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Class 'Hist'

Source: R/Class_definitions.R
Hist-class.Rd

An object for storing information generated by the end of the historical simulations

Slots

Data

The Data object at the end of the historical period

OMPars

A numeric data.frame with nsim rows with sampled Stock, Fleet, Obs, and Imp parameters.

AtAge

A named list with arrays of dimensions: c(nsim, maxage+1, nyears+proyears) or c(nsim, maxage+1, nyears, nareas)

  • Length: Length-at-age for each simulation, age, and year

  • Weight: Weight-at-age for each simulation, age, and year

  • Select: Selectivity-at-age for each simulation, age, and year

  • Retention: Retention-at-age for each simulation, age, and year

  • Maturity: Maturity-at-age for each simulation, age, and year

  • N.Mortality: Natural mortality-at-age for each simulation, age, and year

  • Z.Mortality: Total mortality-at-age for each simulation, age, year and area

  • F.Mortality: Fishing mortality-at-age for each simulation, age, year and area

  • Fret.Mortality: Fishing mortality-at-age for retained fish for each simulation, age, year and area

  • Number: Total numbers by simulation, age, year and area

  • Biomass: Total biomass by simulation, age, year and area

  • VBiomass: Vulnerable biomass by simulation, age, year and area

  • SBiomass: Spawning biomass by simulation, age, year and area

  • Removals: Removals (biomass) by simulation, age, year and area

  • Landings: Landings (biomass) by simulation, age, year and area

  • Discards: Discards (biomass) by simulation, age, year and area

TSdata

A named list with population and fleet dynamics:

  • Number: Total numbers; array dimensions c(nsim, nyears, nareas)

  • Biomass: Total biomass; array dimensions c(nsim, nyears, nareas)

  • VBiomass: Vulnerable biomass; array dimensions c(nsim, nyears, nareas)

  • SBiomass: Spawning Biomass; array dimensions c(nsim, nyears, nareas)

  • Removals: Removals (biomass); array dimensions c(nsim, nyears, nareas)

  • Landings: Landings (biomass); array dimensions c(nsim, nyears, nareas)

  • Discards: Discards (biomass); array dimensions c(nsim, nyears, nareas)

  • Find: Historical fishing mortality (scale-free); matrix dimensions c(nsim, nyears)

  • RecDev: Recruitment deviations (historical and projection); matrix dimensions c(nsim, nyears+proyears+maxage)

  • SPR: Named list with Equilibrium and Dynamic SPR (both matrices iwth dimensions c(nsim, nyears))

  • Unfished_Equilibrium: A named list with unfished equilibrium numbers and biomass-at-age

Ref

A named list with biological reference points:

  • ByYear: A named list with asymptotic reference points (i.e., calculated annually without recruitment deviations) all matrices with dimensions nsim by nyears+proyears:

    • N0: Asymptotic unfished total number

    • SN0: Asymptotic unfished spawning number

    • B0: Asymptotic unfished total biomass

    • SSB0: Asymptotic unfished spawning biomass

    • VB0: Asymptotic unfished vulnerable biomass

    • MSY: Asymptotic MSY

    • FMSY: Fishing mortality corresponding with asymptotic MSY

    • SSBMSY: Spawning stock biomass corresponding with asymptotic MSY

    • BMSY: total biomass corresponding with asymptotic MSY

    • VBMSY: Vulnerable biomass corresponding with asymptotic MSY

    • F01: Fishing mortality where the change in yield per recruit is 10% of that at F = 0

    • Fmax: Fishing mortality that maximizes yield per recruit

    • F_SPR: Fishing mortality corresponding to spawning potential ratio of 20 - 60% in increments of 5%; array dimensions c(nsim, 9, nyears+proyears)

    • Fcrash: Fishing mortality corresponding to the recruits-per-spawner at the origin of the stock-recruit relationship

    • Fmed: Fishing mortality corresponding to the median recruits-per-spawner in the historical period

    • SPRcrash: SPR corresponding to the recruits-per-spawner at the origin of the stock-recruit relationship

  • Dynamic_Unfished: A named list with dynamic unfished reference points for each simulation and year:

    • N0: Unfished total numbers

    • B0: Unfished total biomass

    • SN0: Unfished spawning numbers

    • SSB0: Unfished spawning biomass

    • VB0: Unfished vulnerable biomass

    • Rec: Unfished recruitment

  • ReferencePoints: A data.frame with nsim rows with with biological reference points calculated as an average over age-of-maturity ageM years around the current year (i.e. nyears):

    • N0: Average unfished numbers

    • B0: Average unfished biomass

    • SSB0: Average unfished spawning biomass (used to calculate depletion)

    • SSN0: Average unfished spawning numbers

    • VB0: Average unfished vulnerable biomass (used to calculate depletion if cpar$control$D='VB')

    • MSY: Average maximum sustainable yield (equilibrium)

    • FMSY: Average fishing mortality corresponding with MSY

    • SSBMSY: Average spawning stock biomass corresponding with MSY

    • BMSY: Average total biomass corresponding with MSY

    • VBMSY: Average vulnerable biomass corresponding with MSY

    • UMSY: Average exploitation rate corresponding with MSY

    • FMSY_M: Average FMSY/M ratio

    • SSBMSY_SSB0: Average ratio of SSBMSY to SSB0

    • BMSY_B0: Average ratio of BMSY to B0

    • VBMSY_VB0: Average ratio of VBMSY to VB0

    • RefY: Maximum yield obtained in forward projections with a fixed F

SampPars

A named list with all sampled Stock, Fleet, Obs, and Imp parameters

OM

The OM object (without cpars)

Misc

A list for additional information

Author

A. Hordyk