R/CompEscpmnt.R

In eeholmes/VRAP: VRAP for RER and Viability Computations

#' @title CompEscpmnt
#' @description Compute escapement
#' @param Regime Harvest regime.  
#' @param Year Year to compute the escapement for.
#' @param inputs Inputs from .rav file
#' @param BufTargetU Target ER to use for simulation.  Adjusted if StepFunc=ER.
#' @param Cohort Cohort
#' @param AEQ Adult equivalents
#' @param YearStats list of computed variables for each year: AEQMort, Escpmnt[Year,] = Escpmnt, TotAdultEscpmnt, TotAEQMort, TotEscpmnt,TempCohort.
#' @return Updated YearStats list for value of variables in Year
CompEscpmnt = function(Regime, Year, inputs, BufTargetU, Cohort, AEQ, YearStats){
  # If you have breakpoints, then Regime refers to which of these to use      
  # INITIALIZE PARAMETERS, VARIABLES, AND ARRAYS
  Converge = "No"
  MaxAge=inputs$MaxAge
  
  # SET EXPLOITATION RATE TARGET AFTER ADJUSTMENT FOR MANAGEMENT ERROR.
  # SET INITIAL FISHERY SCALE To 1.0  UNLESS TARGET U=0
  ErrorScale = 1
  if(inputs$MgmtError == "YES") ErrorScale = rgamma(1, inputs$GammaMgmtA, scale=inputs$GammaMgmtB)
  
  if(BufTargetU[Regime] > 0){
    
    BufTargetUError = BufTargetU[Regime] * ErrorScale
    
    if(BufTargetUError >= 1){
      # cat("Warning - Target HR Reduced to 0.99\n")
      BufTargetUError = 0.99  #not allowed to take all fish?
    }    
    FishScale = 1  #there is fishing
  }else{
    TempCohort = Cohort*(1-inputs$MatRate)
    Escpmnt = Cohort * inputs$MatRate
    Escpmnt[Escpmnt < 1] = 0
    AEQMort = rep(0, inputs$MaxAge)
    TotAEQMort = 0
    TotEscpmnt = sum(Escpmnt)
    Converge = "Yes" # don't need to go through the while loop
  }
  
  n = 0
  TotAEQMort.old = -1 
  while(Converge == "No"){
    n = n + 1
    # The pre-terminal and mature harvest will be scaled up or down until
    # the actual exploitation rate ActualU = TotAEQMort / (TotAEQMort + TotEscpmnt)
    # reaches the target for the simulation BufTargetUError.
    
    # COMPUTE PRETERMINAL MORTALITY AND UPDATE COHORT
    tmp=FishScale * inputs$PTU
    tmp[tmp>1] = 1 #can't take more fish than are there
    PTMort = tmp * Cohort
    TempCohort = Cohort - PTMort
    # This VB code not needed since R can work on a vector
    #     for(Age in inputs$MinAge:inputs$MaxAge){
    #       if(FishScale * inputs$PTU[Age] < 1){ #FishScale is 1 or 0
    #         PTMort[Age] = FishScale * Cohort[Age] * inputs$PTU[Age] #take a fraction of fish
    #       }else{
    #         PTMort[Age] = Cohort[Age] #take all fish at that age
    #       }
    #       TempCohort[Age] = Cohort[Age] - PTMort[Age] #pre-term mort
    #     } #end for loop age
    
    # COMPUTE MATURE RUN AND UPDATE COHORT
    MatRun = TempCohort * inputs$MatRate
    TempCohort = TempCohort - MatRun
    # This VB code not needed since R can work on a vector
    #     for(Age in inputs$MinAge:inputs$MaxAge){
    #       MatRun[Age] = TempCohort[Age] * inputs$MatRate[Age]
    #       TempCohort[Age] = TempCohort[Age] - MatRun[Age]
    #     } #end for loop Age
    
    # COMPUTE MATURE MORTALITY AND ESCAPEMENT
    # MatU, MatMort, Escpmnt, MatRun are all 1:MaxAge vectors
    tmp = FishScale * inputs$MatU
    tmp[tmp>1] = 1 #can't take more fish than are there
    MatMort = tmp * MatRun
    Escpmnt = MatRun - MatMort #spawners
    Escpmnt[Escpmnt < 1] = 0
    #     for(Age in inputs$MinAge:inputs$MaxAge){
    #       if(FishScale * inputs$MatU[Age] < 1){ 
    #         MatMort[Age] = FishScale * MatRun[Age] * inputs$MatU[Age] #these are the fish that return and are taken
    #       }else{ #all mature fish taken
    #         MatMort[Age] = MatRun[Age]
    #       }
    #       Escpmnt[Age] = MatRun[Age] - MatMort[Age] #spawners      
    #       if(Escpmnt[Age] < 1) Escpmnt[Age] = 0    
    #     }# end Age for loop
    
    # COMPUTE AEQ TOTAL MORTALITY EXPLOITATION RATE
    AEQMort = AEQ * PTMort + MatMort
    TotAEQMort = sum(AEQMort)
    TotEscpmnt = sum(Escpmnt)
    #     for(Age in inputs$MinAge:inputs$MaxAge){
    #       AEQMort[Age] = (AEQ[Age] * PTMort[Age]) + MatMort[Age]
    #       TotAEQMort = TotAEQMort + AEQMort[Age]
    #       TotEscpmnt = TotEscpmnt + Escpmnt[Age]
    #       #!!! MinAge fish (age 2) not counted
    #       if(Age > inputs$MinAge) TotAdultEscpmnt = TotAdultEscpmnt + Escpmnt[Age]     
    #     } #end for loop
    
    # COMPARE ACTUAL AND TARGET; SCALE EXPLOITATION RATES IF NECESSARY
    # if any of these met, exit
    # Criteria 1: unclear why needed.  Criteria 2: target ER < 0. 
    # Criteria 3: extinct; 
    # Criteria 4: no AEQ mortality from fishing (because no age 2+ fish most likely)
    # Criteria 5: TotAEQMort not changing despite FishScale change.  This happens when FishScale is already maxed out the fishing possible
    if(n > 100 | BufTargetU[Regime] <= 0 | 
       (TotAEQMort + TotEscpmnt) < 1 |
       TotAEQMort == 0 | TotAEQMort==TotAEQMort.old){ 
      Converge = "Yes"
    }else{ # none are met, so determine if converged
      ActualU = TotAEQMort / (TotAEQMort + TotEscpmnt)
      PercentError = abs((ActualU - BufTargetUError) / BufTargetUError)
      if(PercentError > inputs$ConvergeCrit){ 
        FishScale = FishScale * BufTargetUError / ActualU
      }else{ 
        Converge = "Yes" 
      }
    }
    TotAEQMort.old=TotAEQMort 
    # stored as a check against max ER reached without hitting target ER
  } # end of while
  # not needed inside while loop
  # TotAdultEscpmnt = sum(Escpmnt[(inputs$MinAge+1):inputs$MaxAge]) 
  
  YearStats$AEQMort[Year,] = AEQMort
  YearStats$Escpmnt[Year,] = Escpmnt
  YearStats$TotAdultEscpmnt[Year] = sum(Escpmnt[(inputs$MinAge+1):inputs$MaxAge])
  YearStats$TotAEQMort[Year] = TotAEQMort
  YearStats$TotEscpmnt[Year] = TotEscpmnt
  YearStats$TempCohort = TempCohort
  return(YearStats)
}