MMSE-class: Class "MMSE"
In tcarruth/MSEtool: Management Strategy Evaluation Toolkit

Description Slots Objects from the Class Author(s)

A Multi Management Strategy Evaluation object that contains information about simulation conditions and performance of MPs for a multi-stock, multi-fleet operating model.

Name: Name of the MMSE 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.
MPcond: The MP condition. Character ('bystock': an MP per stock, 'byfleet' and MP per stock and fleet, 'MMP' an MP for all stocks and fleets)
MPrefs: The names of the MPs applied for each stock (row) and fleet (column). An array.
nsim: Number of simulations. Single value. Positive integer
nstocks: Number of stocks. Single value. Positive integer
nfleets: Number of fleets. Single value. Positive integer
Snames: Names of the stocks
Fnames: Names of the fleets (matrix nstocks x nfleets)
Stocks: The stock operating model objects. List of Stocks
Fleets: The fleet operating model objects. Hierarchical list, fleets nested in stocks.
Obss: The fleet specific observation error operating model objects. Hierarchical list, fleets nested in stocks.
Imps: The fleet soecific implementation error operating model objects. Hierarchical list, fleets nested in stocks.
OM: A table of sampled parameters of the operating model. Data frame of nsim rows.
Obs: A table of sampled parameters of the observation model. Data frame of nsim rows.
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, 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.
MSY_P: Array of projected MSY by year with dimensions: nsim, nstock, nMP, proyears.
FMSY_P: Array of projected FMSY by year with dimensions: nsim, nstock, nMP, proyears.
SSBMSY_P: Array of projected Spawning Stock Biomass at MSY by year with dimensions: nsim, nstock, nMP, proyears.
Misc: Miscellanenous output such as posterior predictive data

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

T. Carruthers

tcarruth/MSEtool documentation built on Oct. 19, 2020, 6:09 a.m.