R/func_ShakerMethod.R
In catarinawor/ERAR: This package is a loose translation of the Chinook Technical committee ERA model
Defines functions
ShakerMethod1
#ERA function ShakerMethod1() and ShakerMethod4()
#Translated from VB ERA CIS code
#June 2018 -2019
#Author: Catarina Wor
#'@title ShakerMethod1
#'
#'@description calculates the sublegal shakers
#'
#'
#'@param M A list passed to MainSub
#'
#'@param D A list contining the outputs of GetSizeLimitLengthVulnerable
#'
#'@details Calculates stock,age,fishery,year specific PNV values using ND function and input values.
#'
#'@return
#'
#'
#'@export
#'
#'@examples
#'
#'
ShakerMethod1 <- function(D,M){
allCalYr <- (D$FirstBY + D$OceanStartAge) : M$LastCalendarYear
allBY <- D$FirstBY:D$LastBY
SublegalShakerMortalities <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
SublegalDropoffMortalities <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
ExtraLegalShakerMortality <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
ExtraLegalShakerDropoffs <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
TempLegalDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempTerminalShakers <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempSublegalShakers <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempTerminalShakerDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempTerminalLegalDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempSublegalShakerDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
#TotalTerminalShakers <- matrix(0,nrow=length(allBY),ncol=D$MaxAge)
#TotalTerminalShakerDropoffs <- matrix(0,nrow=length(allBY),ncol=D$MaxAge)
CalendarYearShakers <- matrix(0,M$LastCalendarYear,M$NumberPSCFisheries)
#'calculates the sublegal shakers
if(M$isReplicateCohShak){
lastYear <- max(D$IMdf$CalendarYear)
}else{
lastYear <- M$LastCalendarYear
}
valbroodyr <- TRUE
valcalyr <- TRUE
for(PSCFishery in seq_len( M$NumberPSCFisheries - 3 )){
#'excludes escapement but not strays?
for(CalYr in seq_along(allCalYr)){
NonVulnerableCohort <- rep(0, D$MaxAge)
TotalVulnerableCohort <- 0
#'Broodyear not defined yet. This makes zero sense.
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2878", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt should be zero")
valcalyr <- TRUE
for(age in D$OceanStartAge:D$MaxAge){
valbroodyr <- TRUE
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2880", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt start of age loop")
#'derive either brood and calendar year from age as appropriate
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2882 shakerMethod1", CalYr - Age, Age, CalYr, LastIMDataYear, FirstBY, LastBY, TotalVulnerableCohort)
if(M$ShakerMethod=="C"){ #'CalendarYr method
BroodYear <- allCalYr[CalYr] - age
yr_ <- allCalYr[CalYr]
}else{ #'Brood Year method
BroodYear <- allCalYr[CalYr] - D$OceanStartAge
yr_ <- BroodYear + age
}
BYind <- which(allBY==BroodYear)
if(length(BYind)==0) BYind <- BroodYear-allBY[1]
if((BroodYear + age) > max(D$IMdf$CalendarYear)){
#GoTo NxtAge
valbroodyr <- FALSE
#print("GoTo NxtAge")
}
if(M$ShakerMethod == "C"){ #'CalendarYr
if(BroodYear < D$FirstBY){
next
}
if(BroodYear > D$LastBY){
valbroodyr <- FALSE
#print("GoTo NxtAge")
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2895 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2896 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY, TotalVulnerableCohort)
if(D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY==BroodYear]){
valbroodyr <- FALSE
#print("GoTo NxtAge")
}
}else if(M$ShakerMethod == "B"){
if(BroodYear > D$LastBY){
valcalyr <- FALSE
#print("GoTo SkipYR")
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2900 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2901 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY)
if(D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY==BroodYear]){
valcalyr <- FALSE
#print("GoTo SkipYR")
}
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2904", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnchrt before cohrt=")
if(valbroodyr & valcalyr){
if( D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BYind]]){
if(!D$terminal[PSCFishery, age]){
#'PreTerm cohrt after natural mortality
cohrt <- D$Cohort[BYind, age] * D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
}else{
#'total terminal landed catch + terminal shakers + terminal CNR + escapement
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2911 ShakMeth1 call TotalTerminalcatcg_Age", ShakerMethod, BroodYear, Age)
cohrt <- TotalTerminalCatch_Age(D, M, BYind, age) + D$Escape[BYind, age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
}
}else{ #'cohorts estimated for incomplete broods
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2917 shakerMethod1", BroodYear, ShakerMethod, "1", Age, LastAge(BroodYear), TotalVulnerableCohort)
if(M$ShakerMethod == "C" | age <= D$LastAge[BYind]){
cohrt <- CalcEstmCohrt2( D, M, BYind,age )
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 incom BY shakCalcFg 1",ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt2(BroodYear, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
}else{
cohrt <- CalcEstmCohrt( D, M, BYind, age)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
}
#'for all terminal fishery ages
if(D$terminal[PSCFishery,age]){
cohrt <- cohrt * (1 - D$AveragePreTermER[age]) * D$AverageMatRate[age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
}
}#'CompleteBYFlag(BroodYear) = True
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
NonVulnerableCohort[age] <- cohrt * D$PNV[[age - D$OceanStartAge + 1]][BYind + age, PSCFishery ]
TotalVulnerableCohort <- TotalVulnerableCohort + cohrt * D$PV[[age - D$OceanStartAge + 1]][BYind + age, PSCFishery ]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
