Slots
Name- Name of the MSE object
nyears- The number of years for the historical simulation
proyears- The number of years for the projections - closed loop simulations
nMPs- Number of management procedures simulation tested
MPs- The names of the MPs that were tested
nsim- Number of simulations
OM- A table of nsim rows with a column for each sampled parameter of the operating model
- 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)
- CALcv: variability in lengths at age around the growth curve (normal CV)
- 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)
- recgrad: gradient in recruitment strength (age 1 population numbers) over last 10 years of historical simulations
- 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.
- 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 nsim rows with a column for each sampled parameter of the observation model
- 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- Stored biomass relative to BMSY over the projection (an array with dimensions nsim, nMPs, proyears)
F_FMSY- Stored fishing mortality rate relative to FMSY over the projection (an array with dimensions nsim, nMPs, proyears)
B- Stored stock biomass over the projection (an array with dimensions nsim, nMPs, proyears)
SSB- Stored spawning stock biomass over the projection (an array with dimensions nsim, nMPs, proyears)
VB- Stored vulnerable biomass over the projection (an array with dimensions nsim, nMPs, proyears)
FM- Stored fishing mortality rate over the projection (an array with dimensions nsim, nMPs, proyears)
C- Stored catches (taken) over the projection (an array with dimensions nsim, nMPs, proyears)
TAC- Stored Total Allowable Catch (prescribed) over the projection (an array with dimensions nsim, nMPs, proyears)(note that this is NA for input controls)
SSB_hist- Stored historical spawning stock biomass (historical simulations - an array with dimensions nsim, nages, nyears, nareas)
CB_hist- Stored historical catches in weight (historical simulations - an array with dimensions nsim, nages, nyears, nareas)
FM_hist- Stored historical fishing mortality rate (historical simulations - an array with dimensions nsim, nages, nyears, nareas)
Effort- Stored relative fishing effort in the projection years
Extra- A list for additional information
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)