R/func_RedimensionArrays.R

In catarinawor/ERAR: This package is a loose translation of the Chinook Technical committee ERA model

#=======================================================
#ERA function GetFirstAndLastBY()
#Translated from VB ERA CIS code
#October 2018
#Author: Catarina Wor
#=======================================================

#=======================================================


#source(utils.R)




#' @title RedimensionArrays
#'
#' @description  Most.Useless.Thing.Ever =)
#' 
#' 
#'
#' @param M A list passed to MainSub
#'
#' @details
#'
#' @return D: A list 
#' 
#' 
#' 
#' @export
#'
#' @examples
#' 
#' 
RedimensionArrays <- function(D,M){

	#Redimension variables with correct number of BroodYear,Age, and Fishery dimensions
	#I think this function might be useless for the R vession. Will return to it if there is need. 

	D1<-list(AverageMatRate = vector(mode="numeric",length = D$MaxAge),
 				AverageAEQ = vector(mode="numeric",length = D$MaxAge),
   				CompleteBYFlag = vector(length = D$LastBY),
 				MissingBroodYearFlag = vector(length = D$LastBY),
 				CWTRelease = vector(length = D$LastBY),
 				TotalRelease = vector(length = D$LastBY),
 				RelRatio = vector(length = D$LastBY),
 				Escape = matrix(NA,nrow = D$LastBY, ncol=D$MaxAge),
 				EscStray_CA = matrix(NA, nrow = D$LastBY, ncol=D$MaxAge),
 				EscStray_US = matrix(NA,nrow = D$LastBY, ncol=D$MaxAge),
 				TotalMortalities = array(NA,dim = c(M$NumberPSCFisheries, D$MaxAge, D$LastBY)),
				TotalMortalityHarvestRate = array(NA, dim = c(M$NumberPSCFisheries, D$MaxAge, D$LastBY)),
 				CohortAfterNaturalMortality = matrix(NA, nrow= D$LastBY, ncol=D$MaxAge) 
 				)
 	TerminalRun <- matrix(NA,nrow = LastBY, ncol = MaxAge)
 	terminal <- matrix(NA, nrow = NumberPSCFisheries, ncol = MaxAge)
	SurvivalRate <- numeric(length = MaxAge + 1)
  	LastAge <- numeric(length = LastBY)
 	Cohort <- matrix(NA, nrow = LastBY, ncol = MaxAge + 1)
	MatRate <- matrix(NA, nrow = LastBY,ncol = MaxAge)
 	AEQ <- matrix(NA, nrow = LastBY, ncol = MaxAge + 1)
 	#landed catch variables
 	if(!isReplicateCohShak){
 		LandedCatch <- array(NA, dim = c(NumberPSCFisheries, 7, LastBY))
 	}else{
 		LandedCatch <- array(NA, dim = c(NumberPSCFisheries, 7, LastBY))
 	}
 	LegalDropoffMortality <-array(NA, dim = c(NumberPSCFisheries, 7, LastBY))
    TotalTerminalLandedCatch <- matrix(NA, nrow = LastBY, ncol = MaxAge)
 	TotalLandedCatch <- matrix(NA, nrow = LastBY, ncol = MaxAge)
 	TotalLandedCatch_ByFishery <- matrix(NA, nrow = LastBY, ncol =NumberPSCFisheries)
 	LandedCatchHarvestRate <- array(NA, dim = c(NumberPSCFisheries, MaxAge, LastBY))
 	AEQPreTermLandedCatch <- matrix(NA, nrow = LastBY, ncol= MaxAge)
 	AEQLandedCatchPreTermER <- matrix(NA, nrow = LastBY, ncol = MaxAge)
	LandedCatchTermER  <- matrix(NA, nrow = LastBY, ncol = MaxAge)
	AEQLandedCatchTotER <- matrix(NA, nrow = LastBY, ncol = MaxAge)
	TotalMortTermER <- matrix(NA, nrow = LastBY, ncol = MaxAge)
 	AEQTotalMortTotER <- matrix(NA, nrow = LastBY, ncol = MaxAge)
 	AEQTotalMortPreTermER <- matrix(NA, nrow= LastBY, ncol= MaxAge)
	PreTermIncidentalMortalities <- matrix(NA, nrow = LastBY, ncol = MaxAge)
 	AEQPreTermTotalMorts <- matrix(NA, nrow= LastBY, ncol = MaxAge)
 	AEQLandedCatchTotalRun <- numeric(length = LastBY)
	AEQTotalMortTotalRun <- numeric(length = LastBY)
	LandedCatchTerminalRun <- numeric(length = LastBY)
 	TotalMortTerminalRun <- numeric(length = LastBY)
 	AEQPreTermLandedCatchAllAges <- numeric(length = LastBY)
 	AEQPreTermTotalMortsAllAges <- numeric(length = LastBY)
 	TerminalLandedCatchAllAges <- numeric(length = LastBY)
	TerminalTotalMortsAllAges <- numeric(length = LastBY)
 	AEQLandedCatchAllAgesPreTermER <- numeric(length = LastBY)
 	AEQTotalMortAllAgesPreTermER <- numeric(length = LastBY)
 	LandedCatchAllAgesTerminalER <- numeric(length = LastBY)
 	TotalMortAllAgesTerminalER <- numeric(length = LastBY)
 	AEQLandedCatchAllAgesTotalER <- numeric(length = LastBY)
 	AEQTotalMortsAllAgesTotalER <- numeric(length = LastBY)
 	#shaker variables
 	TotalTerminalLegalDropoffs <- matrix(NA, nrow=LastBY, ncol=MaxAge)
 	TotalTerminalShakers <- matrix(NA, nrow=LastBY, ncol=MaxAge)
 	TotalTerminalShakerDropoffs <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalLegalDropoffs <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalSublegalShakerDropoffs<- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalSublegalShakers<- matrix(NA, nrow=LastBY, ncol=MaxAge)
 	#cnr variables
 	TotalCNR<- matrix(NA, nrow = LastBY, ncol=MaxAge)
 	TotalTerminalCNR <- matrix(NA, nrow=LastBY, ncol=MaxAge)
 	LegalCNRMortality <- array(NA, dim = c(NumberPSCFisheries, MaxAge, LastBY))
 	SubLegalCNRMortality <- array(NA,dim = c(NumberPSCFisheries, MaxAge, LastBY))
	LegalCNRDropoffs <- array(NA, dim = c(NumberPSCFisheries, MaxAge, LastBY))
	SubLegalCNRDropoffs <- array(NA, dim = c(NumberPSCFisheries, MaxAge, LastBY))
 	TotalCNRLegal <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalCNRLegalDropoffs <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalCNRSubLegal <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalCNRSubLegalDropoffs <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalTerminalCNRLegal <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalTerminalCNRLegalDropoffs <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalTerminalCNRSubLegal <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	TotalTerminalCNRSubLegalDropoffs <- matrix(NA, nrow=LastBY, ncol=MaxAge)
	ExtraLegalCNRMortality <- array(NA, dim=c(NumberPSCFisheries, MaxAge, LastBY))
	ExtraLegalCNRDropoffs <- array(NA,dim=c(NumberPSCFisheries, MaxAge, LastBY))
 	AdultInterDamSurvivalRate <- numeric(LastBY + MaxAge)
 	JackInterDamSurvivalRate <- numeric(LastBY + MaxAge)
	