#'If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2939 nonVuln", BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr = 1983 Then WriteLine(debug_CohortID, "line 2940 totVuln", CalYr, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age), cohrt * PV(Broo
#If BroodYear + Age > LastIMDataYear Then GoTo NxtAge
#If ShakerMethod = "C" Then
#}valbroodyr
}
} #next age
if(valcalyr){
if(M$ShakerMethod == "C"){
TempCatch <- D$CalendarYearLandedCatch[CalYr, PSCFishery]
}else{
TempCatch <- D$TotalLandedCatch_ByFishery[BYind, PSCFishery]
}
#nxtagefun()
for(aged in D$OceanStartAge:D$MaxAge){
#'derive either brood and calendar year from age as appropriate
if(M$ShakerMethod == "C"){
#'CalendarYr
BroodYear <- allCalYr[CalYr] - aged
yr_ <- allCalYr[CalYr]
}else{
#'Brood Year method
BroodYear <- allCalYr[CalYr] - D$OceanStartAge
yr_ <- BroodYear + aged
if(M$isReplicateCohShak & D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY == BroodYear]){
yr_ <- allCalYr[CalYr]
}
}#'ShakerMethod = "C"
BYind <- which(allBY==BroodYear)
if(length(BYind)==0) BYind <- BroodYear-allBY[1]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2960 calyr", yr_, "age", Age, "brood", BroodYear, "ShakerMethod", ShakerMethod, TotalVulnerableCohort)
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2961", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "FirstBY", FirstBY, "ShakerMethod", ShakerMethod, "yr_", yr_, "LastIMDataYear", LastIMDataYear)
if(BroodYear < D$FirstBY | yr_ > max(D$IMdf$CalendarYear)){
next
}
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2963", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "yr_", yr_, "CNRMethod", CNRMethod(yr_, PSCFishery), "lastby", LastBY, "ShakerMethod", ShakerMethod)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2969", yr_, PSCFishery, CNRMethod(yr_, PSCFishery), TotalVulnerableCohort)
if( length(D$IMdf$CNRMethod[D$IMdf$CalendarYear==yr_& D$IMdf$PSCFishery==PSCFishery])>0){
if( D$IMdf$CNRMethod[D$IMdf$CalendarYear==yr_& D$IMdf$PSCFishery==PSCFishery]!=3){
if(TotalVulnerableCohort !=0){
encounterRate = 0.00001
if(NonVulnerableCohort[aged] > 0 & TotalVulnerableCohort > 0){
encounterRate <- NonVulnerableCohort[aged] / TotalVulnerableCohort
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_CohortID, "line 2971 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_matShakersID, "line 2972 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
}else{
encounterRate <- 0
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973 encounterRate & TotalVulnerableCohort=0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2973 encounterrate =0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973", BroodYear, PSCFishery, Age, TotalVulnerableCohort, " totVuln after goto NxtAge and If CNRMethod(yr_, PSCFishery) <> 3")
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2973", ShakerMethod, PSCFishery, Age, BroodYear, encounterRate, TotalVulnerableCohort)
if(allBY[BYind] <= D$LastBY){
SublegalShakerMortalities[PSCFishery, aged, BYind] <-
TempCatch *
D$IMdf$SublegalIMRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] *
encounterRate
SublegalDropoffMortalities[PSCFishery, aged, BYind] <-
TempCatch *
D$IMdf$DropoffRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery== PSCFishery] *
encounterRate
#'external shaker algorithm needs more development, as is it will produce too many shakers at the older ages
if(D$IMdf$RetentionMethod[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] == 1){
warning("External Shaker algorithm is not valid. Do not trust output.\n")
#'handles external shaker estimates
SublegalShakerMortalities[PSCFishery, aged, BYind] <-
((D$IMdf$SubLegalShakerEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] *
D$LandedCatch[PSCFishery, aged, BYind]) /
D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]) *
D$IMdf$SublegalIMRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]
SublegalDropoffMortalities[PSCFishery, aged, BYind] <- ((D$IMdf$SubLegalShakerEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] *
D$LandedCatch[PSCFishery, aged, BYind]) /
D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]) *
D$IMdf$DropoffRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]
}
#'total (PreTerm and terminal) sublegal shakers BroodYear age
#'add up sublegal shakers for all fisheries and add in sublegal dropoffs
TempSublegalShakers[ BYind, aged] <- TempSublegalShakers[ BYind, aged] + SublegalShakerMortalities[PSCFishery, aged, BYind]
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then
TempSublegalShakerDropoffs[BYind, aged] <- TempSublegalShakerDropoffs[BYind, aged] + SublegalDropoffMortalities[PSCFishery, aged, BYind]
#'totalLegalDropoffs moved here to compare against Coshak12, remove when done testing
TempLegalDropoffs[BYind, aged] <- TempLegalDropoffs[BYind, aged] + D$LegalDropoffMortality[PSCFishery, aged, BYind]
#'TempAgeShak(BroodYear, age) = TempAgeShak(BroodYear, age) + SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)
if(D$terminal[PSCFishery, aged-D$OceanStartAge+1]){
TempTerminalShakers[BYind, aged] <- TempTerminalShakers[BYind, aged] + SublegalShakerMortalities[PSCFishery, aged, BYind]
TempTerminalShakerDropoffs[BYind, aged] <- TempTerminalShakerDropoffs[BYind, aged] + SublegalDropoffMortalities[PSCFishery, aged, BYind]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then WriteLine(debug_matShakersID, "2999 term shakers", BroodYear, Age, PSCFishery, TempSublegalShakers(BroodYear, Age), TempTerminalShakers(BroodYear, Age), SublegalShakerMortalities(PSCFishery, Age, BroodYear), "calYr", CalYr, "catch", TempCatch, "endRte", encounterRate, "shakerRate", SublegalIMRate(CalYr, PSCFishery), "dropoffRate", DropoffRate(CalYr, PSCFishery))
