R/SimulatorFn.R

In nwfscAgeingError: Ageing error

SimulatorFn <-
function(Nreaders, M, SelexForm, ErrorParams, BiasParams, SelexParams, ReadsMat, RecCv=0.6, RecAr1=0.8, Amax=100){

  RecDev = rnorm(Amax, mean=0, sd=RecCv)
    for(i in 2:length(RecDev)){RecDev[i] = RecDev[i]*sqrt(1-RecAr1) + RecDev[i-1]*sqrt(RecAr1)}
  AgeStruct = 1 * exp(-M*1:Amax) * exp(RecDev - RecCv^2/2)
  if(SelexForm=="Logistic"){
    SelexAtAge = 1 / (1 + exp((SelexParams[1]-1:Amax)*SelexParams[2]))
  }else{
    stop("Selex not implemented")
  }
  Ages = sample(x=1:Amax, size=sum(ReadsMat[,1]), prob=AgeStruct*SelexAtAge, replace=TRUE)

  AgeReads = vector()

  IndexI = 0
  for(RowI in 1:nrow(ReadsMat)){
  for(OtolithI in 1:ReadsMat[RowI,1]){
    IndexI = IndexI + 1
    Row = vector()
    for(ReaderI in 1:Nreaders){
      if(ReadsMat[RowI,ReaderI+1]==0){
        Row = c(Row, NA)
      }else{
        Row = c(Row, round(Ages[IndexI]*BiasParams[ReaderI] + rnorm(1, mean=0, sd=Ages[IndexI]*ErrorParams[ReaderI])))
      }
    }
    AgeReads = rbind(AgeReads,Row)
  }}
  return(AgeReads)
}