R/func_CalcCNR.R
In catarinawor/ERAR: This package is a loose translation of the Chinook Technical committee ERA model
Defines functions
CalcCNR
CNRNoDir
#ERA function ShakerMethod1() and ShakerMethod4()
#Translated from VB ERA CIS code
#June 2018 -2019
#Author: Catarina Wor
#' @title CalcCNR
#'
#' @description Calculate Catch non retention after shakermethod.
#'
#'
#' @param M A list passed to MainSub
#' @param D A list containing the outputs of GetWithinBYWeightFlagAndPNVRegionAndAvgMatRates
#'
#' @details
#'
#' @return D1: A list
#'
#' @export
#'
#' @examples
#'
#'
#'
CalcCNR <- function(D, M){
#'calculates legal and sublegal CNR using data from ERA_IMInputs database table
allBY <- D$FirstBY:D$LastBY
allCalYr <- (D$FirstBY + D$OceanStartAge) : M$LastCalendarYear
LegalCNRMortality <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
LegalCNRDropoffs <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
SubLegalCNRMortality <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
SubLegalCNRDropoffs <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
TotalCNRLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalCNRLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalCNRSubLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalCNRSubLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRSubLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRSubLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
for(BroodYear in seq_along(allBY)){
#'skip missing brood years
if(!D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY == allBY[BroodYear]]){
for(PSCFishery in seq_len(M$NumberPSCFisheries-3)){
for(age in D$OceanStartAge:D$LastAge[BroodYear]){
#If isTraceCalc = True Then WriteLine(debug_subLegalCNRID, "9999 follow BY 2013 age 3 CENTRL T", BroodYear, PSCFishery, age, SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
CalYr <- allBY[BroodYear] + age
CalYrind <- allCalYr[allCalYr==CalYr]
#'If CalYr > LastIMYear Then GoTo SkipAge
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1957", PSCFishery, BroodYear, age, CalYr, "CNRMethod", CNRMethod(CalYr, PSCFishery))
AA = as.character(D$IMdf$CNRMethod[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery])
if(AA=="1"|AA=="4"|AA=="5"){
switch(AA,
"1"={
# 'season length method
ratio = D$IMdf$CNRSeasonLength[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$SeasonLength[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
},
"4"={
# 'season effort method, same algorithms as method 1 and 5 but different data
ratio = D$IMdf$CNREffort[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$RetentionEffort[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
},
"5"={
# 'Monitored Catch and monitored release method
ratio = D$IMdf$MonitoredLegalReleases[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$MonitoredLegalCatch[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
},
{
stop('CNR method not defined')
}
)
LegalCNRMortality[PSCFishery, age, BroodYear] <- D$LandedCatch[PSCFishery, age, BroodYear] * ratio * D$IMdf$LegalSelectivityFactor[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] * D$IMdf$LegalIMRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
LegalCNRDropoffs[PSCFishery, age, BroodYear] <- D$LandedCatch[PSCFishery, age, BroodYear] * ratio * D$IMdf$LegalSelectivityFactor[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] * D$IMdf$DropoffRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), CalYr)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
#'**********
#'old code included legal dropoffs and sublegal dropoffs in shakers so I added them here, they should be removed in final code
SubLegalCNRMortality[PSCFishery, age, BroodYear] <- (D$SublegalShakerMortalities[PSCFishery, age, BroodYear] + D$SublegalDropoffMortalities[PSCFishery, age, BroodYear] + D$LegalDropoffMortality[PSCFishery, age, BroodYear]) * ratio * D$IMdf$SublegalSelectivityFactor[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
#If isTraceCalc = True And BroodYear >= traceThisYear Then WriteLine(debug_subLegalCNRID, "1830 CaclCNR", PSCFishery, BroodYear, age, SubLegalCNRMortality(PSCFishery, age, BroodYear), SublegalShakerMortalities(PSCFishery, age, BroodYear), SublegalDropoffMortalities(PSCFishery, age, BroodYear), LegalDropoffMortality(PSCFishery, age, BroodYear), ratio, SublegalSelectivityFactor(CalYr, PSCFishery))
}else{
switch(AA,
"2"={
LegalCNRMortality[PSCFishery, age, BroodYear] <- (D$LandedCatch[PSCFishery, age, BroodYear] * D$IMdf$CNRLegalEncounterEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]) * D$IMdf$LegalIMRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
LegalCNRDropoffs[PSCFishery, age, BroodYear] <- (D$LandedCatch[PSCFishery, age, BroodYear] * D$IMdf$CNRLegalEncounterEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]) * D$IMdf$DropoffRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1836 legalCNR", "Shaker", "Method2", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), CNRLegalEncounterEst(CalYr, PSCFishery), LandedCatchEst(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
if(D$CalendarYearShakers[CalYr, PSCFishery] != 0){
CNRSublegalEncounters <- (D$IMdf$CNRSubLegalEncounterEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] *
D$CalendarYearLandedCatch[CalYrind, PSCFishery] /
D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]) *
((D$SublegalShakerMortalities[PSCFishery, age, BroodYear] +
D$SublegalDropoffMortalities[PSCFishery, age, BroodYear] +
D$LegalDropoffMortality[PSCFishery, age, BroodYear]) /
D$CalendarYearShakers[CalYrind, PSCFishery])
SubLegalCNRMortality[PSCFishery, age, BroodYear] <- CNRSublegalEncounters *
(D$IMdf$SublegalIMRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] +
D$IMdf$DropoffRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery])
}
},
"3"={
#'catchability coefficient method used when there was no retention fishery
d2 <- CNRNoDir(CalYr, BroodYear, PSCFishery, age)
SubLegalCNRMortality[PSCFishery, age, BroodYear] <- d2$SubLegalCNRMortality
LegalCNRMortality[PSCFishery, age, BroodYear] <- d2$LegalCNRMortality
},
"9"={ #'no cnr fishery or data
#'There is no CNR for this year and fishery, go to next year
},
{
stop('CNR method not defined')
}
)
}
}
}
}
}
#'MOVED THIS SECTION OF CODE FROM TOP OF ROUTINE SO THAT
#' CNR MORTALITIES IN LAST PASS WOULD BE AVAILABLE FOR METHOD 3
#' IN NEXT PASS 9/24/97
for(BroodYear in seq_along(allBY)){
for(age in D$OceanStartAge:D$LastAge[BroodYear]){
D$TotalCNRLegal[BroodYear, age] <- 0
D$TotalCNRLegalDropoffs[BroodYear, age] <- 0
D$TotalCNRSubLegal[BroodYear, age] <- 0
D$TotalCNRSubLegalDropoffs[BroodYear, age] <- 0
D$TotalTerminalCNRLegal[BroodYear, age] <- 0
D$TotalTerminalCNRLegalDropoffs[BroodYear, age] <- 0
D$TotalTerminalCNRSubLegal[BroodYear, age] <- 0
D$TotalTerminalCNRSubLegalDropoffs[BroodYear, age] <- 0
}
}
#'MOVED THIS SECTION OF CODE FROM LOOP ABOVE FOR REASON NOTED ABOVE
for(BroodYear in seq_along(allBY)){
#'skip missing brood years
if(!D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY==allBY[BroodYear]]){
CalYr <- BroodYear + age