#'moved to ShakerMethod1 to compare against Coshak12, remove from ShakerMethod1 when done testing
TempTerminalLegalDropoffs[BYind, aged] <- TempTerminalLegalDropoffs[BYind, aged] + D$LegalDropoffMortality[PSCFishery, aged, BYind]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_terminalCatchID, "3011 ShakerMethod`", BroodYear, Age, PSCFishery, "TerminalLegalDropoffs", TempTerminalLegalDropoffs(BroodYear, Age), "dropoff", LegalDropoffMortality(PSCFishery, Age, BroodYear))
}
} #end if 'BroodYear <= LastBY
} #endif D$IMdf$CNRMethod[D$IMdf$CalendarYear==yr_& D$IMdf$PSCFishery==PSCFishery]!=3
}
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt before next age")
}# aged
} #if valcalyr
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt before next yr")
#SkipYR:
} #CalYr
} #PSCFishery
#'code below is necessary outside of loop above so that function TotalCatch_Age works correctly - excluded and done in the return statement
#'calculate shakers for each calendar year and fishery
#'old code errantly added legal dropoffs to shakers so I have added them for now to allow testing against old code output
#'************legal dropoffs should be removed from here for final code
isOK <-TRUE
for(CalYr in seq_along(allCalYr)){
for(PSCFishery in seq_len( M$NumberPSCFisheries )){
if(M$PSCFisheryGear[PSCFishery]=="STRAY"){
isOK <- FALSE
}
if(M$PSCFisheryGear[PSCFishery]=="ESC"){
isOK <- FALSE
}
if(isOK){
for(age in D$OceanStartAge:D$MaxAge){
if(CalYr-age>=D$FirstBY & CalYr-age <= D$LastBY){
CalendarYearShakers[CalYr, PSCFishery] <- CalendarYearShakers[CalYr, PSCFishery] +
SublegalShakerMortalities[PSCFishery, age, CalYr - age] +
SublegalDropoffMortalities[PSCFishery, age, CalYr - age] +
D$LegalDropoffMortality[PSCFishery, age, CalYr - age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr - Age >= traceThisYear And PSCFishery = 8 Then WriteLine(debug_CalYrShakersID, "3038 CalYrShakers", CalYr, PSCFishery, Age, "accum by fishery", CalendarYearShakers(CalYr, PSCFishery), "shaker+dropoff", (SublegalShakerMortalities(PSCFishery, Age, CalYr - Age) + SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age) + LegalDropoffMortality(PSCFishery, Age, CalYr - Age)), "shaker", SublegalShakerMortalities(PSCFishery, Age, CalYr - Age), "SL dropoff", SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age), "L dropoff", LegalDropoffMortality(PSCFishery, Age, CalYr - Age))
}
}
}
}
}
return(list(new=list(
CalendarYearShakers=CalendarYearShakers,
SublegalShakerMortalities=SublegalShakerMortalities,
SublegalDropoffMortalities=SublegalDropoffMortalities,
SublegalShakerMortalities=SublegalShakerMortalities),
old=list(
TotalSublegalShakers=TempSublegalShakers,
TotalSublegalShakerDropoffs=TempSublegalShakerDropoffs,
TotalLegalDropoffs=TempLegalDropoffs,
TotalTerminalShakers=TempTerminalShakers,
TotalTerminalShakerDropoffs=TempTerminalShakerDropoffs,
TotalTerminalLegalDropoffs=TempTerminalLegalDropoffs)
))
#original VB code
#=============================================================
# 'calculates the sublegal shakers
# Dim BroodYear As Integer
# Dim yr_ As Integer
# Dim isOK As Boolean
# Dim lastYear As Integer
# Dim NonVulnerableCohort() As Single
# Dim cohrt, encounterRate As Single
# Dim TempCatch, TotalVulnerableCohort As Single
# Dim TempAgeShak(LastBY, MaxAge) As Single
# ReDim CalendarYearShakers(LastCalendarYear, NumberPSCFisheries)
# ReDim SublegalShakerMortalities(NumberPSCFisheries, MaxAge, LastBY)
# ReDim SublegalDropoffMortalities(NumberPSCFisheries, MaxAge, LastBY)
# ReDim ExtraLegalShakerMortality(NumberPSCFisheries, MaxAge, LastBY)
# ReDim ExtraLegalShakerDropoffs(NumberPSCFisheries, MaxAge, LastBY)
# Dim TempLegalDropoffs(LastBY, MaxAge) As Single
# Dim TempTerminalShakers(LastBY, MaxAge) As Single
# Dim TempTerminalShakerDropoffs(LastBY, MaxAge) As Single
# Dim TempTerminalLegalDropoffs(LastBY, MaxAge) As Single
# Dim TempSublegalShakerDropoffs(LastBY, MaxAge) As Single
# Dim TempSublegalShakers(LastBY, MaxAge) As Single
#
# If isReplicateCohShak = True Then
# lastYear = LastIMDataYear
# Else
# lastYear = LastCalendarYear
# End If
# For PSCFishery As Integer = 1 To NumberPSCFisheries - 1 'excludes escapement
# For CalYr As Integer = FirstBY + OceanStartAge To LastCalendarYear 'LastBY + LastAge(LastBY)
# ReDim NonVulnerableCohort(MaxAge)
# TotalVulnerableCohort = 0
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2878", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt should be zero")
#
# For Age = OceanStartAge To MaxAge
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2880", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt start of age loop")
#
# 'derive either brood and calendar year from age as appropriate
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2882 shakerMethod1", CalYr - Age, Age, CalYr, LastIMDataYear, FirstBY, LastBY, TotalVulnerableCohort)
# If ShakerMethod = "C" Then 'CalendarYr
# BroodYear = CalYr - Age
# yr_ = CalYr
# Else 'Brood Year method
# BroodYear = CalYr - OceanStartAge
# yr_ = BroodYear + Age
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2890 shakerMethod1", ShakerMethod, CalYr, Age, BroodYear, LastIMDataYear, "oceanstartage", OceanStartAge, "ShakerMethod", ShakerMethod, "BY", BroodYear, "age", Age, TotalVulnerableCohort)
# If BroodYear + Age > LastIMDataYear Then GoTo NxtAge
# If ShakerMethod = "C" Then
# If BroodYear < FirstBY Then Exit For
# If BroodYear > LastBY Then GoTo NxtAge
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2895 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2896 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY, TotalVulnerableCohort)
