Add SAM assessement (via FLSAM) in MP

[iambaim]

Add SAM (https://github.com/fishfollower/SAM) as one of the assessment methods.
Example:

devtools::install_github("flr/FLSAM")

library(FLBEIA)
library(FLSAM)

rm(list=ls())
data(one)

oneAssC.sam <- oneAssC
oneAssC.sam[["stk1"]]$assess.model <- "sam2flbeia"
oneAssC.sam[["stk1"]]$harvest.units <- "f"
oneAssC.sam[["stk1"]]$control$indices.type <- "number" # This can be number, biomass or con


s1 <- FLBEIA( biols       = oneBio,    # FLBiols: FLBiol for stk1.
              SRs         = oneSR,     # List: FLSRSim for stk1.
              BDs         = NULL,        # Not population with biomass dynamics.
              fleets      = oneFl,     # FLFleets: one fleet.
              covars      = oneCv,     # List: covars related to economy.
              indices     = oneIndAge, # Age-structured index.
              advice      = oneAdv,    # List: 'TAC' and 'quota.share'
              main.ctrl   = oneMainC,  # List: info on start and end of the simulation.
              biols.ctrl  = oneBioC,   # List: model to simulate the stock dynamics.
              fleets.ctrl = oneFlC,    # List: fleet dynamics models select. and other params.
              covars.ctrl = oneCvC,    # List: covariates dynamics ("fixedCovar").
              obs.ctrl    = oneObsCIndAge, # List: type of stock and index observation
                                           #       ("age2ageDat","ageInd").
              assess.ctrl = oneAssC.sam,   # List: assessment model used ("sca2flbeia").
              advice.ctrl = oneAdvC)  # List: rule for TAC advice ("IcesHCR").


stk1.mp1 <- s1$stocks[['stk1']]
stk1.om1 <- FLBEIA:::perfectObs(s1$biols[['stk1']], s1$fleets, year = dim(s1$biols[['stk1']]@n)[2])
adf <- as.data.frame
s1_pop <- rbind( data.frame( population='obs', indicator='SSB', as.data.frame(ssb(stk1.mp1))), 
                 data.frame( population='obs', indicator='Harvest', as.data.frame(fbar(stk1.mp1))), 
                 data.frame( population='obs', indicator='Catch', as.data.frame(catch(stk1.mp1))),
                 data.frame( population='obs', indicator='Recruitment', as.data.frame(rec(stk1.mp1))),
                 data.frame( population='real', indicator='SSB', as.data.frame(ssb(stk1.om1))), 
                 data.frame( population='real', indicator='Harvest', as.data.frame(fbar(stk1.om1))), 
                 data.frame( population='real', indicator='Catch', as.data.frame(catch(stk1.om1))),
                 data.frame( population='real', indicator='Recruitment', as.data.frame(rec(stk1.om1))))
p <- ggplot( data=s1_pop, aes(x=year, y=data, color=population)) + 
  geom_line() +
  facet_grid(indicator ~ ., scales="free") + 
  geom_vline(xintercept = oneMainC$sim.years[['initial']]-1, linetype = "longdash")+
  theme_bw()+
  theme(text=element_text(size=15),
        title=element_text(size=15,face="bold"),
        strip.text=element_text(size=15), 
        legend.position="top")+
  ylab("")
print(p)

Thanks!

-Ibrahim