TotalCNRLegal[BroodYear, ] <- apply(LegalCNRMortality[, , BroodYear],2,sum)
TotalCNRLegalDropoffs[BroodYear, ] <- apply(LegalCNRDropoffs[, , BroodYear],2,sum)
TotalCNRSubLegal[BroodYear, ] <- apply(SubLegalCNRMortality[, , BroodYear],2,sum)
TotalCNRSubLegalDropoffs[BroodYear, ] <- apply(SubLegalCNRDropoffs[, , BroodYear],2,sum)
TotalTerminalCNRLegal[BroodYear,] <- apply(LegalCNRMortality[D$terminal[, age], , BroodYear],2,sum)
TotalTerminalCNRLegalDropoffs[BroodYear,] <- apply(LegalCNRDropoffs[D$terminal[, age], , BroodYear],2,sum)
TotalTerminalCNRSubLegal[BroodYear,] <- apply(SubLegalCNRMortality[D$terminal[, age], , BroodYear],2,sum)
TotalTerminalCNRSubLegalDropoffs[BroodYear,] <- apply(SubLegalCNRDropoffs[D$terminal[, age], , BroodYear],2,sum)
}
}
return(list(TotalCNRLegal=TotalCNRLegal,
TotalCNRLegalDropoffs=TotalCNRLegalDropoffs,
TotalCNRSubLegal=TotalCNRSubLegal,
TotalCNRSubLegalDropoffs=TotalCNRSubLegalDropoffs,
TotalTerminalCNRLegal=TotalTerminalCNRLegal,
TotalTerminalCNRLegalDropoffs=TotalTerminalCNRLegalDropoffs,
TotalTerminalCNRSubLegal=TotalTerminalCNRSubLegal,
TotalTerminalCNRSubLegalDropoffs=TotalTerminalCNRSubLegalDropoffs,
LegalCNRMortality = LegalCNRMortality,
LegalCNRDropoffs = LegalCNRDropoffs,
SubLegalCNRMortality = SubLegalCNRMortality,
LegalCNRDropoffs = LegalCNRDropoffs))
#Original VB code
#'calculates legal and sublegal CNR using data from ERA_IMInputs database table
# Dim CNRSublegalEncounters As Single
# Dim CalYr As Integer
# Dim ratio As Single
# For BroodYear As Integer = FirstBY To LastBY
# 'skip missing brood years
# If MissingBroodYearFlag(BroodYear) = False Then
# For PSCFishery As Integer = 1 To NumberPSCFisheries
# For age As Integer = OceanStartAge To LastAge(BroodYear)
# If isTraceCalc = True Then WriteLine(debug_subLegalCNRID, "9999 follow BY 2013 age 3 CENTRL T", BroodYear, PSCFishery, age, SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
# CalYr = BroodYear + age
# 'If CalYr > LastIMYear Then GoTo SkipAge
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1957", PSCFishery, BroodYear, age, CalYr, "CNRMethod", CNRMethod(CalYr, PSCFishery))
# Select Case CNRMethod(CalYr, PSCFishery)
# Case 1, 4, 5 'season length, season effort, and monitored release methods, same algorithms, different data in ratio
# Select Case CNRMethod(CalYr, PSCFishery)
# Case 1 'season length method
# ratio = CNRSeasonLength(CalYr, PSCFishery) / SeasonLength(CalYr, PSCFishery)
# Case 4 'season effort method, same algorithms as method 1 and 5 but different data
# ratio = CNREffort(CalYr, PSCFishery) / RetentionEffort(CalYr, PSCFishery)
# Case 5 'Monitored Catch and monitored release method
# ratio = MonitoredLegalReleases(CalYr, PSCFishery) / MonitoredLegalCatch(CalYr, PSCFishery)
# End Select
# LegalCNRMortality(PSCFishery, age, BroodYear) = LandedCatch(PSCFishery, age, BroodYear) * ratio * LegalSelectivityFactor(CalYr, PSCFishery) * LegalIMRate(CalYr, PSCFishery)
# LegalCNRDropoffs(PSCFishery, age, BroodYear) = LandedCatch(PSCFishery, age, BroodYear) * ratio * LegalSelectivityFactor(CalYr, PSCFishery) * DropoffRate(CalYr, PSCFishery)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), CalYr)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
# '**********
# 'old code included legal dropoffs and sublegal dropoffs in shakers so I added them here, they should be removed in final code
# SubLegalCNRMortality(PSCFishery, age, BroodYear) = (SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)) * ratio * SublegalSelectivityFactor(CalYr, PSCFishery)
# If isTraceCalc = True And BroodYear >= traceThisYear Then WriteLine(debug_subLegalCNRID, "1830 CaclCNR", PSCFishery, BroodYear, age, SubLegalCNRMortality(PSCFishery, age, BroodYear), SublegalShakerMortalities(PSCFishery, age, BroodYear), SublegalDropoffMortalities(PSCFishery, age, BroodYear), LegalDropoffMortality(PSCFishery, age, BroodYear), ratio, SublegalSelectivityFactor(CalYr, PSCFishery))
# Case 2 'reported encounters method
# LegalCNRMortality(PSCFishery, age, BroodYear) = (LandedCatch(PSCFishery, age, BroodYear) * CNRLegalEncounterEst(CalYr, PSCFishery) / LandedCatchEst(CalYr, PSCFishery)) * LegalIMRate(CalYr, PSCFishery)
# LegalCNRDropoffs(PSCFishery, age, BroodYear) = (LandedCatch(PSCFishery, age, BroodYear) * CNRLegalEncounterEst(CalYr, PSCFishery) / LandedCatchEst(CalYr, PSCFishery)) * DropoffRate(CalYr, PSCFishery)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1836 legalCNR", "Shaker", "Method2", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), CNRLegalEncounterEst(CalYr, PSCFishery), LandedCatchEst(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
# If CalendarYearShakers(CalYr, PSCFishery) <> 0 Then
# CNRSublegalEncounters = (CNRSubLegalEncounterEst(CalYr, PSCFishery) * CalendarYearLandedCatch(CalYr, PSCFishery) / LandedCatchEst(CalYr, PSCFishery)) * ((SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)) / CalendarYearShakers(CalYr, PSCFishery))
# SubLegalCNRMortality(PSCFishery, age, BroodYear) = CNRSublegalEncounters * (SublegalIMRate(CalYr, PSCFishery) + DropoffRate(CalYr, PSCFishery))
# If isTraceCalc = True Then
# If BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then Write(debug_subLegalCNRID, "1837 sublegalCNR", PSCFishery, age, "rpt enc", CNRSubLegalEncounterEst(CalYr, PSCFishery), "rpt cat", LandedCatchEst(CalYr, PSCFishery), "SL IMrate", SublegalIMRate(CalYr, PSCFishery), "dropoffRate", DropoffRate(CalYr, PSCFishery), "relRatio", RelRatio(BroodYear))
# If BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then Write(debug_subLegalCNRID, "CNR sublegal", "method2", SubLegalCNRMortality(PSCFishery, age, BroodYear), "enc", CNRSubLegalEncounterEst(CalYr, PSCFishery), "*calYrCatch", CalendarYearLandedCatch(CalYr, PSCFishery), "/rpt catch*(SL shaker", SublegalShakerMortalities(PSCFishery, age, BroodYear), "+ SL dropoff", SublegalDropoffMortalities(PSCFishery, age, BroodYear), "+ L dropoff)", LegalDropoffMortality(PSCFishery, age, BroodYear), "/calYrShakers", CalendarYearShakers(CalYr, PSCFishery))
# If BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_subLegalCNRID, "*(SL IMRate + dropoff rate)", CalYr)
# End If
# End If
# Case 3 'catchability coefficient method used when there was no retention fishery
# Call CNRNoDir(CalYr, BroodYear, PSCFishery, age)
# Case 9 'no cnr fishery or data
# 'There is no CNR for this year and fishery, go to next year
# End Select
# 'SkipAge:
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "2042", "CNRMethod", CNRMethod(CalYr, PSCFishery), BroodYear, PSCFishery, age, "CNRlegal", LegalCNRMortality(PSCFishery, age, BroodYear), "shakers", LegalCNRDropoffs(PSCFishery, age, BroodYear), "relratio", RelRatio(BroodYear))
