MSE Object

Objects of class MSE are returned by the Project and runMSE functions, and contain all of the output from the MSE. In this section we will examine the MSE object in more detail.

First we will run an MSE so that we have an MSE object to work with. We will then briefly examine some of the contents of the MSE object.

We create an OM based on the Blue Shark stock object and other built-in objects:

OM <- new('OM', Blue_shark, Generic_Fleet, Imprecise_Biased, Perfect_Imp, nsim=200)

Note that we have increased the number of simulations from the default 48 to 200:

## [1] 200

Let’s choose an arbitrary set of MPs:

MPs <- c("Fratio", "DCAC", "Fdem", "DD", "matlenlim") 

Set up parallel processing:

## R Version:  R version 4.0.3 (2020-10-10) 
## Library MSEtool loaded.
## Library DLMtool loaded.
## Library SAMtool loaded.

And run the MSE using parallel processing and save the output to an object called BSharkMSE:

BSharkMSE <- runMSE(OM, MPs, parallel = TRUE, silent=TRUE)

The names of the slots in an object of class MSE can be displayed using the slotNames function:

##  [1] "Name"     "nyears"   "proyears" "nMPs"     "MPs"      "nsim"    
##  [7] "OM"       "Obs"      "SB_SBMSY" "F_FMSY"   "N"        "B"       
## [13] "SSB"      "VB"       "FM"       "SPR"      "Catch"    "Removals"
## [19] "Effort"   "TAC"      "TAE"      "BioEco"   "RefPoint" "CB_hist" 
## [25] "FM_hist"  "SSB_hist" "Hist"     "PPD"      "Misc"

MSE objects contain all of the information from the MSE, stored in 29 slots.

The following section describe the contents of the MSE object.