	#Sub RedimensionArrays()
	#       'Redimension variables with correct number of BroodYear,Age, and Fishery dimensions
	#       ReDim AverageMatRate(MaxAge)
	#       ReDim AverageAEQ(MaxAge)
	#       ReDim CompleteBYFlag(LastBY)
	#       ReDim MissingBroodYearFlag(LastBY)
	#       ReDim CWTRelease(LastBY)
	#       ReDim TotalRelease(LastBY)
	#       ReDim RelRatio(LastBY)
	#       ReDim Escape(LastBY, MaxAge)
	#       ReDim EscStray_CA(LastBY, MaxAge)
	#       ReDim EscStray_US(LastBY, MaxAge)
	#       ReDim TotalMortalities(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim TotalMortalityHarvestRate(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim CohortAfterNaturalMortality(LastBY, MaxAge)
	#       ReDim TerminalRun(LastBY, MaxAge)
	#       ReDim terminal(NumberPSCFisheries, MaxAge)
	#       ReDim SurvivalRate(MaxAge + 1)
	#       ReDim LastAge(LastBY)
	#       ReDim Cohort(LastBY, MaxAge + 1)
	#       ReDim MatRate(LastBY, MaxAge)
	#       ReDim AEQ(LastBY, MaxAge + 1)
	#       'landed catch variables
	#       If isReplicateCohShak = False Then
	#           ReDim LandedCatch(NumberPSCFisheries, 7, LastBY)
	#       Else
	#           ReDim LandedCatch(NumberERAFisheries, 7, LastBY)
	#       End If
	#

