Table 3: AGEPRO Keyword structure

Note: lengthSeqYears is representing the length a model’s sequential year time period beginning from the first projection year (NFyear) to the last projection year (NXyear).

Table 3: Structure of AGEPRO VERSION 4.25 input file by keyword.
Keyword Input Variable
GENERAL
  1. Single Line contains 9 Integer values:
    • NFyear (I) - this is the first year of the projection
    • NXYear (I) - this is the last year of the projection
    • NFAge (I) – this is the first age in the population model
    • NXAge (I) – this is the plus-group age in the population model
    • NSims (I) – this is the number of simulations to conduct for each bootstrap replicate of initial population size
    • NFleet (I) – this is the number of fleets in the harvest model
    • NRecModel (I) – this is the number of recruitment submodels in the population model
    • DiscFlag (I) – this is a logical flag to indicate whether discards are included in the harvest model (1=true, 0=false)
    • ISeed (I) – this is a positive integer seed to initialize the random number generator
CASEID
  1. Single Line contains a character string:
    • Model (S) – this is a string that describes the projection model run
BOOTSTRAP
  1. Single Line of containing 2 Numeric Values:
    • NBoot (I)- this is the number of bootstrap replicates of initial population size
    • BootFac (F) – this is the multiplicative factor to convert the relative bootstrap population numbers at age to absolute numbers at age
  2. Single Line containing a character string:
    • BootFile (S) – this is the name of the bootstrap filename including the file path
HARVEST
  1. Single Line containing a numerical vector:
    • HarvestSpec [0:NYears-1] (F) – this is the harvest specification by year vector where an input of zero indicates an F-based harvest rate and any positive input indicates a quota-based harvest rate (that is, input=0 for F and input>0 for catch biomass)
  2. The following is the logic for to determine HarvestValue [0:NYears-1][0:Nfleet-1] (F), which is the harvest amount by year and fleet array where an input row is the set of annual F values or catches (in metric tons) depending on the harvest specification by year.
    • If NFleet = 1, read in addittional line
    • else if NFleet > 2, read additional NFLEET-1 lines
RETROADJUST
  1. Single line containing a numerical value:
    • RetroAdjust [0:NAges-1] (F) – this is the vector of age-specific numbers at age multipliers for an initial population size at age vector if retrospective bias adjustment is applied
NATMORT
  1. Single line containing 2 Interger Values:
    • NatMortFlag (I) – this is the logical flag that indicates if the average natural mortality rate at age vector is to be read from an existing data file (input=1) or not (input≠)
    • NatMortTimeFlag (I) – this is the logical flag that indicates if the average natural mortality rate at age vector is a time-varying array (input =1) ordered by year (row) and age (column); otherwise the average natural mortality rate at age vector does not vary by year
  2. This is the logic for to determine how the average natural mortality rate at age AvgNatMort (F) vector is read:
    • If NatMortFlag = 1, read DataFiles[*] (S)
    • Else, presume NatMortFlag = 0,
      • If NatMortTimeFlag = 1, read additional NYears-1 rows: AvgNatMort[0:NAges-1]\[0:NYears-1] (F):
      • Else (NatMortTimeFlag = 0), read 1 more row: AvgNatMort[0:NAges-1] (F):
  3. Single Line containg numerical values:
    • NatMortErr[0:NAges-1] (F) This is the vector of age-specific CVs for sampling the natural mortality rate at age vector with lognormal process error
BIOLOGICAL
  1. Single Line containing an integer:
    • ZFracTimeFlag (I) – this is the logical flag that indicates if the within-year fractions of fishing (TF) and natural (TM) mortality that occur from January \(1^{st}\) to the spawning season are a time-varying array (input =1) or constant values (input≠1) where 0≤TF≤1 and 0≤TM≤1. For example, if the spawning season begins in July and input=0 then TF=TM=½
  2. This is the logic to read TF
    • If (ZFracTimeFlag = 1), then read NYears-1 rows: TF[0:NYears-1] (F)
    • Else read TF (F)
  3. This is the logic to read TM
    • If (ZFracTimeFlag = 1), then read NYears-1 rows: TM[0:NYears-1] (F)
    • Else read read TM (F)
MATURITY
  1. Single Line containing 2 integers:
    • MaturityFlag (I) – this is the logical flag that indicates if the average fraction mature at age vector is to be read from an existing data file (input =1) or not (input≠1)
    • MaturityTimeFlag (I) – this is the logical flag that indicates if the average fraction mature at age vector is a time-varying array (input =1) ordered by year (row) and age (column); otherwise the average fraction mature at age vector does not vary by year.