# If MissingBroodYearFlag(BroodYear) = True Then GoTo NxtAge
# ElseIf ShakerMethod = "B" Then
# If BroodYear > LastBY Then GoTo SkipYR
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2900 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2901 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY)
# If MissingBroodYearFlag(BroodYear) = True Then GoTo SkipYR
# End If
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2904", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnchrt before cohrt=")
#
# If CompleteBYFlag(BroodYear) = True Then 'cohorts estimated for complete broods
# If terminal(PSCFishery, Age) = False Then
# 'PreTerm cohrt after natural mortality
# cohrt = Cohort(BroodYear, Age) * SurvivalRate(Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
# Else
# 'total terminal landed catch + terminal shakers + terminal CNR + escapement
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2911 ShakMeth1 call TotalTerminalcatcg_Age", ShakerMethod, BroodYear, Age)
#
# cohrt = TotalTerminalCatch_Age(BroodYear, Age, pass) + Escape(BroodYear, Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
# End If
# Else 'cohorts estimated for incomplete broods
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2917 shakerMethod1", BroodYear, ShakerMethod, "1", Age, LastAge(BroodYear), TotalVulnerableCohort)
# If ShakerMethod = "C" Or Age <= LastAge(BroodYear) Then
# cohrt = CalcEstmCohrt2(BroodYear, Age)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 incom BY shakCalcFg 1",ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt2(BroodYear, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
# Else
# cohrt = CalcEstmCohrt(BroodYear, Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
# End If
# 'for all terminal fishery ages
# If terminal(PSCFishery, Age) = True Then
# cohrt = cohrt * (1 - AveragePreTermER(Age)) * AverageMatRate(Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
# End If
# End If 'CompleteBYFlag(BroodYear) = True
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
# NonVulnerableCohort(Age) = cohrt * PNV(BroodYear + Age, PSCFishery, Age)
# TotalVulnerableCohort = TotalVulnerableCohort + cohrt * (PV(BroodYear + Age, PSCFishery, Age))
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
# 'If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2939 nonVuln", BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr = 1983 Then WriteLine(debug_CohortID, "line 2940 totVuln", CalYr, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age), cohrt * PV(BroodYear + Age, PSCFishery, Age))
#NxtAge:
# Next Age
# If ShakerMethod = "C" Then 'calendar year method
# TempCatch = CalendarYearLandedCatch(CalYr, PSCFishery)
# Else 'brood year method
# TempCatch = TotalLandedCatch_ByFishery(BroodYear, PSCFishery)
# End If
# For Age = OceanStartAge To MaxAge
# 'derive either brood and calendar year from age as appropriate
# If ShakerMethod = "C" Then 'CalendarYr
# BroodYear = CalYr - Age
# yr_ = CalYr
# Else 'Brood Year method
# BroodYear = CalYr - OceanStartAge
# yr_ = BroodYear + Age
# If isReplicateCohShak = True And CompleteBYFlag(BroodYear) = True Then
# yr_ = CalYr
# End If
# End If 'ShakerMethod = "C"
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2960 calyr", yr_, "age", Age, "brood", BroodYear, "ShakerMethod", ShakerMethod, TotalVulnerableCohort)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2961", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "FirstBY", FirstBY, "ShakerMethod", ShakerMethod, "yr_", yr_, "LastIMDataYear", LastIMDataYear)
# If BroodYear < FirstBY Or yr_ > LastIMDataYear Then Exit For
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2963", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "yr_", yr_, "CNRMethod", CNRMethod(yr_, PSCFishery), "lastby", LastBY, "ShakerMethod", ShakerMethod)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2969", yr_, PSCFishery, CNRMethod(yr_, PSCFishery), TotalVulnerableCohort)
# If CNRMethod(yr_, PSCFishery) <> 3 Then
# If TotalVulnerableCohort <> 0 Then
# encounterRate = 0.00001
# If NonVulnerableCohort(Age) > 0 And TotalVulnerableCohort > 0 Then
# encounterRate = NonVulnerableCohort(Age) / TotalVulnerableCohort
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_CohortID, "line 2971 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_matShakersID, "line 2972 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
# Else
# encounterRate = 0
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973 encounterRate & TotalVulnerableCohort=0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2973 encounterrate =0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
# End If
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973", BroodYear, PSCFishery, Age, TotalVulnerableCohort, " totVuln after goto NxtAge and If CNRMethod(yr_, PSCFishery) <> 3")
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2973", ShakerMethod, PSCFishery, Age, BroodYear, encounterRate, TotalVulnerableCohort)
#
# If BroodYear <= LastBY Then
# SublegalShakerMortalities(PSCFishery, Age, BroodYear) = TempCatch * SublegalIMRate(CalYr, PSCFishery) * encounterRate
# SublegalDropoffMortalities(PSCFishery, Age, BroodYear) = TempCatch * DropoffRate(CalYr, PSCFishery) * encounterRate
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2979 SL dropoff", ShakerMethod, PSCFishery, Age, BroodYear, "dropoff", SublegalDropoffMortalities(PSCFishery, Age, BroodYear), "catch", TempCatch, "dropOffRate", DropoffRate(CalYr, PSCFishery), "encRte", encounterRate, "relRatio", RelRatio(BroodYear))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2980 SL shaker", ShakerMethod, PSCFishery, Age, BroodYear, "shakers", SublegalShakerMortalities(PSCFishery, Age, BroodYear), "catch", TempCatch, "SublegalIMRat", SublegalIMRate(CalYr, PSCFishery), "encRte", encounterRate, "relRatio", RelRatio(BroodYear))