# Next age
# Next PSCFishery
# End If
# Next BroodYear
# 'MOVED THIS SECTION OF CODE FROM TOP OF ROUTINE SO THAT
# ' CNR MORTALITIES IN LAST PASS WOULD BE AVAILABLE FOR METHOD 3
# ' IN NEXT PASS 9/24/97
# For BroodYear As Integer = FirstBY To LastBY
# For Age = OceanStartAge To LastAge(BroodYear)
# TotalCNRLegal(BroodYear, Age) = 0
# TotalCNRLegalDropoffs(BroodYear, Age) = 0
# TotalCNRSubLegal(BroodYear, Age) = 0
# TotalCNRSubLegalDropoffs(BroodYear, Age) = 0
# TotalTerminalCNRLegal(BroodYear, Age) = 0
# TotalTerminalCNRLegalDropoffs(BroodYear, Age) = 0
# TotalTerminalCNRSubLegal(BroodYear, Age) = 0
# TotalTerminalCNRSubLegalDropoffs(BroodYear, Age) = 0
# Next Age
# Next BroodYear
# 'MOVED THIS SECTION OF CODE FROM LOOP ABOVE FOR REASON NOTED ABOVE
# For BroodYear As Integer = FirstBY To LastBY
# 'skip missing brood years
# If MissingBroodYearFlag(BroodYear) = False Then
# For PSCFishery = 1 To NumberPSCFisheries
# For age As Integer = OceanStartAge To LastAge(BroodYear)
# CalYr = BroodYear + age
# TotalCNRLegal(BroodYear, age) += LegalCNRMortality(PSCFishery, age, BroodYear)
# TotalCNRLegalDropoffs(BroodYear, age) += LegalCNRDropoffs(PSCFishery, age, BroodYear)
# TotalCNRSubLegal(BroodYear, age) += SubLegalCNRMortality(PSCFishery, age, BroodYear)
# TotalCNRSubLegalDropoffs(BroodYear, age) += SubLegalCNRDropoffs(PSCFishery, age, BroodYear)
# If terminal(PSCFishery, age) = True And PSCFisheryGear(PSCFishery) <> "STRAY" Then
# TotalTerminalCNRLegal(BroodYear, age) += LegalCNRMortality(PSCFishery, age, BroodYear)
# TotalTerminalCNRLegalDropoffs(BroodYear, age) += LegalCNRDropoffs(PSCFishery, age, BroodYear)
# TotalTerminalCNRSubLegal(BroodYear, age) += SubLegalCNRMortality(PSCFishery, age, BroodYear)
# TotalTerminalCNRSubLegalDropoffs(BroodYear, age) += SubLegalCNRDropoffs(PSCFishery, age, BroodYear)
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then
# WriteLine(debug_LegalDropoffID, "2368 CalcCNR", PSCFishery, age, BroodYear, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), SubLegalCNRMortality(PSCFishery, age, BroodYear), SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
# WriteLine(debug_terminalCatchID, "2368 CalcCNR fishery specific", PSCFishery, age, BroodYear, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), SubLegalCNRMortality(PSCFishery, age, BroodYear), SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
# WriteLine(debug_terminalCatchID, "2368 CalcCNR total", PSCFishery, age, BroodYear, TotalTerminalCNRLegal(BroodYear, age), TotalTerminalCNRLegalDropoffs(BroodYear, age), TotalTerminalCNRSubLegal(BroodYear, age), TotalTerminalCNRSubLegalDropoffs(BroodYear, age))
# End If
# Next age
# Next PSCFishery
# End If
# Next BroodYear
}
#' @title CNRNoDir
#'
#' @description Calculate Catch non retention after shakermethod when there was no retention fishery.
#'
#'
#' @param M A list passed to MainSub
#' @param D A list containing the outputs of GetWithinBYWeightFlagAndPNVRegionAndAvgMatRates
#'
#' @details
#'
#' @return D1: A list
#'
#' @export
#'
#' @examples
#'
#'
#'
CNRNoDir <- function(YR, BroodYear, PSCFishery,age){
#'Calculation of legal-sized CNR mortalities
# 'when estimated encounter of legal-sized During CNR is unknown
# 'use boat days to estimate
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches)
# 'local variables
IMortRt <-matrix(NA, nrow=2, ncol=2)
sublegal <- 1
legal <- 2
Instantaneous <- 1
Annual <- 2
#'DM = DropoffRate(YR, PSCFishery) dropoff rate is not used, SHould it be????
#'Note: removed division by Drop-off rate, Oct. 29 1997; included in external Q
#' For this algorithm to work correctly, the q values must be computed
#' with dropoff mortality included.
for(sizeGroup in sublegal:legal){
#'get annual landing rate for hypothetical retention fishery: catchability * selectivity * boat-days
if(sizeGroup == sublegal){
SubLegalCatchabilityCoefficient<- D$catchabilitydf$AvgQ[D$catchabilitydf$SizeClass == "S" & D$catchabilitydf$PSCFishery == PSCFishery&D$catchabilitydf$Age==age]
SublegalSelectivityFactor <- D$IMdf$SublegalSelectivityFactor[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
CNREffort <- D$IMdf$CNREffort[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
AnnualRetentionEncounterRate <- 1 - exp(-SubLegalCatchabilityCoefficient * SublegalSelectivityFactor * CNREffort )
}else if(sizeGroup == sublegal){
LegalCatchabilityCoefficient <- D$catchabilitydf$AvgQ[D$catchabilitydf$SizeClass == "L" & D$catchabilitydf$PSCFishery == PSCFishery&D$catchabilitydf$Age==age]
LegalSelectivityFactor <- D$IMdf$LegalSelectivityFactor[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
CNREffort <- D$IMdf$CNREffort[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
AnnualRetentionEncounterRate <- 1 - exp(- LegalCatchabilityCoefficient * LegalSelectivityFactor * CNREffort)
}
#'convert to Instantaneous rate
InstantaneousRetentionEncounterRate <- -log(1 - AnnualRetentionEncounterRate)
#'difference between hypothetical retention and CNR rates is
#'replacement of boat-days with boat-reavailability day
#'i.e. boat-days /(CNR season in days/availability in days)
CNRSeasonLength <- D$IMdf$CNRSeasonLength[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
Reavailability <- D$IMdf$Reavailability[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
tp = CNRSeasonLength / Reavailability
#'convert hypothetical retention rate to CNR rate
InstantaneousCNREncounterRate <- InstantaneousRetentionEncounterRate / tp
#'convert Instantaneous rate back to annual rate
AnnualCNREncounterRate <- 1 - exp(-InstantaneousCNREncounterRate)
if(sizeGroup == sublegal){
IMortRt[Annual, 1] <- AnnualCNREncounterRate
}else if(sizeGroup == legal){
LegalIMRate <- D$IMdf$LegalIMRate[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
IMortRt[Annual, 1] = AnnualCNREncounterRate * LegalIMRate
}
IMortRt[Instantaneous, 1] <- -log(1 - IMortRt[Annual, 1]) #'this is already computed above
IMortRt[Annual, 2] = 1 - exp(-IMortRt[Instantaneous, 1] * tp) #'this is already computed above
if(D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY == allBY[BroodYear]]){
if(!D$terminal[PSCFishery,age]){
cohrt <- D$Cohort[BroodYear, age] * D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
}else{
cohrt <- TotalTerminalCatch_Age(D, M, BY=BroodYear, age) + D$Escape[BroodYear, age]
}
}else{
if(M$ShakerMethod == "C"| age <= D$LastAge[BroodYear] ){
cohrt <- CalcEstmCohrt2(D, M, BroodYear, age)
}else{
cohrt <- CalcEstmCohrt(D, M, BroodYear, age)
}
if(D$terminal[PSCFishery, age]){
cohrt <- cohrt * (1 - D$AveragePreTermER[age]) * D$AverageMatRate[age]
}
}
if(sizeGroup == sublegal){
SubLegalCNRMortality <- IMortRt[Annual, 2] * cohrt
}else if(sizeGroup == legal){
LegalCNRMortality <- IMortRt[Annual, 2] * cohrt
}
}
return(list(SubLegalCNRMortality=SubLegalCNRMortality,
LegalCNRMortality=LegalCNRMortality))
# -----------------------------------------------------------------------------------------
#Original VB code
# Sub CNRNoDir(ByRef YR As Integer, ByRef BroodYear As Integer, ByRef PSCFishery As Integer, ByRef age As Integer) 'no directed fishery
# 'Calculation of legal-sized CNR mortalities
# 'when estimated encounter of legal-sized During CNR is unknown
# 'use boat days to estimate
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches)
#
# 'local variables
# Dim cohrt As Single
# Dim Annual, Instantaneous As Integer
# Dim AnnualRetentionEncounterRate, InstantaneousRetentionEncounterRate, AnnualCNREncounterRate, InstantaneousCNREncounterRate As Single