  2. This is the logic for to determine how the average fraction mature at age vector, AvgMaturity (F) is read:
    • If (MaturityFlag = 1), read DataFiles[*] (S)
    • Else, MaturutyFlag = 0,
      • If MaturityTimeFlag = 1, read additional NYears-1 rows: Avgmaturity[0:NAges-1]\[0:NYears-1] (F):
      • Else (MaturityTimeFlag = 0), read 1 more row: AvgMaturity[0:NAges-1] (F):
  3. Single line contining a numerical vector:
    • MaturityErr[0:NAges-1] (F) – this is the vector of age-specific CVs for sampling the fraction mature at age vector with lognormal process error
STOCK_WEIGHT
  1. Single Line containing 2 integers:
    • StockWtFlag (I) – this is the logical flag that indicates if the average stock weight at age vector is to be read from an existing data file (input =1) or not (input≠1)
    • StockWtTimeFlag (I) – this is the logical flag that indicates if the average stock weight at age vector is a time-varying array (input =1) ordered by year (row) and age (column); otherwise the average stock weight at age vector does not vary by year
  2. This is the logic for to determine how the average stock weight of age vector inputs, AvgStockWeight (F) is read:
    • If (StockWtFlag = 1), read DataFiles[*] (S)
    • Else, StockWtFlag = 0,
      • If (StockWtTimeFlag = 1), read additional NYears-1 rows: AvgStockWeight[0:NAges-1]\[0:NYears-1] (F)
      • Else (StockWtTimeFlag = 0), read 1 more row: AvgStockWeight[0:NAges-1] (F)
  3. Single line containing a numerical Vector
    • StockWtErr[0:NAges-1] (F) – this is the vector of age-specific CVs for sampling the stock weight at age vector with lognormal process error
SSB_WEIGHT
  1. Single Line containing 2 integers:
    • SpawnWtFlag (I) – this is the logical flag that indicates if the average spawning weight at age vector is:
      • (input>0) to be read from an existing data file
      • or (input=0) to be read from the input file
      • or (input=-1) to be set equal to the average stock weight at age vector
    • SpawnWtTimeFlag (I) – this is the logical flag that indicates if the average spawning weight at age vector is a time-varying array (input=1) ordered by year (row) and age (column); otherwise (input=0) the average spawning weight at age vector does not vary by year
  2. This is the logic for to determine how the average spawning weight of age vector inputs AvgSpawnWeight (F) is read:
    • If (SpawnWtFlag = 1), read DataFiles[*] (S)
    • Else if SpawnWtFlag = -1 then set average spawning weight at age vector to equal the average stock weight at age vector
    • Else, SpawnWtFlag = 0,
      • If (SpawnWtTimeFlag = 1), read additional NYears-1 rows: AvgSpawnWeight[0:NAges-1]\[0:NYears-1] (F)
      • Else (SpawnWtTimeFlag = 0), read 1 more row: AvgSpawnWeight[0:NAges-1] (F)
  3. Single Line containing numericial vector :
    • SpawnWtErr[0:NAges-1] (F) – this is the vector of age-specific CVs for sampling the spawning weight at age vector with lognormal process error
MEAN_WEIGHT
  1. Single Line containing 2 integers:
    • MeanStockWtFlag (I) – this is the logical flag that indicates if the average mean weight at age vector is to be read:
      • (input=1) from an existing data file
      • or (input=0) from the input file itself
    • MeanStockWtTimeFlag (I) – this is the logical flag that indicates if the average mean weight at age vector is a time-varying array (input=1) ordered by year (row) and age (column); otherwise (input=0) the average mean weight at age vector does not vary by year
  2. This is the logic for to determine how the average mean weight of age vector inputs AvgMeanStockWeight (F) is read:
    • If (MeanStockWtFlag = 1), read DataFiles[*] (S)
    • Else, presume MeanStockWtFlag = 0,
      • If (MeanStockWtTimeFlag = 1), read additional Nyears-1 rows: AvgMeanStockWeight [0:NAges-1][0:NYears-1] (F)
      • Else (MeanStockWtTimeFlag = 0), read 1 more row: AvgMeanWeight[0:NAges-1][0] (F)