# 'external shaker algorithm needs more development, as is it will produce too many shakers at the older ages
# If RetentionMethod(CalYr, PSCFishery) = 1 Then 'handles external shaker estimates
# MsgBox("External Shaker algorithm is not valid. Do not trust output.")
# SublegalShakerMortalities(PSCFishery, Age, BroodYear) = ((SubLegalShakerEst(CalYr, PSCFishery) * LandedCatch(PSCFishery, Age, BroodYear)) / LandedCatchEst(CalYr, PSCFishery)) * SublegalIMRate(CalYr, PSCFishery)
# SublegalDropoffMortalities(PSCFishery, Age, BroodYear) = ((SubLegalShakerEst(CalYr, PSCFishery) * LandedCatch(PSCFishery, Age, BroodYear)) / LandedCatchEst(CalYr, PSCFishery)) * DropoffRate(CalYr, PSCFishery)
# End If
# 'total (PreTerm and terminal) sublegal shakers BroodYear age
# 'add up sublegal shakers for all fisheries and add in sublegal dropoffs
# TempSublegalShakers(BroodYear, Age) = TempSublegalShakers(BroodYear, Age) + SublegalShakerMortalities(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then WriteLine(debug_matShakersID, "2990 TempSublegalShakers", BroodYear, Age, PSCFishery, TempSublegalShakers(BroodYear, Age), TempSublegalShakers(BroodYear, Age), SublegalShakerMortalities(PSCFishery, Age, BroodYear), TempCatch, SublegalIMRate(CalYr, PSCFishery), encounterRate)
# TempSublegalShakerDropoffs(BroodYear, Age) = TempSublegalShakerDropoffs(BroodYear, Age) + SublegalDropoffMortalities(PSCFishery, Age, BroodYear)
# 'totalLegalDropoffs moved here to compare against Coshak12, remove when done testing
# TempLegalDropoffs(BroodYear, Age) = TempLegalDropoffs(BroodYear, Age) + LegalDropoffMortality(PSCFishery, Age, BroodYear)
# 'TempAgeShak(BroodYear, age) = TempAgeShak(BroodYear, age) + SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)
# If terminal(PSCFishery, Age) = True Then
# TempTerminalShakers(BroodYear, Age) = TempTerminalShakers(BroodYear, Age) + SublegalShakerMortalities(PSCFishery, Age, BroodYear)
# TempTerminalShakerDropoffs(BroodYear, Age) = TempTerminalShakerDropoffs(BroodYear, Age) + SublegalDropoffMortalities(PSCFishery, Age, BroodYear)
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then WriteLine(debug_matShakersID, "2999 term shakers", BroodYear, Age, PSCFishery, TempSublegalShakers(BroodYear, Age), TempTerminalShakers(BroodYear, Age), SublegalShakerMortalities(PSCFishery, Age, BroodYear), "calYr", CalYr, "catch", TempCatch, "endRte", encounterRate, "shakerRate", SublegalIMRate(CalYr, PSCFishery), "dropoffRate", DropoffRate(CalYr, PSCFishery))
# 'moved to ShakerMethod1 to compare against Coshak12, remove from ShakerMethod1 when done testing
# TempTerminalLegalDropoffs(BroodYear, Age) = TempTerminalLegalDropoffs(BroodYear, Age) + LegalDropoffMortality(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_terminalCatchID, "3011 ShakerMethod`", BroodYear, Age, PSCFishery, "TerminalLegalDropoffs", TempTerminalLegalDropoffs(BroodYear, Age), "dropoff", LegalDropoffMortality(PSCFishery, Age, BroodYear))
# End If
# End If 'BroodYear <= LastBY
# End If 'CNRMethod(yr_, PSCFishery) <> 3
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt before next age")
# Next Age
#SkipYR:
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt before next yr")
# Next CalYr
# Next PSCFishery
# 'code below is necessary outside of loop above so that function TotalCatch_Age works correctly
# For BroodYear = FirstBY To LastBY
# For Age = OceanStartAge To MaxAge
# 'total (PreTerm and terminal) sublegal shakers by age
# 'add up sublegal shakers for all fisheries and add in sublegal dropoffs
# TotalSublegalShakers(BroodYear, Age) = TempSublegalShakers(BroodYear, Age)
# TotalSublegalShakerDropoffs(BroodYear, Age) = TempSublegalShakerDropoffs(BroodYear, Age)
# 'totalLegalDropoffs moved here to compare against Coshak12, remove when done testing
# TotalLegalDropoffs(BroodYear, Age) = TempLegalDropoffs(BroodYear, Age)
# TotalTerminalShakers(BroodYear, Age) = TempTerminalShakers(BroodYear, Age)
# TotalTerminalShakerDropoffs(BroodYear, Age) = TempTerminalShakerDropoffs(BroodYear, Age)
# 'moved to ShakerMethod1 to compare against Coshak12, remove from ShakerMethod1 when done testing
# TotalTerminalLegalDropoffs(BroodYear, Age) = TempTerminalLegalDropoffs(BroodYear, Age)
# Next Age
# Next BroodYear
#
# 'calculate shakers for each calendar year and fishery
# 'old code errantly added legal dropoffs to shakers so I have added them for now to allow testing against old code output
# '************legal dropoffs should be removed from here for final code
# For CalYr As Integer = FirstBY + OceanStartAge To LastCalendarYear
# For PSCFishery As Integer = 1 To NumberPSCFisheries
# isOK = True
# If PSCFisheryGear(PSCFishery) = "STRAY" Then isOK = False
# If PSCFisheryGear(PSCFishery) = "ESC" Then isOK = False
# If isOK = True Then
# For Age = OceanStartAge To MaxAge
# If CalYr - Age >= FirstBY And CalYr - Age <= LastBY Then
# CalendarYearShakers(CalYr, PSCFishery) += SublegalShakerMortalities(PSCFishery, Age, CalYr - Age) + SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age) + LegalDropoffMortality(PSCFishery, Age, CalYr - Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr - Age >= traceThisYear And PSCFishery = 8 Then WriteLine(debug_CalYrShakersID, "3038 CalYrShakers", CalYr, PSCFishery, Age, "accum by fishery", CalendarYearShakers(CalYr, PSCFishery), "shaker+dropoff", (SublegalShakerMortalities(PSCFishery, Age, CalYr - Age) + SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age) + LegalDropoffMortality(PSCFishery, Age, CalYr - Age)), "shaker", SublegalShakerMortalities(PSCFishery, Age, CalYr - Age), "SL dropoff", SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age), "L dropoff", LegalDropoffMortality(PSCFishery, Age, CalYr - Age))
# End If
# Next Age
# End If
# Next PSCFishery
# Next CalYr
}
catarinawor/ERAR documentation built on Sept. 21, 2019, 8:25 a.m.
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Defines functions ShakerMethod1
#ERA function ShakerMethod1() and ShakerMethod4()
#Translated from VB ERA CIS code
#June 2018 -2019
#Author: Catarina Wor
#'@title ShakerMethod1
#'
#'@description calculates the sublegal shakers
#'
#'
#'@param M A list passed to MainSub
#'
#'@param D A list contining the outputs of GetSizeLimitLengthVulnerable
#'
#'@details Calculates stock,age,fishery,year specific PNV values using ND function and input values.