# Dim IMortRt(1, 1) As Single
# Dim tp As Single
# Dim sublegal As Integer = 1
# Dim legal As Integer = 2
# Instantaneous = 0
# Annual = 1
# 'DM = DropoffRate(YR, PSCFishery) dropoff rate is not used, SHould it be????
# 'Note: removed division by Drop-off rate, Oct. 29 1997; included in external Q
# ' For this algorithm to work correctly, the q values must be computed
# ' with dropoff mortality included.
# For sizeGroup As Integer = sublegal To legal
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And sizeGroup = sublegal And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2920 SL", SubLegalCatchabilityCoeifficient(age, PSCFishery), SublegalSelectivityFactor(YR, PSCFishery), CNREffort(YR, PSCFishery))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And sizeGroup = legal And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2921 L", LegalCatchabilityCoeifficient(age, PSCFishery), LegalSelectivityFactor(YR, PSCFishery), CNREffort(YR, PSCFishery))
# 'get annual landing rate for hypothetical retention fishery: catchability * selectivity * boat-days
# If sizeGroup = sublegal Then
# AnnualRetentionEncounterRate = 1 - System.Math.Exp(-SubLegalCatchabilityCoeifficient(age, PSCFishery) * SublegalSelectivityFactor(YR, PSCFishery) * CNREffort(YR, PSCFishery))
# ElseIf sizeGroup = legal Then
# AnnualRetentionEncounterRate = 1 - System.Math.Exp(-LegalCatchabilityCoeifficient(age, PSCFishery) * LegalSelectivityFactor(YR, PSCFishery) * CNREffort(YR, PSCFishery))
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2928 ann", AnnualRetentionEncounterRate)
# 'convert to Instantaneous rate
# InstantaneousRetentionEncounterRate = -System.Math.Log(1 - AnnualRetentionEncounterRate)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2932 inst", AnnualRetentionEncounterRate)
#
# 'difference between hypothetical retention and CNR rates is
# 'replacement of boat-days with boat-reavailability day
# 'i.e. boat-days /(CNR season in days/availability in days)
# tp = CNRSeasonLength(YR, PSCFishery) / Reavailability(YR, PSCFishery)
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2873", sizeGroup, YR, "AnnRetenEncRte", AnnualRetentionEncounterRate, "InstantaneousRetentionEncounterRate", InstantaneousRetentionEncounterRate, "tp", tp)
#
#
# 'convert hypothetical retention rate to CNR rate
# InstantaneousCNREncounterRate = InstantaneousRetentionEncounterRate / tp
# 'convert Instantaneous rate back to annual rate
# AnnualCNREncounterRate = 1 - System.Math.Exp(-InstantaneousCNREncounterRate)
# If sizeGroup = sublegal Then
# IMortRt(Annual, 0) = AnnualCNREncounterRate
# ElseIf sizeGroup = legal Then
# IMortRt(Annual, 0) = AnnualCNREncounterRate * LegalIMRate(YR, PSCFishery)
# End If
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2879", sizeGroup, BroodYear, age, YR, "AnnRetenEncRte", LegalCatchabilityCoeifficient(age, PSCFishery), LegalSelectivityFactor(YR, PSCFishery), CNREffort(YR, PSCFishery), "tp", CNRSeasonLength(YR, PSCFishery), Reavailability(YR, PSCFishery), "IMortRT", AnnualCNREncounterRate, LegalIMRate(YR, PSCFishery))
#
# IMortRt(Instantaneous, 0) = -System.Math.Log(1 - IMortRt(Annual, 0)) 'this is already computed above
# IMortRt(Annual, 1) = 1 - System.Math.Exp(-IMortRt(Instantaneous, 0) * tp) 'this is already computed above
# If CompleteBYFlag(BroodYear) = True Then
# If terminal(PSCFishery, age) = False Then
# cohrt = Cohort(BroodYear, age) * SurvivalRate(age)
# Else
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "3045 CNRNoDir callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
# cohrt = TotalTerminalCatch_Age(BroodYear, age, pass) + Escape(BroodYear, age)
# End If
# Else
# If ShakerMethod = "C" Or age <= LastAge(BroodYear) Then
# cohrt = CalcEstmCohrt2(BroodYear, age)
# If isTraceCalc = True And shakermethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "3010 CNRNoDir", ShakerMethod, BroodYear, age, PSCFishery, cohrt)
# Else
# cohrt = CalcEstmCohrt(BroodYear, age)
# End If
# If terminal(PSCFishery, age) = True Then
# cohrt = cohrt * (1 - AveragePreTermER(age)) * AverageMatRate(age)
# End If
# End If
# If sizeGroup = sublegal Then
# SubLegalCNRMortality(PSCFishery, age, BroodYear) = IMortRt(Annual, 1) * cohrt
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2899", BroodYear, PSCFishery, age, "CNRNoDir SL", SubLegalCNRMortality(PSCFishery, age, BroodYear), IMortRt(Annual, 1), cohrt, "calYr", YR, "relratio", RelRatio(BroodYear))
# ElseIf sizeGroup = legal Then
# LegalCNRMortality(PSCFishery, age, BroodYear) = IMortRt(Annual, 1) * cohrt
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2903", BroodYear, PSCFishery, age, "CNRNoDir L", LegalCNRMortality(PSCFishery, age, BroodYear), IMortRt(Annual, 1), cohrt, "calYr", YR, "relratio", RelRatio(BroodYear))
# End If
# Next sizeGroup
#
# End Sub
}
catarinawor/ERAR documentation built on Sept. 21, 2019, 8:25 a.m.
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Defines functions CalcCNR CNRNoDir
#ERA function ShakerMethod1() and ShakerMethod4()
#Translated from VB ERA CIS code
#June 2018 -2019
#Author: Catarina Wor
#' @title CalcCNR
#'
#' @description Calculate Catch non retention after shakermethod.
