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DLMtool (version 5.0)

MSE-class: Class 'MSE'

Description

A Management Strategy Evaluation object that contains information about simulation conditions and performance of data-limited methods

Arguments

Slots

Name

Name of the MSE object. Single value. Character string

nyears

The number of years for the historical simulation. Single value. Positive integer

proyears

The number of years for the projections - closed loop simulations. Single value. Positive integer

nMPs

Number of management procedures simulation tested. Single value. Positive integer.

MPs

The names of the MPs that were tested. Vector of length nMPs. Character strings.

nsim

Number of simulations. Single value. Positive integer

OM

A table of sampled parameter of the operating model. Table object of nsim rows. Real numbers

  • RefY: reference yield, the highest long-term yield (mean over last five years of projection) obtained from a fixed F strategy. This is a useful reference point for framing performance of MPs because it standardizes for starting point and future productivity.

  • M: instantaneous natural mortality rate

  • Depletion: stock depletion (biomass / unfished biomass) in the final historical year (prior to projection)

  • A: abundance (biomass) updated in each management update of projection

  • BMSY_B0: most productive stock size relative to unfished

  • FMSY_M: fishing mortality rate divided by natural mortality rate

  • Mgrad: mean average percentage gradient in natural mortality rate (percentage per time step)

  • Msd: interannual variability in natural mortality rate (lognormal CV)

  • procsd: process error - CV in log-normal recruitment deviations

  • Esd: interannual variability in historical effort (fishing mortality rate)

  • dFfinal: gradient in fishing mortality rate over final five years of the historical simulation

  • MSY: Maximum Sustainable Yield

  • qinc: mean percentage increase in fishing efficiency (catchability) in projected years (input controls only)

  • qcv: interannual variability in future fishing efficiency (catchability) in projected years (input controls only)

  • FMSY: Fishing mortality rate at Maximum Sustainable Yield

  • Linf: maximum length (von Bertalanffy Linf parameter)

  • K: maximum growth rate (von Bertalanffy K parameter)

  • t0: theoretical length at age zero (von Bertalanffy t0 parameter)

  • hs: steepness of the stock recruitment relationship (the fraction of unfished recruitment at a fifth of unfished stock levels)

  • Linfgrad: mean gradient in maximum length (per cent per time step)

  • Kgrad: mean gradient in maximum growth rate (per cent per time step)

  • Linfsd: interannual variability in maximum length (log normal CV)

  • Ksd: interannual variability in maximum growth rate (log normal CV)

  • ageM: age at 50 per cent maturity

  • LFS: length at full selection (the shortest length class where fishery selectivity is 100 per cent)

  • age05: the age at 5 percent selectivity (ascending limb of selectivity curve)

  • Vmaxage: the selectivity of the oldest age class (controls dome shape of selectivity curve)

  • LFC: length at first capture, the smallest length that can be caught by the gear

  • OFLreal: the true simulated Over Fishing Limit (FMSY x biomass) updated in each management update of the projection

  • Spat_targ: spatial targetting parameter, fishing mortality rate across areas is proportional to vulnerable biomass raised to the power of this number.

  • Size_area_1: The size of area 1 relative to area 2

  • Frac_area_1: the fraction of unfished biomass inhabiting area 1 (can be seen as fraction of habitat in area 1 or relative size of area 1)

  • Prob_staying: the probability that individuals in area 1 remain there between time-steps

  • AC: autocorrelation in recruitment

Obs

A table of sampled parameters of the observation model. Table of nsim rows. Real numbers

  • Cbias: bias in observed catches

  • Csd: observation error in observed catches (lognormal CV)

  • CAA_nsamp: the number of catch-at-age observations per time step

  • CAA_ESS: the effective sample size of multinomial catch-at-age observation model (number of independent draws)

  • CAL_nsamp: the number of catch-at-length observations per time step

  • CAL_ESS: the effective sample size of multinomial catch-at-length observation model (number of independent draws)

  • Isd: observation error in relative abundance index (lognormal CV)

  • Dbias: bias in observed stock depletion (also applies to depletion Dt for DCAC)

  • Mbias: bias in observed natural mortality rate

  • FMSY_Mbias: bias in ratio of FMSY to natural mortality rate

  • BMSY_B0bias: bias in ratio of most productive stock size relative to unfished

  • AMbias: bias in age at 50 per cent maturity

  • LFCbias: bias in length at first capture

  • LFSbias: bias in length at full selection

  • Abias: bias in observed current absolute stock biomass

  • Kbias: bias in maximum growth rate (von Bertalanffy K parameter)

  • t0bias: bias in theoretical length at age zero (von Bertalanffy t0 parameter)

  • Linfbias: bias in maximum length (von Bertalanffy Linf parameter)

  • hbias: bias in observed steepness of the stock recruitment relationship

  • Irefbias: bias in abundance index corresponding to BMSY stock levels

  • Crefbias: bias in MSY prediction (target or reference catch)

  • Brefbias: bias in BMSY stock levels (target or reference biomass levels)

B_BMSY

Simulated biomass relative to BMSY over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

F_FMSY

Simulated fishing mortality rate relative to FMSY over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

B

Simulated stock biomass over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

SSB

Simulated spawning stock biomass over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

VB

Simulated vulnerable biomass over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

FM

Simulated fishing mortality rate over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

C

Simulated catches (taken) over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

TAC

Simulated Total Allowable Catch (prescribed) over the projection (this is NA for input controls). An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

SSB_hist

Simulated historical spawning stock biomass. An array with dimensions: nsim, nages, nMPs, proyears. Non-negative real numbers

CB_hist

Simulated historical catches in weight. An array with dimensions: nsim, nages, nMPs, proyears. Non-negative real numbers

FM_hist

Simulated historical fishing mortality rate. An array with dimensions: nsim, nages, nMPs, proyears. Non-negative real numbers

Effort

Simulated relative fishing effort in the projection years. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers

PAA

Population at age in last projection year. An array with dimensions: nsim, nMPs, nages. Non-negative real numbers

CAA

Catch at age in last projection year. An array with dimensions: nsim, nMPs, nages. Non-negative real numbers

CAL

Catch at length in last projection year. An array with dimensions: nsim, nMPs, nCALbins. Non-negative real numbers

CALbins

Mid-points of the catch-at-length bins. Vector of length nCALbins. Positive real numbers.

Objects from the Class

Objects can be created by calls of the form new('MSE', Name, nyears, proyears, nMPs, MPs, nsim, OMtable, Obs, B_BMSYa, F_FMSYa, Ba, FMa, Ca, OFLa, Effort, PAA, CAA, CAL, CALbins)