  3. Single Line containing a numerical vector:
    • MeanStockWtErr[0:NAges-1] (F) – this is the vector of age-specific CVs for sampling the mean weight at age vector with lognormal process error
FISHERY
  1. Single Line containing 2 integers:
    • FSelecFlag (I) – this is the logical flag that indicates if the average fishery selectivity at age vectors by fleet are to be read:
      • (input=1) from an existing data file
      • or (input=0) from the input file itself
    • FSelecTimeFlag (I) – this is the logical flag that indicates if the average fishery selectivity at age vectors by fleet are a time-varying array (input=1) ordered by fleet (index 1), year (index 2), and age (index 3); otherwise (input=0) the average fishery selectivity at age vectors by fleet do not vary by year
  2. This is the logic for the average fishery selectivity at age vectors by fleet inputs AvgFSelec (F) is read:
    • If (FSelecFlag = 1), read DataFiles[*] (S)
    • Else, FSelectFlag = 0,
      • If (FSelecTimeFlag = 1), read (Nyears*Fleets)-1 rows: AvgFSelec [0:NAges-1][0:NYears-1][0:NFleets-1] (F)
      • Else (FSelectTimeFlag = 0), read NFleets rows: AvgFSelec[0:NAges-1][0][0:NFleets-1] (F)
  3. Single Line Containing a numerical vector:
    • FSelecErr[0:NAges-1][0:NFleets-1] (F) – this is the array of age-specific and fleet-specific CVs for sampling the fishery selectivity at age vectors by fleet with lognormal process error
DISCARD
  1. Single Line containing 2 integers:
    • DiscFracFlag (I) – this is the logical flag that indicates if the average discard fraction at age vectors by fleet are to be read from:
      • (input=1) an existing data file (input=1)
      • or (input≠1) from the input file itself.
    • DiscFracTimeFlag (I) – this is the logical flag that indicates if the average discard fraction at age vectors by fleet are a time-varying array (input=1) ordered by fleet (index 1), year (index 2), and age (index 3); otherwise (input=0) the average discard fraction at age vectors by fleet do not vary by year
  2. This is the logic for the average discard fraction at age vectors by fleet inputs AvgDiscFrac[0:NAges-1][0][0:NFleets-1] (F) is read:
    • If (DiscFracFlag = 1), read DataFiles[*] (S)
    • Else, DiscFracFlag = 0
      • If (DiscFracTimeFlag = 0), read an addtitional (Nyears*Fleets)-1 rows: AvgDiscFrac [0:NAges-1][0:NYears-1][0:NFleets-1] (F)
      • Else (FSelectTimeFlag = 1), read Nfleets row(s): AvgDiscFrac[0:NAges-1][0][0:NFleets-1] (F)
  3. Single Line Containing a numerical vector:
    • DiscFracErr[0:NAges-1][0:NFleets-1] (F) – this is the array of age-specific and fleet-specific CVs for sampling the discard fraction at age vectors by fleet with lognormal process error
CATCH_WEIGHT
  1. Single Line containing 2 integers:
    • CatchWtFlag (I) – this is the logical flag that indicates if the average catch weight at age vectors by fleet are to be read from:
      • (input=1) an existing data file
      • or (input=0) to be read from the input file
      • or (input=-1) to be set equal to the average stock weight at age vector
      • or (input=-2) to be set equal to the average spawning weight at age vector
      • or (input=-3) to be set equal to the average mean weight at age vector
    • CatchWtTimeFlag (I) – this is the logical flag that indicates if the average catch weight at age vectors by fleet are a time-varying array (input=1) ordered by fleet (index 1), year (index 2), and age (index 3); otherwise the average catch weight at age vectors by fleet do not vary by year
  2. This is the logic for the average catch weight at age vector inputs AvgCatchWeight (F) is read:
    • If (CatchWtFlag = 1), read DataFiles[*] (S)
    • Else if (CatchWtFlag = -1), then set average catch weight at age vector to equal the average stock weight at age vector
    • Else if (CatchWtFlag = -2), then set average catch weight at age vector to equal the average spawning weight at age vector
