Learn R Programming
DLMtool (version 5.4.1)

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

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

  • AC: autocorrelation in recruitment

  • ageM: age at 50 per cent maturity

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

  • Blow: SSB where it takes MGThorizon x MGT to reach Bfrac of BMSY (spawning biomass)

  • BMSY: NA

  • BMSY_B0: ratio of BMSY to unfished total biomass in last historical year

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

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

  • DR: the fraction of caught fish that are discarded

  • Esd: inter-annual variability in fishing mortality rate

  • Fdisc: fraction of discarded fish that die

  • FinF: F in last historical year

  • FMSY: fishing mortality at MSY in last historical year

  • FMSY_M: ratio of FMSY to M in last historical year

  • Frac_area_1: fraction of the unfished biomass in stock 1

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

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

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

  • L5: length at 5/

  • L50: length at 50/

  • L50_95: increment between L50 and L95

  • L95: length at 95/

  • LenCV: CV of length-at-age

  • LFR: first length at full retention

  • LFS: first length at full selection

  • Linf: asymptotic length

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

  • LR5: first length at 5/

  • M: instantaneous natural mortality rate

  • maxF: NA

  • maxlen: NA

  • Mexp: exponent of Lorezen M-weight relationship

  • MGT: mean generation time

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

  • MSY: maximum sustainable yield in last historical year

  • OFLreal: A * FMSY the true simulated Over Fishing Limit in last historical year

  • Prob_staying: probability of inviduals in area 1 remaining in area 1 over the course of one year

  • procmu: NA

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

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

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

  • R0: NA

  • 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.

  • Rmaxlen: retention of fish at asymptotic length

  • Size_area_1: size of Area 1 relative to Area 2

  • SizeLimFrac: fraction of average implementation error of size regulations

  • SizeLimSD: log-normal coefficient of variation controlling mismatch between a minimum size limit and the real minimum size retained.

  • Spat_targ: distribution of fishing in relation to spatial biomass: fishing distribution is proportional to B^Spat_targ

  • SRrel: NA

  • SSB0: unfished spawning biomass

  • SSBMSY: NA

  • SSBMSY_SSB0: ratio of SSB_MSY/SSB0 in last historical year

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

  • TACFrac: mean fraction of TAC taken

  • TACSD: log-normal coefficient of variation in the fraction of Total Allowable Catch (TAC) taken

  • TAEFrac: mean fraction of TAE taken

  • TAESD: log-normal coefficient of variation in the fraction of TAE

  • UMSY: MSY exploitation rate

  • Vmaxlen: selection of fish at asymptotic length

Obs

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

  • Abias: bias in observed current absolute stock biomass

  • Aerr: error in observed current absolute stock biomass

  • betas: hyper-stability/hyper-depletion parameter

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

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

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

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

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

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

  • Cbias: bias in observed catches

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

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

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

  • Derr: error in observed stock depletion

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

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

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

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

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

  • lenMbias: bias in length at 50 per cent maturity

  • LFCbias: bias in length at first capture

  • LFSbias: bias in length at full selection

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

  • Mbias: bias in observed natural mortality rate

  • Recsd: error in observed recruitment

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

B_BMSY

Simulated spawning biomass relative to spawning 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, nyears, nareas. Non-negative real numbers

CB_hist

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

FM_hist

Simulated historical fishing mortality rate. An array with dimensions: nsim, nages, nyears, nareas. 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.

Misc

Miscellanenous output such as posterior predictive data

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)