#'
#'@return
#'
#'
#'@export
#'
#'@examples
#'
#'
ShakerMethod1 <- function(D,M){
allCalYr <- (D$FirstBY + D$OceanStartAge) : M$LastCalendarYear
allBY <- D$FirstBY:D$LastBY
SublegalShakerMortalities <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
SublegalDropoffMortalities <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
ExtraLegalShakerMortality <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
ExtraLegalShakerDropoffs <- array(NA, dim=c(M$NumberPSCFisheries, D$MaxAge, length(allBY)))
TempLegalDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempTerminalShakers <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempSublegalShakers <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempTerminalShakerDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempTerminalLegalDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
TempSublegalShakerDropoffs <- matrix(0,nrow=length(allBY), ncol= D$MaxAge)
#TotalTerminalShakers <- matrix(0,nrow=length(allBY),ncol=D$MaxAge)
#TotalTerminalShakerDropoffs <- matrix(0,nrow=length(allBY),ncol=D$MaxAge)
CalendarYearShakers <- matrix(0,M$LastCalendarYear,M$NumberPSCFisheries)
#'calculates the sublegal shakers
if(M$isReplicateCohShak){
lastYear <- max(D$IMdf$CalendarYear)
}else{
lastYear <- M$LastCalendarYear
}
valbroodyr <- TRUE
valcalyr <- TRUE
for(PSCFishery in seq_len( M$NumberPSCFisheries - 3 )){
#'excludes escapement but not strays?
for(CalYr in seq_along(allCalYr)){
NonVulnerableCohort <- rep(0, D$MaxAge)
TotalVulnerableCohort <- 0
#'Broodyear not defined yet. This makes zero sense.
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2878", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt should be zero")
valcalyr <- TRUE
for(age in D$OceanStartAge:D$MaxAge){
valbroodyr <- TRUE
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2880", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt start of age loop")
#'derive either brood and calendar year from age as appropriate
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2882 shakerMethod1", CalYr - Age, Age, CalYr, LastIMDataYear, FirstBY, LastBY, TotalVulnerableCohort)
if(M$ShakerMethod=="C"){ #'CalendarYr method
BroodYear <- allCalYr[CalYr] - age
yr_ <- allCalYr[CalYr]
}else{ #'Brood Year method
BroodYear <- allCalYr[CalYr] - D$OceanStartAge
yr_ <- BroodYear + age
}
BYind <- which(allBY==BroodYear)
if(length(BYind)==0) BYind <- BroodYear-allBY[1]
if((BroodYear + age) > max(D$IMdf$CalendarYear)){
#GoTo NxtAge
valbroodyr <- FALSE
#print("GoTo NxtAge")
}
if(M$ShakerMethod == "C"){ #'CalendarYr
if(BroodYear < D$FirstBY){
next
}
if(BroodYear > D$LastBY){
valbroodyr <- FALSE
#print("GoTo NxtAge")
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2895 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2896 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY, TotalVulnerableCohort)
if(D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY==BroodYear]){
valbroodyr <- FALSE
#print("GoTo NxtAge")
}
}else if(M$ShakerMethod == "B"){
if(BroodYear > D$LastBY){
valcalyr <- FALSE
#print("GoTo SkipYR")
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2900 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2901 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY)
if(D$MissingBroodYearFlag$Flag[D$MissingBroodYearFlag$BY==BroodYear]){
valcalyr <- FALSE
#print("GoTo SkipYR")
}
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2904", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnchrt before cohrt=")
if(valbroodyr & valcalyr){
if( D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BYind]]){
if(!D$terminal[PSCFishery, age]){
#'PreTerm cohrt after natural mortality
cohrt <- D$Cohort[BYind, age] * D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
}else{
#'total terminal landed catch + terminal shakers + terminal CNR + escapement
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2911 ShakMeth1 call TotalTerminalcatcg_Age", ShakerMethod, BroodYear, Age)
cohrt <- TotalTerminalCatch_Age(D, M, BYind, age) + D$Escape[BYind, age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
}
}else{ #'cohorts estimated for incomplete broods
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2917 shakerMethod1", BroodYear, ShakerMethod, "1", Age, LastAge(BroodYear), TotalVulnerableCohort)
if(M$ShakerMethod == "C" | age <= D$LastAge[BYind]){
cohrt <- CalcEstmCohrt2( D, M, BYind,age )
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 incom BY shakCalcFg 1",ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt2(BroodYear, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
}else{
cohrt <- CalcEstmCohrt( D, M, BYind, age)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
}
#'for all terminal fishery ages
if(D$terminal[PSCFishery,age]){
cohrt <- cohrt * (1 - D$AveragePreTermER[age]) * D$AverageMatRate[age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
}
}#'CompleteBYFlag(BroodYear) = True
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
NonVulnerableCohort[age] <- cohrt * D$PNV[[age - D$OceanStartAge + 1]][BYind + age, PSCFishery ]
TotalVulnerableCohort <- TotalVulnerableCohort + cohrt * D$PV[[age - D$OceanStartAge + 1]][BYind + age, PSCFishery ]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
#'If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2939 nonVuln", BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr = 1983 Then WriteLine(debug_CohortID, "line 2940 totVuln", CalYr, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age), cohrt * PV(Broo
#If BroodYear + Age > LastIMDataYear Then GoTo NxtAge
#If ShakerMethod = "C" Then
#}valbroodyr
}
} #next age
if(valcalyr){
if(M$ShakerMethod == "C"){
TempCatch <- D$CalendarYearLandedCatch[CalYr, PSCFishery]
}else{
TempCatch <- D$TotalLandedCatch_ByFishery[BYind, PSCFishery]
}
#nxtagefun()
for(aged in D$OceanStartAge:D$MaxAge){