    • Else if (CatchWtFlag = -3), then set average catch weight at age vector to equal the average mean weight at age vector
    • Else, CatchWtFlag = 1, then
      • If (CatchWtTimeFlag = 1), read an addtitional (Nyears*Fleets)-1 rows for AvgCatchWeight [0:NAges-1][0:NYears-1][0:NFleets-1] (F)
      • Else (CatchWtTimeFlag = 0), read Nfleet rows for AvgCatchWeight [0:NAges-1][0][0:NFleets-1] (F)
  3. Single Line containing a numeric vector:
    • CatchWtErr[0:NAges-1][0:NFleets-1] (F) – this is the array of age-specific and fleet-specific CVs for sampling the catch weight at age vectors by fleet with lognormal process error
DISC_WEIGHT
  1. Single Line containing 2 integers:
    • DiscWtFlag (I) – this is the logical flag that indicates if the average discard weight at age vectors by fleet are to be read from:
      • (input=1) an existing data file
      • or (input=0) to be read from the input file
      • or (input=-1) to be set equal to the average stock weight at age vector
      • or (input=-2) to be set equal to the average spawning weight at age vector
      • or (input=-3) to be set equal to the average mean weight at age vector
      • or (input=-4) to be set equal to the average catch weight at age vector
    • DiscWtTimeFlag (I) – this is the logical flag that indicates if the average discard weight at age vectors by fleet are a time-varying array (input=1) ordered by fleet (index 1), year (index 2), and age (index 3); otherwise (input=0) the average discard weight at age vectors by fleet do not vary by year.
  2. This is the logic for the average discard weight at age vector inputs AvgDiscWeight (F) is read:
    • If (DiscWtFlag = 1), read DataFiles[*] (S)
    • Else if (DiscWtFlag = -1), then set average discard weight at age vector to equal the average stock weight at age vector
    • Else if (DiscWtFlag = -2), then set average discard weight at age vector to equal the average spawning weight at age vector
    • Else if (DiscWtFlag = -3), then set average discard weight at age vector to equal the average mean weight at age vector
    • Else if (DiscWtFlag = -4), then set average discard weight at age vector to equal the average catch weight at age vector
    • Else, DiscWtFlag = 0
      • If (DiscWtTimeFlag = 1), then read AvgDiscWeight [0:NAges-1][0:NYears-1][0:NFleets-1] (F)
      • Else (DiscWtTimeFlag = 0), read AvgDiscWeight[0:NAges-1][0][0:NFleets-1] (F)
  3. Single Line containing a numeric vector
    • DiscWtErr[0:NAges-1][0:NFleets-1] (F) – this is the array of age-specific and fleet-specific CVs for sampling the discard weight at age vectors by fleet with lognormal process error
RECRUIT
  1. Single line containing 3 integers
    • RecFac (F) – this is the multiplier to convert recruitment submodel units for recruitment to absolute numbers of fish
    • SSBFac (F) – this is the multiplier to convert recruitment submodel units for spawning biomass to absolute spawning weight of fish in kilograms
    • MaxRecObs (I) – this is the maximum number of recruitment observations for an empirical recruitment submodel (up to the maximum value of a long int, or about 2 billion array elements)
  2. Single line containing a numeric vector
    • RecruitType[0:NRecModel-1] (I) – this is the vector of recruitment submodel types in the projection
  3. Numerical matrix array of lengthSeqYears rows (lines) and count of submodel types columns
    • RecruitProb[0:NYears-1][0:NRecModel-1] (F) – this is the array of recruitment submodel probabilities ordered by year (row) and submodel (column) with row sums equal to unity
  4. RecruitData: For each recruitment submodel in RecruitType vector, j=0 to (NRecModel – 1), is a the set of function calls to read in the input data needed for each recruitment submodel. See Table 4: Input data structure for AGEPRO Recruitment Models for specific details where the required input data for each submodel RecruitType is read.