#'
#'
#' @param M A list passed to MainSub
#' @param D A list containing the outputs of GetWithinBYWeightFlagAndPNVRegionAndAvgMatRates
#'
#' @details
#'
#' @return D1: A list
#'
#' @export
#'
#' @examples
#'
#'
#'
CalcCNR <- function(D, M){
#'calculates legal and sublegal CNR using data from ERA_IMInputs database table
allBY <- D$FirstBY:D$LastBY
allCalYr <- (D$FirstBY + D$OceanStartAge) : M$LastCalendarYear
LegalCNRMortality <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
LegalCNRDropoffs <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
SubLegalCNRMortality <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
SubLegalCNRDropoffs <- array(0, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
TotalCNRLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalCNRLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalCNRSubLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalCNRSubLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRSubLegal <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
TotalTerminalCNRSubLegalDropoffs <- matrix(0, nrow=length(allBY),ncol=D$MaxAge)
for(BroodYear in seq_along(allBY)){
#'skip missing brood years
if(!D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY == allBY[BroodYear]]){
for(PSCFishery in seq_len(M$NumberPSCFisheries-3)){
for(age in D$OceanStartAge:D$LastAge[BroodYear]){
#If isTraceCalc = True Then WriteLine(debug_subLegalCNRID, "9999 follow BY 2013 age 3 CENTRL T", BroodYear, PSCFishery, age, SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
CalYr <- allBY[BroodYear] + age
CalYrind <- allCalYr[allCalYr==CalYr]
#'If CalYr > LastIMYear Then GoTo SkipAge
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1957", PSCFishery, BroodYear, age, CalYr, "CNRMethod", CNRMethod(CalYr, PSCFishery))
AA = as.character(D$IMdf$CNRMethod[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery])
if(AA=="1"|AA=="4"|AA=="5"){
switch(AA,
"1"={
# 'season length method
ratio = D$IMdf$CNRSeasonLength[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$SeasonLength[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
},
"4"={
# 'season effort method, same algorithms as method 1 and 5 but different data
ratio = D$IMdf$CNREffort[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$RetentionEffort[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
},
"5"={
# 'Monitored Catch and monitored release method
ratio = D$IMdf$MonitoredLegalReleases[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$MonitoredLegalCatch[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
},
{
stop('CNR method not defined')
}
)
LegalCNRMortality[PSCFishery, age, BroodYear] <- D$LandedCatch[PSCFishery, age, BroodYear] * ratio * D$IMdf$LegalSelectivityFactor[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] * D$IMdf$LegalIMRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
LegalCNRDropoffs[PSCFishery, age, BroodYear] <- D$LandedCatch[PSCFishery, age, BroodYear] * ratio * D$IMdf$LegalSelectivityFactor[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] * D$IMdf$DropoffRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), CalYr)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
#'**********
#'old code included legal dropoffs and sublegal dropoffs in shakers so I added them here, they should be removed in final code
SubLegalCNRMortality[PSCFishery, age, BroodYear] <- (D$SublegalShakerMortalities[PSCFishery, age, BroodYear] + D$SublegalDropoffMortalities[PSCFishery, age, BroodYear] + D$LegalDropoffMortality[PSCFishery, age, BroodYear]) * ratio * D$IMdf$SublegalSelectivityFactor[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
#If isTraceCalc = True And BroodYear >= traceThisYear Then WriteLine(debug_subLegalCNRID, "1830 CaclCNR", PSCFishery, BroodYear, age, SubLegalCNRMortality(PSCFishery, age, BroodYear), SublegalShakerMortalities(PSCFishery, age, BroodYear), SublegalDropoffMortalities(PSCFishery, age, BroodYear), LegalDropoffMortality(PSCFishery, age, BroodYear), ratio, SublegalSelectivityFactor(CalYr, PSCFishery))
}else{
switch(AA,
"2"={
LegalCNRMortality[PSCFishery, age, BroodYear] <- (D$LandedCatch[PSCFishery, age, BroodYear] * D$IMdf$CNRLegalEncounterEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]) * D$IMdf$LegalIMRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
LegalCNRDropoffs[PSCFishery, age, BroodYear] <- (D$LandedCatch[PSCFishery, age, BroodYear] * D$IMdf$CNRLegalEncounterEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] / D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]) * D$IMdf$DropoffRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1836 legalCNR", "Shaker", "Method2", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), CNRLegalEncounterEst(CalYr, PSCFishery), LandedCatchEst(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
if(D$CalendarYearShakers[CalYr, PSCFishery] != 0){
CNRSublegalEncounters <- (D$IMdf$CNRSubLegalEncounterEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] *
D$CalendarYearLandedCatch[CalYrind, PSCFishery] /
D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery]) *
((D$SublegalShakerMortalities[PSCFishery, age, BroodYear] +
D$SublegalDropoffMortalities[PSCFishery, age, BroodYear] +
D$LegalDropoffMortality[PSCFishery, age, BroodYear]) /
D$CalendarYearShakers[CalYrind, PSCFishery])
SubLegalCNRMortality[PSCFishery, age, BroodYear] <- CNRSublegalEncounters *
(D$IMdf$SublegalIMRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery] +
D$IMdf$DropoffRate[D$IMdf$CalendarYear==CalYr&D$IMdf$PSCFishery==PSCFishery])
}
},
"3"={
#'catchability coefficient method used when there was no retention fishery
d2 <- CNRNoDir(CalYr, BroodYear, PSCFishery, age)
SubLegalCNRMortality[PSCFishery, age, BroodYear] <- d2$SubLegalCNRMortality
LegalCNRMortality[PSCFishery, age, BroodYear] <- d2$LegalCNRMortality
},
"9"={ #'no cnr fishery or data
#'There is no CNR for this year and fishery, go to next year
},
{
stop('CNR method not defined')
}
)
}
}
}
}
}
#'MOVED THIS SECTION OF CODE FROM TOP OF ROUTINE SO THAT
#' CNR MORTALITIES IN LAST PASS WOULD BE AVAILABLE FOR METHOD 3
#' IN NEXT PASS 9/24/97
for(BroodYear in seq_along(allBY)){
for(age in D$OceanStartAge:D$LastAge[BroodYear]){
D$TotalCNRLegal[BroodYear, age] <- 0
D$TotalCNRLegalDropoffs[BroodYear, age] <- 0
D$TotalCNRSubLegal[BroodYear, age] <- 0
D$TotalCNRSubLegalDropoffs[BroodYear, age] <- 0
D$TotalTerminalCNRLegal[BroodYear, age] <- 0
D$TotalTerminalCNRLegalDropoffs[BroodYear, age] <- 0
D$TotalTerminalCNRSubLegal[BroodYear, age] <- 0
D$TotalTerminalCNRSubLegalDropoffs[BroodYear, age] <- 0
}
}