#'derive either brood and calendar year from age as appropriate
if(M$ShakerMethod == "C"){
#'CalendarYr
BroodYear <- allCalYr[CalYr] - aged
yr_ <- allCalYr[CalYr]
}else{
#'Brood Year method
BroodYear <- allCalYr[CalYr] - D$OceanStartAge
yr_ <- BroodYear + aged
if(M$isReplicateCohShak & D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY == BroodYear]){
yr_ <- allCalYr[CalYr]
}
}#'ShakerMethod = "C"
BYind <- which(allBY==BroodYear)
if(length(BYind)==0) BYind <- BroodYear-allBY[1]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2960 calyr", yr_, "age", Age, "brood", BroodYear, "ShakerMethod", ShakerMethod, TotalVulnerableCohort)
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2961", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "FirstBY", FirstBY, "ShakerMethod", ShakerMethod, "yr_", yr_, "LastIMDataYear", LastIMDataYear)
if(BroodYear < D$FirstBY | yr_ > max(D$IMdf$CalendarYear)){
next
}
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2963", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "yr_", yr_, "CNRMethod", CNRMethod(yr_, PSCFishery), "lastby", LastBY, "ShakerMethod", ShakerMethod)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2969", yr_, PSCFishery, CNRMethod(yr_, PSCFishery), TotalVulnerableCohort)
if( length(D$IMdf$CNRMethod[D$IMdf$CalendarYear==yr_& D$IMdf$PSCFishery==PSCFishery])>0){
if( D$IMdf$CNRMethod[D$IMdf$CalendarYear==yr_& D$IMdf$PSCFishery==PSCFishery]!=3){
if(TotalVulnerableCohort !=0){
encounterRate = 0.00001
if(NonVulnerableCohort[aged] > 0 & TotalVulnerableCohort > 0){
encounterRate <- NonVulnerableCohort[aged] / TotalVulnerableCohort
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_CohortID, "line 2971 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_matShakersID, "line 2972 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
}else{
encounterRate <- 0
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973 encounterRate & TotalVulnerableCohort=0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2973 encounterrate =0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973", BroodYear, PSCFishery, Age, TotalVulnerableCohort, " totVuln after goto NxtAge and If CNRMethod(yr_, PSCFishery) <> 3")
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2973", ShakerMethod, PSCFishery, Age, BroodYear, encounterRate, TotalVulnerableCohort)
if(allBY[BYind] <= D$LastBY){
SublegalShakerMortalities[PSCFishery, aged, BYind] <-
TempCatch *
D$IMdf$SublegalIMRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] *
encounterRate
SublegalDropoffMortalities[PSCFishery, aged, BYind] <-
TempCatch *
D$IMdf$DropoffRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery== PSCFishery] *
encounterRate
#'external shaker algorithm needs more development, as is it will produce too many shakers at the older ages
if(D$IMdf$RetentionMethod[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] == 1){
warning("External Shaker algorithm is not valid. Do not trust output.\n")
#'handles external shaker estimates
SublegalShakerMortalities[PSCFishery, aged, BYind] <-
((D$IMdf$SubLegalShakerEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] *
D$LandedCatch[PSCFishery, aged, BYind]) /
D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]) *
D$IMdf$SublegalIMRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]
SublegalDropoffMortalities[PSCFishery, aged, BYind] <- ((D$IMdf$SubLegalShakerEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery] *
D$LandedCatch[PSCFishery, aged, BYind]) /
D$IMdf$LandedCatchEst[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]) *
D$IMdf$DropoffRate[D$IMdf$CalendarYear==allCalYr[CalYr] & D$IMdf$PSCFishery==PSCFishery]
}
#'total (PreTerm and terminal) sublegal shakers BroodYear age
#'add up sublegal shakers for all fisheries and add in sublegal dropoffs
TempSublegalShakers[ BYind, aged] <- TempSublegalShakers[ BYind, aged] + SublegalShakerMortalities[PSCFishery, aged, BYind]
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then
TempSublegalShakerDropoffs[BYind, aged] <- TempSublegalShakerDropoffs[BYind, aged] + SublegalDropoffMortalities[PSCFishery, aged, BYind]
#'totalLegalDropoffs moved here to compare against Coshak12, remove when done testing
TempLegalDropoffs[BYind, aged] <- TempLegalDropoffs[BYind, aged] + D$LegalDropoffMortality[PSCFishery, aged, BYind]
#'TempAgeShak(BroodYear, age) = TempAgeShak(BroodYear, age) + SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)
if(D$terminal[PSCFishery, aged-D$OceanStartAge+1]){
TempTerminalShakers[BYind, aged] <- TempTerminalShakers[BYind, aged] + SublegalShakerMortalities[PSCFishery, aged, BYind]
TempTerminalShakerDropoffs[BYind, aged] <- TempTerminalShakerDropoffs[BYind, aged] + SublegalDropoffMortalities[PSCFishery, aged, BYind]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then WriteLine(debug_matShakersID, "2999 term shakers", BroodYear, Age, PSCFishery, TempSublegalShakers(BroodYear, Age), TempTerminalShakers(BroodYear, Age), SublegalShakerMortalities(PSCFishery, Age, BroodYear), "calYr", CalYr, "catch", TempCatch, "endRte", encounterRate, "shakerRate", SublegalIMRate(CalYr, PSCFishery), "dropoffRate", DropoffRate(CalYr, PSCFishery))
#'moved to ShakerMethod1 to compare against Coshak12, remove from ShakerMethod1 when done testing
TempTerminalLegalDropoffs[BYind, aged] <- TempTerminalLegalDropoffs[BYind, aged] + D$LegalDropoffMortality[PSCFishery, aged, BYind]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_terminalCatchID, "3011 ShakerMethod`", BroodYear, Age, PSCFishery, "TerminalLegalDropoffs", TempTerminalLegalDropoffs(BroodYear, Age), "dropoff", LegalDropoffMortality(PSCFishery, Age, BroodYear))
}
} #end if 'BroodYear <= LastBY
} #endif D$IMdf$CNRMethod[D$IMdf$CalendarYear==yr_& D$IMdf$PSCFishery==PSCFishery]!=3
}
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt before next age")