	#       ReDim LegalDropoffMortality(NumberPSCFisheries, 7, LastBY)
	#       ReDim TotalTerminalLandedCatch(LastBY, MaxAge)
	#       ReDim TotalLandedCatch(LastBY, MaxAge)
	#       ReDim TotalLandedCatch_ByFishery(LastBY, NumberPSCFisheries)
	#       ReDim LandedCatchHarvestRate(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim AEQPreTermLandedCatch(LastBY, MaxAge)
	#       ReDim AEQLandedCatchPreTermER(LastBY, MaxAge)
	#       ReDim LandedCatchTermER(LastBY, MaxAge)
	#       ReDim AEQLandedCatchTotER(LastBY, MaxAge)
	#       ReDim TotalMortTermER(LastBY, MaxAge)
	#       ReDim AEQTotalMortTotER(LastBY, MaxAge)
	#       ReDim AEQTotalMortPreTermER(LastBY, MaxAge)
	#       ReDim PreTermIncidentalMortalities(LastBY, MaxAge)
	#       ReDim AEQPreTermTotalMorts(LastBY, MaxAge)
	#       ReDim AEQLandedCatchTotalRun(LastBY)
	#       ReDim AEQTotalMortTotalRun(LastBY)
	#       ReDim LandedCatchTerminalRun(LastBY)
	#       ReDim TotalMortTerminalRun(LastBY)
	#       ReDim AEQPreTermLandedCatchAllAges(LastBY)
	#       ReDim AEQPreTermTotalMortsAllAges(LastBY)
	#       ReDim TerminalLandedCatchAllAges(LastBY)
	#       ReDim TerminalTotalMortsAllAges(LastBY)
	#       ReDim AEQLandedCatchAllAgesPreTermER(LastBY)
	#       ReDim AEQTotalMortAllAgesPreTermER(LastBY)
	#       ReDim LandedCatchAllAgesTerminalER(LastBY)
	#       ReDim TotalMortAllAgesTerminalER(LastBY)
	#       ReDim AEQLandedCatchAllAgesTotalER(LastBY)
	#       ReDim AEQTotalMortsAllAgesTotalER(LastBY)
	#       'shaker variables
	#       ReDim TotalTerminalLegalDropoffs(LastBY, MaxAge)
	#       ReDim TotalTerminalShakers(LastBY, MaxAge)
	#       ReDim TotalTerminalShakerDropoffs(LastBY, MaxAge)
	#       ReDim TotalLegalDropoffs(LastBY, MaxAge)
	#       ReDim TotalSublegalShakerDropoffs(LastBY, MaxAge)
	#       ReDim TotalSublegalShakers(LastBY, MaxAge)
	#       'cnr variables
	#       ReDim TotalCNR(LastBY, MaxAge)
	#       ReDim TotalTerminalCNR(LastBY, MaxAge)
	#       ReDim LegalCNRMortality(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim SubLegalCNRMortality(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim LegalCNRDropoffs(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim SubLegalCNRDropoffs(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim TotalCNRLegal(LastBY, MaxAge)
	#       ReDim TotalCNRLegalDropoffs(LastBY, MaxAge)
	#       ReDim TotalCNRSubLegal(LastBY, MaxAge)
	#       ReDim TotalCNRSubLegalDropoffs(LastBY, MaxAge)
	#       ReDim TotalTerminalCNRLegal(LastBY, MaxAge)
	#       ReDim TotalTerminalCNRLegalDropoffs(LastBY, MaxAge)
	#       ReDim TotalTerminalCNRSubLegal(LastBY, MaxAge)
	#       ReDim TotalTerminalCNRSubLegalDropoffs(LastBY, MaxAge)
	#       ReDim ExtraLegalCNRMortality(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim ExtraLegalCNRDropoffs(NumberPSCFisheries, MaxAge, LastBY)
	#       ReDim AdultInterDamSurvivalRate(LastBY + MaxAge)
	#       ReDim JackInterDamSurvivalRate(LastBY + MaxAge)
	#   End Sub
}