#'MOVED THIS SECTION OF CODE FROM LOOP ABOVE FOR REASON NOTED ABOVE
for(BroodYear in seq_along(allBY)){
#'skip missing brood years
if(!D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY==allBY[BroodYear]]){
CalYr <- BroodYear + age
TotalCNRLegal[BroodYear, ] <- apply(LegalCNRMortality[, , BroodYear],2,sum)
TotalCNRLegalDropoffs[BroodYear, ] <- apply(LegalCNRDropoffs[, , BroodYear],2,sum)
TotalCNRSubLegal[BroodYear, ] <- apply(SubLegalCNRMortality[, , BroodYear],2,sum)
TotalCNRSubLegalDropoffs[BroodYear, ] <- apply(SubLegalCNRDropoffs[, , BroodYear],2,sum)
TotalTerminalCNRLegal[BroodYear,] <- apply(LegalCNRMortality[D$terminal[, age], , BroodYear],2,sum)
TotalTerminalCNRLegalDropoffs[BroodYear,] <- apply(LegalCNRDropoffs[D$terminal[, age], , BroodYear],2,sum)
TotalTerminalCNRSubLegal[BroodYear,] <- apply(SubLegalCNRMortality[D$terminal[, age], , BroodYear],2,sum)
TotalTerminalCNRSubLegalDropoffs[BroodYear,] <- apply(SubLegalCNRDropoffs[D$terminal[, age], , BroodYear],2,sum)
}
}
return(list(TotalCNRLegal=TotalCNRLegal,
TotalCNRLegalDropoffs=TotalCNRLegalDropoffs,
TotalCNRSubLegal=TotalCNRSubLegal,
TotalCNRSubLegalDropoffs=TotalCNRSubLegalDropoffs,
TotalTerminalCNRLegal=TotalTerminalCNRLegal,
TotalTerminalCNRLegalDropoffs=TotalTerminalCNRLegalDropoffs,
TotalTerminalCNRSubLegal=TotalTerminalCNRSubLegal,
TotalTerminalCNRSubLegalDropoffs=TotalTerminalCNRSubLegalDropoffs,
LegalCNRMortality = LegalCNRMortality,
LegalCNRDropoffs = LegalCNRDropoffs,
SubLegalCNRMortality = SubLegalCNRMortality,
LegalCNRDropoffs = LegalCNRDropoffs))
#Original VB code
#'calculates legal and sublegal CNR using data from ERA_IMInputs database table
# Dim CNRSublegalEncounters As Single
# Dim CalYr As Integer
# Dim ratio As Single
# For BroodYear As Integer = FirstBY To LastBY
# 'skip missing brood years
# If MissingBroodYearFlag(BroodYear) = False Then
# For PSCFishery As Integer = 1 To NumberPSCFisheries
# For age As Integer = OceanStartAge To LastAge(BroodYear)
# If isTraceCalc = True Then WriteLine(debug_subLegalCNRID, "9999 follow BY 2013 age 3 CENTRL T", BroodYear, PSCFishery, age, SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
# CalYr = BroodYear + age
# 'If CalYr > LastIMYear Then GoTo SkipAge
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1957", PSCFishery, BroodYear, age, CalYr, "CNRMethod", CNRMethod(CalYr, PSCFishery))
# Select Case CNRMethod(CalYr, PSCFishery)
# Case 1, 4, 5 'season length, season effort, and monitored release methods, same algorithms, different data in ratio
# Select Case CNRMethod(CalYr, PSCFishery)
# Case 1 'season length method
# ratio = CNRSeasonLength(CalYr, PSCFishery) / SeasonLength(CalYr, PSCFishery)
# Case 4 'season effort method, same algorithms as method 1 and 5 but different data
# ratio = CNREffort(CalYr, PSCFishery) / RetentionEffort(CalYr, PSCFishery)
# Case 5 'Monitored Catch and monitored release method
# ratio = MonitoredLegalReleases(CalYr, PSCFishery) / MonitoredLegalCatch(CalYr, PSCFishery)
# End Select
# LegalCNRMortality(PSCFishery, age, BroodYear) = LandedCatch(PSCFishery, age, BroodYear) * ratio * LegalSelectivityFactor(CalYr, PSCFishery) * LegalIMRate(CalYr, PSCFishery)
# LegalCNRDropoffs(PSCFishery, age, BroodYear) = LandedCatch(PSCFishery, age, BroodYear) * ratio * LegalSelectivityFactor(CalYr, PSCFishery) * DropoffRate(CalYr, PSCFishery)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), CalYr)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "1966", "ShakerMethod1", BroodYear, PSCFishery, age, LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), ratio, LegalSelectivityFactor(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
# '**********
# 'old code included legal dropoffs and sublegal dropoffs in shakers so I added them here, they should be removed in final code
# SubLegalCNRMortality(PSCFishery, age, BroodYear) = (SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)) * ratio * SublegalSelectivityFactor(CalYr, PSCFishery)
# If isTraceCalc = True And BroodYear >= traceThisYear Then WriteLine(debug_subLegalCNRID, "1830 CaclCNR", PSCFishery, BroodYear, age, SubLegalCNRMortality(PSCFishery, age, BroodYear), SublegalShakerMortalities(PSCFishery, age, BroodYear), SublegalDropoffMortalities(PSCFishery, age, BroodYear), LegalDropoffMortality(PSCFishery, age, BroodYear), ratio, SublegalSelectivityFactor(CalYr, PSCFishery))
# Case 2 'reported encounters method
# LegalCNRMortality(PSCFishery, age, BroodYear) = (LandedCatch(PSCFishery, age, BroodYear) * CNRLegalEncounterEst(CalYr, PSCFishery) / LandedCatchEst(CalYr, PSCFishery)) * LegalIMRate(CalYr, PSCFishery)
# LegalCNRDropoffs(PSCFishery, age, BroodYear) = (LandedCatch(PSCFishery, age, BroodYear) * CNRLegalEncounterEst(CalYr, PSCFishery) / LandedCatchEst(CalYr, PSCFishery)) * DropoffRate(CalYr, PSCFishery)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And age = traceThisAge Then WriteLine(debug_LegalCNRID, "1836 legalCNR", "Shaker", "Method2", BroodYear, PSCFishery, age, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), LandedCatch(PSCFishery, age, BroodYear), CNRLegalEncounterEst(CalYr, PSCFishery), LandedCatchEst(CalYr, PSCFishery), LegalIMRate(CalYr, PSCFishery), DropoffRate(CalYr, PSCFishery), CalYr)
# If CalendarYearShakers(CalYr, PSCFishery) <> 0 Then
# CNRSublegalEncounters = (CNRSubLegalEncounterEst(CalYr, PSCFishery) * CalendarYearLandedCatch(CalYr, PSCFishery) / LandedCatchEst(CalYr, PSCFishery)) * ((SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)) / CalendarYearShakers(CalYr, PSCFishery))
# SubLegalCNRMortality(PSCFishery, age, BroodYear) = CNRSublegalEncounters * (SublegalIMRate(CalYr, PSCFishery) + DropoffRate(CalYr, PSCFishery))
# If isTraceCalc = True Then
# If BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then Write(debug_subLegalCNRID, "1837 sublegalCNR", PSCFishery, age, "rpt enc", CNRSubLegalEncounterEst(CalYr, PSCFishery), "rpt cat", LandedCatchEst(CalYr, PSCFishery), "SL IMrate", SublegalIMRate(CalYr, PSCFishery), "dropoffRate", DropoffRate(CalYr, PSCFishery), "relRatio", RelRatio(BroodYear))
# If BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then Write(debug_subLegalCNRID, "CNR sublegal", "method2", SubLegalCNRMortality(PSCFishery, age, BroodYear), "enc", CNRSubLegalEncounterEst(CalYr, PSCFishery), "*calYrCatch", CalendarYearLandedCatch(CalYr, PSCFishery), "/rpt catch*(SL shaker", SublegalShakerMortalities(PSCFishery, age, BroodYear), "+ SL dropoff", SublegalDropoffMortalities(PSCFishery, age, BroodYear), "+ L dropoff)", LegalDropoffMortality(PSCFishery, age, BroodYear), "/calYrShakers", CalendarYearShakers(CalYr, PSCFishery))
# If BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_subLegalCNRID, "*(SL IMRate + dropoff rate)", CalYr)
# End If
# End If
# Case 3 'catchability coefficient method used when there was no retention fishery
# Call CNRNoDir(CalYr, BroodYear, PSCFishery, age)
# Case 9 'no cnr fishery or data
# 'There is no CNR for this year and fishery, go to next year
# End Select
# 'SkipAge:
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_LegalCNRID, "2042", "CNRMethod", CNRMethod(CalYr, PSCFishery), BroodYear, PSCFishery, age, "CNRlegal", LegalCNRMortality(PSCFishery, age, BroodYear), "shakers", LegalCNRDropoffs(PSCFishery, age, BroodYear), "relratio", RelRatio(BroodYear))
