R/fillTrueOM.R

In cmlegault/WKFORBIAS: Create and anlyze retro assessments

#' Fill True OM values
#' 
#' @param om operating model list from createOM
#' @export

fillTrueOM <- function(om){
  
  blankmat <- matrix(NA, nrow=om$nYear, ncol=om$nAge)
  if (is.null(om$NAA)) om$NAA <- blankmat
  if (is.null(om$FAA)) om$FAA <- blankmat
  if (is.null(om$MAA)) om$MAA <- blankmat
  if (is.null(om$WAA)) om$WAA <- blankmat
  if (is.null(om$indices)){ 
    om$indices <- list()
    for (ind in 1:om$nInd){
      om$indices[[ind]] <- list()
      om$indices[[ind]]$IAA <- blankmat 
    }
  }
   
  if (om$Flist$type == "constant"){
    om$FAA <- om$Flist$values
  }
  
  if (om$Mlist$type == "constant"){
    om$MAA <- om$Mlist$values
  }
  
  if (om$Wlist$type == "constant"){
    om$WAA <- om$Wlist$values
  }
  
  if (om$nyear1list$type == "constant"){
    om$NAA[1, ] <- om$nyear1list$values
  }
  
  if (om$Rlist$type == "constant"){
    om$NAA[, 1] <- om$Rlist$values
  }
  
  # fill in NAA matrix using F and M matrices
  for (iyear in 1:(om$nYear-1)){
    survs <- calcSurvival(om$NAA[iyear, ], om$MAA[iyear, ], om$FAA[iyear], TRUE)
    om$NAA[(iyear+1), 2:(om$nAge)] <- survs[-(om$nAge - 1)]
  }
  
  # calculate catch matrix using N, F, and M matrices
  om$CAA <- calcCatch(om$NAA, om$MAA, om$FAA)
  
  # calculate total catch in weight
  om$Ctot <- rep(NA, om$nYear)
  for (iyear in 1:om$nYear){
    om$Ctot[iyear] <- calcAggregateBiomass(om$CAA[iyear, ], om$WAA[iyear, ])
  }
  
  # generate surveys
  for (ind in 1:om$nInd){
    for (iyear in 1:om$nYear){
      om$indices[[ind]]$IAA[iyear, ] <- om$NAA[iyear, ] * om$indexlist[[ind]]$selxvalues * om$indexlist[[ind]]$qvalues  
    }
  }

  return(om)  
}

# example call 
# myomTrue <- fillTrueOM(myom)
# names(myomTrue)