
`NAA0`	`n_regions, n_ages, n_years, n_sexes, n_sims`	Dynamic unfished numbers-at-age
`Dynamic_SSB0`	`n_regions, n_years, n_sims`	Dynamic unfished spawning stock biomass
`SSB`	`n_regions, n_years, n_sims`	Spawning stock biomass
`Total_Biom`	`n_regions, n_years, n_sims`	Total biomass
`ln_RecDevs`	`n_regions, n_years, n_sims`	Log-scale recruitment deviations
`ln_InitDevs`	`n_regions, n_ages - 1, n_sims`	Log-scale initial age deviations
`natmort`	`n_regions, n_ages, n_sexes, n_sims`	Natural mortality-at-age
`ZAA`	`n_regions, n_years, n_ages, n_sexes, n_sims`	Total mortality
`WAA`	`n_regions, n_years, n_ages, n_sexes, n_sims`	Mean weight-at-age
`WAA_fish`	`n_regions, n_years, n_ages, n_sexes, n_fish_fleets, n_sims`	Weight-at-age for fishery
`WAA_srv`	`n_regions, n_years, n_ages, n_sexes, n_srv_fleets, n_sims`	Weight-at-age for survey
`MatAA`	`n_regions, n_years, n_ages, n_sexes, n_sims`	Proportion mature-at-age
`SizeAgeTrans`	`n_regions, n_years, n_lens, n_ages, n_sexes, n_sims`	Size–age transition array
`AgeingError`	`n_years, n_model_ages, n_obs_ages, n_sims`	Ageing error array
`Movement`	`n_regions, n_regions, n_years, n_ages, n_sexes, n_sims`	Movement array

Fishery Processes

Element	Dimension	Description
`init_F`	`n_regions, n_fish_fleets`	Initial fishing mortality rate
`Fmort`	`n_regions, n_years, n_fish_fleets, n_sims`	Annual fishing mortality
`ln_sigmaC`	`n_regions, n_years, n_fish_fleets`	Standard deviation for catch likelihood
`fish_sel`	`n_regions, n_years, n_ages, n_sexes, n_fish_fleets, n_sims`	Fishery selectivity-at-age
`fish_q`	`n_regions, n_years, n_fish_fleets, n_sims`	Fishery catchability
`TrueCatch`	`n_regions, n_years, n_fish_fleets, n_sims`	True catch
`ObsCatch`	`n_regions, n_years, n_fish_fleets, n_sims`	Observed catch
`ObsFishIdx`	`n_regions, n_years, n_fish_fleets, n_sims`	Observed fishery index
`TrueFishIdx`	`n_regions, n_years, n_fish_fleets, n_sims`	True fishery index
`ObsFishIdx_SE`	`n_regions, n_years, n_fish_fleets, n_sims`	Standard error of observed index
`CAA`	`n_regions, n_years, n_ages, n_sexes, n_fish_fleets, n_sims`	Catch-at-age
`CAL`	`n_regions, n_years, n_lens, n_sexes, n_fish_fleets, n_sims`	Catch-at-length
`ObsFishAgeComps`	`n_regions, n_years, n_ages, n_sexes, n_fish_fleets, n_sims`	Observed fishery age comps
`ObsFishLenComps`	`n_regions, n_years, n_lens, n_sexes, n_fish_fleets, n_sims`	Observed fishery length comps
`ISS_FishAgeComps`	`n_regions, n_years, n_fish_fleets, n_sexes, n_sims`	Input sample size for fishery age comps
`ISS_FishLenComps`	`n_regions, n_years, n_fish_fleets, n_sexes, n_sims`	Input sample size for fishery length comps

Survey Processes

Element	Dimension	Description
`srv_sel`	`n_regions, n_years, n_ages, n_sexes, n_srv_fleets, n_sims`	Survey selectivity-at-age
`srv_q`	`n_regions, n_years, n_srv_fleets, n_sims`	Survey catchability
`ObsSrvIdx`	`n_regions, n_years, n_srv_fleets, n_sims`	Observed survey index
`TrueSrvIdx`	`n_regions, n_years, n_srv_fleets, n_sims`	True survey index
`ObsSrvIdx_SE`	`n_regions, n_years, n_srv_fleets, n_sims`	Standard error of observed index
`Srv_IAA`	`n_regions, n_years, n_ages, n_sexes, n_srv_fleets, n_sims`	Survey index-at-age
`Srv_IAL`	`n_regions, n_years, n_lens, n_sexes, n_srv_fleets, n_sims`	Survey index-at-length
`ObsSrvAgeComps`	`n_regions, n_years, n_ages, n_sexes, n_srv_fleets, n_sims`	Observed survey age comps
`ObsSrvLenComps`	`n_regions, n_years, n_lens, n_sexes, n_srv_fleets, n_sims`	Observed survey length comps
`ISS_SrvAgeComps`	`n_regions, n_years, n_srv_fleets, n_sexes, n_sims`	Input sample size for survey age comps
`ISS_SrvLenComps`	`n_regions, n_years, n_srv_fleets, n_sexes, n_sims`	Input sample size for survey length comps

Tagging

Element	Dimension	Description
`tag_release_indicator`	`n_tag_cohorts, 2 (Column 1 = tag region, Column 2 = tag year)`	Indicator for tag release events
`Tag_Reporting`	`n_regions, n_years, n_sims`	Tag reporting rate
`Tagged_Fish`	`n_regions, n_years, n_ages, n_sexes, n_sims`	Number of tagged fish
`ln_Init_Tag_Mort`	`1`	Initial tag-induced mortality
`ln_Tag_Shed`	`1`	Tag shedding rate
`Tag_Avail`	`n_regions, n_years, n_ages, n_sexes, n_sims`	Available tagged fish for recapture
`UseTagging`	`1`	Indicator if tagging is simulated
`Pred_Tag_Recap`	`n_regions, n_years, n_ages, n_sexes, n_sims`	True tag recaptures
`Obs_Tag_Recap`	`n_regions, n_years, n_ages, n_sexes, n_sims`	Observed tag recaptures