# Next age
# Next PSCFishery
# End If
# Next BroodYear
# 'MOVED THIS SECTION OF CODE FROM TOP OF ROUTINE SO THAT
# ' CNR MORTALITIES IN LAST PASS WOULD BE AVAILABLE FOR METHOD 3
# ' IN NEXT PASS 9/24/97
# For BroodYear As Integer = FirstBY To LastBY
# For Age = OceanStartAge To LastAge(BroodYear)
# TotalCNRLegal(BroodYear, Age) = 0
# TotalCNRLegalDropoffs(BroodYear, Age) = 0
# TotalCNRSubLegal(BroodYear, Age) = 0
# TotalCNRSubLegalDropoffs(BroodYear, Age) = 0
# TotalTerminalCNRLegal(BroodYear, Age) = 0
# TotalTerminalCNRLegalDropoffs(BroodYear, Age) = 0
# TotalTerminalCNRSubLegal(BroodYear, Age) = 0
# TotalTerminalCNRSubLegalDropoffs(BroodYear, Age) = 0
# Next Age
# Next BroodYear
# 'MOVED THIS SECTION OF CODE FROM LOOP ABOVE FOR REASON NOTED ABOVE
# For BroodYear As Integer = FirstBY To LastBY
# 'skip missing brood years
# If MissingBroodYearFlag(BroodYear) = False Then
# For PSCFishery = 1 To NumberPSCFisheries
# For age As Integer = OceanStartAge To LastAge(BroodYear)
# CalYr = BroodYear + age
# TotalCNRLegal(BroodYear, age) += LegalCNRMortality(PSCFishery, age, BroodYear)
# TotalCNRLegalDropoffs(BroodYear, age) += LegalCNRDropoffs(PSCFishery, age, BroodYear)
# TotalCNRSubLegal(BroodYear, age) += SubLegalCNRMortality(PSCFishery, age, BroodYear)
# TotalCNRSubLegalDropoffs(BroodYear, age) += SubLegalCNRDropoffs(PSCFishery, age, BroodYear)
# If terminal(PSCFishery, age) = True And PSCFisheryGear(PSCFishery) <> "STRAY" Then
# TotalTerminalCNRLegal(BroodYear, age) += LegalCNRMortality(PSCFishery, age, BroodYear)
# TotalTerminalCNRLegalDropoffs(BroodYear, age) += LegalCNRDropoffs(PSCFishery, age, BroodYear)
# TotalTerminalCNRSubLegal(BroodYear, age) += SubLegalCNRMortality(PSCFishery, age, BroodYear)
# TotalTerminalCNRSubLegalDropoffs(BroodYear, age) += SubLegalCNRDropoffs(PSCFishery, age, BroodYear)
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then
# WriteLine(debug_LegalDropoffID, "2368 CalcCNR", PSCFishery, age, BroodYear, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), SubLegalCNRMortality(PSCFishery, age, BroodYear), SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
# WriteLine(debug_terminalCatchID, "2368 CalcCNR fishery specific", PSCFishery, age, BroodYear, LegalCNRMortality(PSCFishery, age, BroodYear), LegalCNRDropoffs(PSCFishery, age, BroodYear), SubLegalCNRMortality(PSCFishery, age, BroodYear), SubLegalCNRDropoffs(PSCFishery, age, BroodYear))
# WriteLine(debug_terminalCatchID, "2368 CalcCNR total", PSCFishery, age, BroodYear, TotalTerminalCNRLegal(BroodYear, age), TotalTerminalCNRLegalDropoffs(BroodYear, age), TotalTerminalCNRSubLegal(BroodYear, age), TotalTerminalCNRSubLegalDropoffs(BroodYear, age))
# End If
# Next age
# Next PSCFishery
# End If
# Next BroodYear
}
#' @title CNRNoDir
#'
#' @description Calculate Catch non retention after shakermethod when there was no retention fishery.
#'
#'
#' @param M A list passed to MainSub
#' @param D A list containing the outputs of GetWithinBYWeightFlagAndPNVRegionAndAvgMatRates
#'
#' @details
#'
#' @return D1: A list
#'
#' @export
#'
#' @examples
#'
#'
#'
CNRNoDir <- function(YR, BroodYear, PSCFishery,age){
#'Calculation of legal-sized CNR mortalities
# 'when estimated encounter of legal-sized During CNR is unknown
# 'use boat days to estimate
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches)
# 'local variables
IMortRt <-matrix(NA, nrow=2, ncol=2)
sublegal <- 1
legal <- 2
Instantaneous <- 1
Annual <- 2
#'DM = DropoffRate(YR, PSCFishery) dropoff rate is not used, SHould it be????
#'Note: removed division by Drop-off rate, Oct. 29 1997; included in external Q
#' For this algorithm to work correctly, the q values must be computed
#' with dropoff mortality included.
for(sizeGroup in sublegal:legal){
#'get annual landing rate for hypothetical retention fishery: catchability * selectivity * boat-days
if(sizeGroup == sublegal){
SubLegalCatchabilityCoefficient<- D$catchabilitydf$AvgQ[D$catchabilitydf$SizeClass == "S" & D$catchabilitydf$PSCFishery == PSCFishery&D$catchabilitydf$Age==age]
SublegalSelectivityFactor <- D$IMdf$SublegalSelectivityFactor[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
CNREffort <- D$IMdf$CNREffort[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
AnnualRetentionEncounterRate <- 1 - exp(-SubLegalCatchabilityCoefficient * SublegalSelectivityFactor * CNREffort )
}else if(sizeGroup == sublegal){
LegalCatchabilityCoefficient <- D$catchabilitydf$AvgQ[D$catchabilitydf$SizeClass == "L" & D$catchabilitydf$PSCFishery == PSCFishery&D$catchabilitydf$Age==age]
LegalSelectivityFactor <- D$IMdf$LegalSelectivityFactor[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
CNREffort <- D$IMdf$CNREffort[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
AnnualRetentionEncounterRate <- 1 - exp(- LegalCatchabilityCoefficient * LegalSelectivityFactor * CNREffort)
}
#'convert to Instantaneous rate
InstantaneousRetentionEncounterRate <- -log(1 - AnnualRetentionEncounterRate)
#'difference between hypothetical retention and CNR rates is
#'replacement of boat-days with boat-reavailability day
#'i.e. boat-days /(CNR season in days/availability in days)
CNRSeasonLength <- D$IMdf$CNRSeasonLength[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
Reavailability <- D$IMdf$Reavailability[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
tp = CNRSeasonLength / Reavailability
#'convert hypothetical retention rate to CNR rate
InstantaneousCNREncounterRate <- InstantaneousRetentionEncounterRate / tp
#'convert Instantaneous rate back to annual rate
AnnualCNREncounterRate <- 1 - exp(-InstantaneousCNREncounterRate)
if(sizeGroup == sublegal){
IMortRt[Annual, 1] <- AnnualCNREncounterRate
}else if(sizeGroup == legal){
LegalIMRate <- D$IMdf$LegalIMRate[D$IMdf$CalendarYear == YR & D$IMdf$PSCFishery == PSCFishery]
IMortRt[Annual, 1] = AnnualCNREncounterRate * LegalIMRate
