The MSE object has 29 slots. As it is an S4 object the slots are accessed with the @ symbol, e.g., MSE@Name.
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
Operating model parameters (last historical year used for time-varying parameters). Data.frame with nsim rows
Obs
Observation parameters (last historical year used for time-varying parameters). Data.frame with nsim rows
SB_SBMSY
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
N
Simulated total numbers over the projection. An array with dimensions: nsim, maxage+1, nMPs, proyears, nareas. 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
SPR
Currently not used.
Catch
Simulated catches (landings) over the projection. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers
Removals
Simulated removals (catch + discards) over the projection. An array with dimensions: nsim, 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
TAC
Simulated Total Allowable Catch prescribed by MPs. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers
TAE
Simulated Total Allowable Effort prescribed by MPs. An array with dimensions: nsim, nMPs, proyears. Non-negative real numbers
BioEco
Named list with bio-economic output Only used if bio-economic parameters are included in OM
RefPoint
Named list of annual MSY reference points MSY, FMSY, and SBMSY. Array with dimensions: nsim, nMPs, nyears+proyears. Will be the same as Hist@Ref$ByYear unless selectivity is changed by MP
CB_hist
Simulated catches (landings) from the spool-up period. An array with dimensions: nsim, nyears. Non-negative real numbers
FM_hist
Simulated fishing mortality rate from the spool-up period. An array with dimensions: nsim, nyears Non-negative real numbers
SSB_hist
Simulated spawning stock biomass from the spool-up period. An array with dimensions: nsim, nyears. Non-negative real numbers
Hist
Information from the historical spool-up period. Object of class Hist . Only returned if extended=TRUE in runMSE
PPD
Posterior predictive data. List of Data objects at the end of the projection period (length nMPs )
Misc
Miscellaneous output