}# aged
} #if valcalyr
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt before next yr")
#SkipYR:
} #CalYr
} #PSCFishery
#'code below is necessary outside of loop above so that function TotalCatch_Age works correctly - excluded and done in the return statement
#'calculate shakers for each calendar year and fishery
#'old code errantly added legal dropoffs to shakers so I have added them for now to allow testing against old code output
#'************legal dropoffs should be removed from here for final code
isOK <-TRUE
for(CalYr in seq_along(allCalYr)){
for(PSCFishery in seq_len( M$NumberPSCFisheries )){
if(M$PSCFisheryGear[PSCFishery]=="STRAY"){
isOK <- FALSE
}
if(M$PSCFisheryGear[PSCFishery]=="ESC"){
isOK <- FALSE
}
if(isOK){
for(age in D$OceanStartAge:D$MaxAge){
if(CalYr-age>=D$FirstBY & CalYr-age <= D$LastBY){
CalendarYearShakers[CalYr, PSCFishery] <- CalendarYearShakers[CalYr, PSCFishery] +
SublegalShakerMortalities[PSCFishery, age, CalYr - age] +
SublegalDropoffMortalities[PSCFishery, age, CalYr - age] +
D$LegalDropoffMortality[PSCFishery, age, CalYr - age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr - Age >= traceThisYear And PSCFishery = 8 Then WriteLine(debug_CalYrShakersID, "3038 CalYrShakers", CalYr, PSCFishery, Age, "accum by fishery", CalendarYearShakers(CalYr, PSCFishery), "shaker+dropoff", (SublegalShakerMortalities(PSCFishery, Age, CalYr - Age) + SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age) + LegalDropoffMortality(PSCFishery, Age, CalYr - Age)), "shaker", SublegalShakerMortalities(PSCFishery, Age, CalYr - Age), "SL dropoff", SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age), "L dropoff", LegalDropoffMortality(PSCFishery, Age, CalYr - Age))
}
}
}
}
}
return(list(new=list(
CalendarYearShakers=CalendarYearShakers,
SublegalShakerMortalities=SublegalShakerMortalities,
SublegalDropoffMortalities=SublegalDropoffMortalities,
SublegalShakerMortalities=SublegalShakerMortalities),
old=list(
TotalSublegalShakers=TempSublegalShakers,
TotalSublegalShakerDropoffs=TempSublegalShakerDropoffs,
TotalLegalDropoffs=TempLegalDropoffs,
TotalTerminalShakers=TempTerminalShakers,
TotalTerminalShakerDropoffs=TempTerminalShakerDropoffs,
TotalTerminalLegalDropoffs=TempTerminalLegalDropoffs)
))
#original VB code
#=============================================================
# 'calculates the sublegal shakers
# Dim BroodYear As Integer
# Dim yr_ As Integer
# Dim isOK As Boolean
# Dim lastYear As Integer
# Dim NonVulnerableCohort() As Single
# Dim cohrt, encounterRate As Single
# Dim TempCatch, TotalVulnerableCohort As Single
# Dim TempAgeShak(LastBY, MaxAge) As Single
# ReDim CalendarYearShakers(LastCalendarYear, NumberPSCFisheries)
# ReDim SublegalShakerMortalities(NumberPSCFisheries, MaxAge, LastBY)
# ReDim SublegalDropoffMortalities(NumberPSCFisheries, MaxAge, LastBY)
# ReDim ExtraLegalShakerMortality(NumberPSCFisheries, MaxAge, LastBY)
# ReDim ExtraLegalShakerDropoffs(NumberPSCFisheries, MaxAge, LastBY)
# Dim TempLegalDropoffs(LastBY, MaxAge) As Single
# Dim TempTerminalShakers(LastBY, MaxAge) As Single
# Dim TempTerminalShakerDropoffs(LastBY, MaxAge) As Single
# Dim TempTerminalLegalDropoffs(LastBY, MaxAge) As Single
# Dim TempSublegalShakerDropoffs(LastBY, MaxAge) As Single
# Dim TempSublegalShakers(LastBY, MaxAge) As Single
#
# If isReplicateCohShak = True Then
# lastYear = LastIMDataYear
# Else
# lastYear = LastCalendarYear
# End If
# For PSCFishery As Integer = 1 To NumberPSCFisheries - 1 'excludes escapement
# For CalYr As Integer = FirstBY + OceanStartAge To LastCalendarYear 'LastBY + LastAge(LastBY)
# ReDim NonVulnerableCohort(MaxAge)
# TotalVulnerableCohort = 0
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2878", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt should be zero")
#
# For Age = OceanStartAge To MaxAge
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2880", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt start of age loop")
#
# 'derive either brood and calendar year from age as appropriate
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2882 shakerMethod1", CalYr - Age, Age, CalYr, LastIMDataYear, FirstBY, LastBY, TotalVulnerableCohort)
# If ShakerMethod = "C" Then 'CalendarYr
# BroodYear = CalYr - Age
# yr_ = CalYr
# Else 'Brood Year method
# BroodYear = CalYr - OceanStartAge
# yr_ = BroodYear + Age
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2890 shakerMethod1", ShakerMethod, CalYr, Age, BroodYear, LastIMDataYear, "oceanstartage", OceanStartAge, "ShakerMethod", ShakerMethod, "BY", BroodYear, "age", Age, TotalVulnerableCohort)
# If BroodYear + Age > LastIMDataYear Then GoTo NxtAge
# If ShakerMethod = "C" Then
# If BroodYear < FirstBY Then Exit For
# If BroodYear > LastBY Then GoTo NxtAge
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2895 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2896 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY, TotalVulnerableCohort)
# If MissingBroodYearFlag(BroodYear) = True Then GoTo NxtAge
# ElseIf ShakerMethod = "B" Then
# If BroodYear > LastBY Then GoTo SkipYR
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2900 shakerMethod1", ShakerMethod, BroodYear, Age, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "2901 shakerMethod1", ShakerMethod, CalYr, BroodYear, Age, PSCFishery, MissingBroodYearFlag(BroodYear), CompleteBYFlag(BroodYear), "lastBY", LastBY)
# If MissingBroodYearFlag(BroodYear) = True Then GoTo SkipYR
# End If
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2904", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnchrt before cohrt=")
#
# If CompleteBYFlag(BroodYear) = True Then 'cohorts estimated for complete broods
# If terminal(PSCFishery, Age) = False Then
# 'PreTerm cohrt after natural mortality
# cohrt = Cohort(BroodYear, