Description of Simulation Dimensions

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

Simulation Settings

Element	Dimension	Description
n_sims	1	Number of simulations
n_pop	1	Number of populations
n_regions	1	Number of regions
n_years	1	Number of years (alias for n_yrs)
n_yrs	1	Number of years
n_ages	1	Number of ages
n_lens	1	Number of length bins
n_sexes	1	Number of sexes
n_seas	1	Number of seasons
n_fish_fleets	1	Number of fishery fleets
n_srv_fleets	1	Number of survey fleets
seasdur	n_seas	Duration of each season as a fraction of the year
spawn_seas	1	Season in which spawning occurs
natal_region	n_pop	Natal region index for each population

Population, Recruitment, and Biological Processes

Element	Dimension	Description
sexratio	n_pop × n_regions × n_years × n_sexes × n_sims	Sex ratio (female proportion) by population, region, year, and sex
R0	n_pop × n_regions × n_years × n_sims	Regional unfished or mean recruitment by population
Rec	n_pop × n_regions × n_years × n_sims	Realized recruitment by population and region
rec_seas_prop	n_pop × n_seas × n_sims	Seasonal recruitment apportionment proportions by population
stray_rate	n_pop × n_years × n_sims	Proportion of each population’s spawning biomass contributing to non-natal regions
NAA	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Numbers-at-age (fished)
NAA0	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Numbers-at-age (unfished)
NAA_bef	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Numbers-at-age before movement is applied
NAA_aft	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Numbers-at-age after movement is applied
Dynamic_SSB0	n_pop × n_regions × n_years × n_sims	Dynamic unfished spawning stock biomass by population and region
SSB	n_pop × n_regions × n_years × n_sims	Spawning stock biomass by population and region
eff_SSB	n_pop × n_years × n_sims	Effective SSB at each population’s natal region, including stray contributions
Total_Biom	n_pop × n_regions × n_years × n_sims	Total biomass by population and region
ln_RecDevs	n_pop × n_regions × n_years × n_sims	Log-scale recruitment deviations
ln_InitDevs	n_pop × n_regions × (n_ages - 1) × n_sims	Log-scale initial age deviations
natmort	n_pop × n_regions × n_years × n_ages × n_sexes × n_sims	Natural mortality-at-age
ZAA	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Total instantaneous mortality (natural + retained F + dead discard F)
WAA	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Mean weight-at-age
WAA_fish	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims	Fishery weight-at-age
WAA_srv	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_srv_fleets × n_sims	Survey weight-at-age
MatAA	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Proportion mature-at-age
SizeAgeTrans	n_pop × n_regions × n_years × n_seas × 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 transition matrix
Movement	n_pop × n_regions × n_regions × n_years × n_seas × n_ages × n_sexes × n_sims	Movement (transition) matrix
sgl_seas_spawning_movement	n_pop × n_regions × n_regions × n_years × n_ages × n_sexes × n_sims	Spawning movement applied when n_seas == 1 and n_pop > 1

Fishery Processes

Fishing Mortality and Selectivity

Element	Dimension	Description
init_F	n_seas	Initial fishing mortality rate
Fmort	n_regions × n_years × n_seas × n_fish_fleets × n_sims	Annual fishing mortality rate by region, season, and fleet
fish_sel	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims	Total fishery selectivity-at-age
ret_sel	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims	Retention selectivity-at-age (fraction of selected fish that are retained)
dmr	n_regions × n_years × n_seas × n_fish_fleets × n_sims	Discard mortality rate (fraction of discarded fish that die); used to compute dead discard fishing mortality
fish_q	n_regions × n_years × n_fish_fleets × n_sims	Fishery catchability

Retained Catch

Element	Dimension	Description
ln_sigmaC	n_regions × n_years × n_seas × n_fish_fleets	Log standard deviation for regional retained catch likelihood
ln_sigmaC_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets	Log standard deviation for population-specific retained catch likelihood
CAA	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims	Retained catch-at-age (Baranov equation, retained component only)
CAL	n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims	Retained catch-at-length
TrueCatch	n_regions × n_years × n_seas × n_fish_fleets × n_sims	True regional retained catch (abundance or biomass)
ObsCatch	n_regions × n_years × n_seas × n_fish_fleets × n_sims	Observed regional retained catch (with lognormal error)
TrueCatch_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets × n_sims	True population-specific retained catch
ObsCatch_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets × n_sims	Observed population-specific retained catch (with lognormal error)

Discards

Element	Dimension	Description
ln_sigmaD	n_regions × n_years × n_seas × n_fish_fleets	Log standard deviation for regional discard likelihood
ln_sigmaD_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets	Log standard deviation for population-specific discard likelihood
DAA	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims	Dead discard catch-at-age (Baranov equation, dead discard component: F × fish_sel × (1 - ret_sel) × dmr / Z)
DAL	n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims	Dead discard catch-at-length
TrueDiscard	n_regions × n_years × n_seas × n_fish_fleets × n_sims	True regional discard index (units determined by discard_units: abundance, biomass, or fraction)
ObsDiscard	n_regions × n_years × n_seas × n_fish_fleets × n_sims	Observed regional discard index (with lognormal error)
TrueDiscard_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets × n_sims	True population-specific discard index
ObsDiscard_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets × n_sims	Observed population-specific discard index (with lognormal error)

Fishery Indices

Element	Dimension	Description
TrueFishIdx	n_regions × n_years × n_seas × n_fish_fleets × n_sims	True regional fishery index (abundance or biomass)
ObsFishIdx	n_regions × n_years × n_seas × n_fish_fleets × n_sims	Observed regional fishery index (with lognormal error)
ObsFishIdx_SE	n_regions × n_years × n_seas × n_fish_fleets	Standard error of observed regional fishery index
TrueFishIdx_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets × n_sims	True population-specific fishery index
ObsFishIdx_pop	n_pop × n_regions × n_years × n_seas × n_fish_fleets × n_sims	Observed population-specific fishery index
ObsFishIdx_pop_SE	n_pop × n_regions × n_years × n_seas × n_fish_fleets	Standard error of population-specific fishery index

Retained Fishery Compositions

Element	Dimension	Description
ObsFishAgeComps	n_regions × n_years × n_seas × n_obs_ages × n_sexes × n_fish_fleets × n_sims	Observed regional retained fishery age compositions
ObsFishLenComps	n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims	Observed regional retained fishery length compositions
ISS_FishAgeComps	n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for regional retained fishery age compositions
ISS_FishLenComps	n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for regional retained fishery length compositions
ObsFishAgeComps_pop	n_pop × n_regions × n_years × n_seas × n_obs_ages × n_sexes × n_fish_fleets × n_sims	Observed population-specific retained fishery age compositions
ObsFishLenComps_pop	n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims	Observed population-specific retained fishery length compositions
ISS_FishAgeComps_pop	n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for population-specific retained fishery age comps
ISS_FishLenComps_pop	n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for population-specific retained fishery length comps

Discard Fishery Compositions

Element	Dimension	Description
ObsFishAgeComps_discard	n_regions × n_years × n_seas × n_obs_ages × n_sexes × n_fish_fleets × n_sims	Observed regional discard fishery age compositions
ObsFishLenComps_discard	n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims	Observed regional discard fishery length compositions
ISS_FishAgeComps_discard	n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for regional discard fishery age compositions
ISS_FishLenComps_discard	n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for regional discard fishery length compositions
ObsFishAgeComps_discard_pop	n_pop × n_regions × n_years × n_seas × n_obs_ages × n_sexes × n_fish_fleets × n_sims	Observed population-specific discard fishery age compositions
ObsFishLenComps_discard_pop	n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets × n_sims	Observed population-specific discard fishery length compositions
ISS_FishAgeComps_discard_pop	n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for population-specific discard fishery age comps
ISS_FishLenComps_discard_pop	n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets × n_sims	Input sample size for population-specific discard fishery length comps

Survey Processes

Survey Selectivity and Indices

Element	Dimension	Description
srv_sel	n_pop × n_regions × n_years × n_seas × 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
TrueSrvIdx	n_regions × n_years × n_seas × n_srv_fleets × n_sims	True regional survey index (abundance or biomass)
ObsSrvIdx	n_regions × n_years × n_seas × n_srv_fleets × n_sims	Observed regional survey index (with lognormal error)
ObsSrvIdx_SE	n_regions × n_years × n_seas × n_srv_fleets	Standard error of observed regional survey index
TrueSrvIdx_pop	n_pop × n_regions × n_years × n_seas × n_srv_fleets × n_sims	True population-specific survey index
ObsSrvIdx_pop	n_pop × n_regions × n_years × n_seas × n_srv_fleets × n_sims	Observed population-specific survey index (with lognormal error)
ObsSrvIdx_pop_SE	n_pop × n_regions × n_years × n_seas × n_srv_fleets	Standard error of population-specific survey index

Survey Compositions

Element	Dimension	Description
SrvIAA	n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_srv_fleets × n_sims	Survey index-at-age
SrvIAL	n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_srv_fleets × n_sims	Survey index-at-length
ObsSrvAgeComps	n_regions × n_years × n_seas × n_obs_ages × n_sexes × n_srv_fleets × n_sims	Observed regional survey age compositions
ObsSrvLenComps	n_regions × n_years × n_seas × n_lens × n_sexes × n_srv_fleets × n_sims	Observed regional survey length compositions
ISS_SrvAgeComps	n_regions × n_years × n_seas × n_sexes × n_srv_fleets × n_sims	Input sample size for regional survey age compositions
ISS_SrvLenComps	n_regions × n_years × n_seas × n_sexes × n_srv_fleets × n_sims	Input sample size for regional survey length compositions
ObsSrvAgeComps_pop	n_pop × n_regions × n_years × n_seas × n_obs_ages × n_sexes × n_srv_fleets × n_sims	Observed population-specific survey age compositions
ObsSrvLenComps_pop	n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_srv_fleets × n_sims	Observed population-specific survey length compositions
ISS_SrvAgeComps_pop	n_pop × n_regions × n_years × n_seas × n_sexes × n_srv_fleets × n_sims	Input sample size for population-specific survey age compositions
ISS_SrvLenComps_pop	n_pop × n_regions × n_years × n_seas × n_sexes × n_srv_fleets × n_sims	Input sample size for population-specific survey length compositions

Tagging

Element	Dimension	Description
use_conv_fish_tagging	n_fish_fleets	Indicator vector for whether conventional tagging is simulated for each fishery fleet
conv_tag_release_indicator	n_conv_tag_cohorts × 3 (col 1 = release region, col 2 = release year, col 3 = release season)	Indicator for tag release events
conv_tag_fish_reporting	n_regions × n_years × n_fish_fleets × n_sims	Tag reporting rate by region, year, and fleet
conv_tagged_fish	n_conv_tag_cohorts × n_pop × n_ages × n_sexes × n_sims	Number of tagged fish released per cohort, population, age, and sex
conv_tagged_fish_attr	n_conv_tag_cohorts × n_pop × n_ages × n_sexes × n_sims	Tagged fish release array marginalised to the attended likelihood resolution (via conv_fish_tag_attr)
ln_init_conv_tag_mort	1	Log-scale initial tag-induced mortality
ln_conv_tag_shed	1	Log-scale chronic tag shedding rate
conv_tag_fish_avail	(conv_tag_max_liberty + 1) × n_seas × n_conv_tag_cohorts × n_pop × n_regions × n_ages × n_sexes × n_sims	Tagged fish available for recapture at each time step
pred_conv_tag_fish_recap	conv_tag_max_liberty × n_seas × n_conv_tag_cohorts × n_pop × n_regions × n_ages × n_sexes × n_fish_fleets × n_sims	Predicted conventional tag recaptures (retained catch only)
obs_conv_tag_fish_recap	conv_tag_max_liberty × n_seas × n_conv_tag_cohorts × n_pop × n_regions × n_ages × n_sexes × n_fish_fleets × n_sims	Observed (simulated) conventional tag recaptures