}
IMortRt[Instantaneous, 1] <- -log(1 - IMortRt[Annual, 1]) #'this is already computed above
IMortRt[Annual, 2] = 1 - exp(-IMortRt[Instantaneous, 1] * tp) #'this is already computed above
if(D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY == allBY[BroodYear]]){
if(!D$terminal[PSCFishery,age]){
cohrt <- D$Cohort[BroodYear, age] * D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
}else{
cohrt <- TotalTerminalCatch_Age(D, M, BY=BroodYear, age) + D$Escape[BroodYear, age]
}
}else{
if(M$ShakerMethod == "C"| age <= D$LastAge[BroodYear] ){
cohrt <- CalcEstmCohrt2(D, M, BroodYear, age)
}else{
cohrt <- CalcEstmCohrt(D, M, BroodYear, age)
}
if(D$terminal[PSCFishery, age]){
cohrt <- cohrt * (1 - D$AveragePreTermER[age]) * D$AverageMatRate[age]
}
}
if(sizeGroup == sublegal){
SubLegalCNRMortality <- IMortRt[Annual, 2] * cohrt
}else if(sizeGroup == legal){
LegalCNRMortality <- IMortRt[Annual, 2] * cohrt
}
}
return(list(SubLegalCNRMortality=SubLegalCNRMortality,
LegalCNRMortality=LegalCNRMortality))
# -----------------------------------------------------------------------------------------
#Original VB code
# Sub CNRNoDir(ByRef YR As Integer, ByRef BroodYear As Integer, ByRef PSCFishery As Integer, ByRef age As Integer) 'no directed fishery
# 'Calculation of legal-sized CNR mortalities
# 'when estimated encounter of legal-sized During CNR is unknown
# 'use boat days to estimate
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches)
#
# 'local variables
# Dim cohrt As Single
# Dim Annual, Instantaneous As Integer
# Dim AnnualRetentionEncounterRate, InstantaneousRetentionEncounterRate, AnnualCNREncounterRate, InstantaneousCNREncounterRate As Single
# Dim IMortRt(1, 1) As Single
# Dim tp As Single
# Dim sublegal As Integer = 1
# Dim legal As Integer = 2
# Instantaneous = 0
# Annual = 1
# 'DM = DropoffRate(YR, PSCFishery) dropoff rate is not used, SHould it be????
# 'Note: removed division by Drop-off rate, Oct. 29 1997; included in external Q
# ' For this algorithm to work correctly, the q values must be computed
# ' with dropoff mortality included.
# For sizeGroup As Integer = sublegal To legal
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And sizeGroup = sublegal And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2920 SL", SubLegalCatchabilityCoeifficient(age, PSCFishery), SublegalSelectivityFactor(YR, PSCFishery), CNREffort(YR, PSCFishery))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And sizeGroup = legal And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2921 L", LegalCatchabilityCoeifficient(age, PSCFishery), LegalSelectivityFactor(YR, PSCFishery), CNREffort(YR, PSCFishery))
# 'get annual landing rate for hypothetical retention fishery: catchability * selectivity * boat-days
# If sizeGroup = sublegal Then
# AnnualRetentionEncounterRate = 1 - System.Math.Exp(-SubLegalCatchabilityCoeifficient(age, PSCFishery) * SublegalSelectivityFactor(YR, PSCFishery) * CNREffort(YR, PSCFishery))
# ElseIf sizeGroup = legal Then
# AnnualRetentionEncounterRate = 1 - System.Math.Exp(-LegalCatchabilityCoeifficient(age, PSCFishery) * LegalSelectivityFactor(YR, PSCFishery) * CNREffort(YR, PSCFishery))
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2928 ann", AnnualRetentionEncounterRate)
# 'convert to Instantaneous rate
# InstantaneousRetentionEncounterRate = -System.Math.Log(1 - AnnualRetentionEncounterRate)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2932 inst", AnnualRetentionEncounterRate)
#
# 'difference between hypothetical retention and CNR rates is
# 'replacement of boat-days with boat-reavailability day
# 'i.e. boat-days /(CNR season in days/availability in days)
# tp = CNRSeasonLength(YR, PSCFishery) / Reavailability(YR, PSCFishery)
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2873", sizeGroup, YR, "AnnRetenEncRte", AnnualRetentionEncounterRate, "InstantaneousRetentionEncounterRate", InstantaneousRetentionEncounterRate, "tp", tp)
#
#
# 'convert hypothetical retention rate to CNR rate
# InstantaneousCNREncounterRate = InstantaneousRetentionEncounterRate / tp
# 'convert Instantaneous rate back to annual rate
# AnnualCNREncounterRate = 1 - System.Math.Exp(-InstantaneousCNREncounterRate)
# If sizeGroup = sublegal Then
# IMortRt(Annual, 0) = AnnualCNREncounterRate
# ElseIf sizeGroup = legal Then
# IMortRt(Annual, 0) = AnnualCNREncounterRate * LegalIMRate(YR, PSCFishery)
# End If
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CNRNoDirID, "2879", sizeGroup, BroodYear, age, YR, "AnnRetenEncRte", LegalCatchabilityCoeifficient(age, PSCFishery), LegalSelectivityFactor(YR, PSCFishery), CNREffort(YR, PSCFishery), "tp", CNRSeasonLength(YR, PSCFishery), Reavailability(YR, PSCFishery), "IMortRT", AnnualCNREncounterRate, LegalIMRate(YR, PSCFishery))
#
# IMortRt(Instantaneous, 0) = -System.Math.Log(1 - IMortRt(Annual, 0)) 'this is already computed above
# IMortRt(Annual, 1) = 1 - System.Math.Exp(-IMortRt(Instantaneous, 0) * tp) 'this is already computed above
# If CompleteBYFlag(BroodYear) = True Then
# If terminal(PSCFishery, age) = False Then
# cohrt = Cohort(BroodYear, age) * SurvivalRate(age)
# Else
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "3045 CNRNoDir callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
# cohrt = TotalTerminalCatch_Age(BroodYear, age, pass) + Escape(BroodYear, age)
# End If
# Else
# If ShakerMethod = "C" Or age <= LastAge(BroodYear) Then
# cohrt = CalcEstmCohrt2(BroodYear, age)
# If isTraceCalc = True And shakermethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "3010 CNRNoDir", ShakerMethod, BroodYear, age, PSCFishery, cohrt)
# Else
# cohrt = CalcEstmCohrt(BroodYear, age)
# End If
# If terminal(PSCFishery, age) = True Then
# cohrt = cohrt * (1 - AveragePreTermER(age)) * AverageMatRate(age)
# End If
# End If
# If sizeGroup = sublegal Then
# SubLegalCNRMortality(PSCFishery, age, BroodYear) = IMortRt(Annual, 1) * cohrt
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2899", BroodYear, PSCFishery, age, "CNRNoDir SL", SubLegalCNRMortality(PSCFishery, age, BroodYear), IMortRt(Annual, 1), cohrt, "calYr", YR, "relratio", RelRatio(BroodYear))
# ElseIf sizeGroup = legal Then
# LegalCNRMortality(PSCFishery, age, BroodYear) = IMortRt(Annual, 1) * cohrt
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_CNRNoDirID, "2903", BroodYear, PSCFishery, age, "CNRNoDir L", LegalCNRMortality(PSCFishery, age, BroodYear), IMortRt(Annual, 1), cohrt, "calYr", YR, "relratio", RelRatio(BroodYear))
# End If
# Next sizeGroup
#
# End Sub
}
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