BOUNDS
  1. Single Line contaning 2 integers:
    • MaxWeight (F) – this is the maximum value of an fish weight, noting that there is lognormal sampling variation for weight at age values
    • MaxNatMort (F) – this is the maximum natural mortality rate, noting that there is lognormal sampling variation for natural mortality at age values
PERC
  1. Single Line containing 1 numeric value:
    • PercReportValue (F) – this is the user-selected percentile for reporting the percentile of the projected distribution of the following by year: spawning stock biomass, stock biomass on January \(1^{st}\), mean biomass, combined catch biomass, landings, fishing mortality, and stock numbers at age
REFPOINT
  1. Single Line containing 4 numeric values:
    • SSBThresh (F) – this is the spawning biomass threshold expressed in biomass output units
    • StockBioThresh (F) – this is the stock biomass threshold expressed in biomass output units
    • MeanBioThresh (F) – this is the mean biomass threshold expressed in biomass output units
    • FMortThresh (F) – this is the fishing mortality threshold
OPTIONS
  1. Single Line containing 3 integers:
    • StockSummaryFlag (I) – this is the logical flag to output stock summary information
      • I=0: No stock summary or auxiliary files
      • I=1. Stock summary in output file and no auxiliary files
      • I=2. Stock summary in output file and auxiliary files 2 through 10 are produced
      • I=3. Stock summary in output file and all auxiliary files are produced
    • DataFlag (I) – this is the logical flag to output population and fishery processes simulated with lognormal process error to auxiliary output files
    • ExportRFlag (I) – this is the logical flag to output projection results to an R dataframe
SCALE
  1. Single Line containing 3 numeric values:
    • scalebio (F) – the output units of biomass expressed in thousand metric tons
    • scalerec (F) – the output units of recruitment numbers
    • scalestk (F) – the output units of stock size numbers
REBUILD
  1. Single Line containing 4 numeric and interger values:
    • TargetYear (I) – this is the user-selected target year for rebuilding to the target value
    • TargetValue (F) – this is the target biomass value in units of thousands of metric tons
    • TargetType (I) – this is the index for the type of population biomass as the target where index=0 is spawning stock biomass, index=1 is stock biomass on January 1st, else target is mean biomass
    • TargetPercent (F) – this is the percent frequency of achieving the target value by the target year where the percent frequency is a value between 0 (indicating zero chance of achieving target) and 100 (indicating 100 percent chance of achieving target).
PSTAR
  1. Single Line containing a Interger value:
    • KPStar (I) – this is the user-selected number of PStar values to be evaluated in the target year
  2. Single Line containing a Numerical Vector:
    • KStar[0:KPStar-1] (F) – these are the PStar values to evaluate where PStar is the probability of exceeding the overfishing level
  3. Single Line containing a numerical value:
    • PStarF (F) – this is the fishing mortality rate that defines the overfishing level
  4. Single Line containing a Integer value:
    • TargetYear (I) – this is user-selected target year for the total annual catch to produce the user-selected PStar values is calculated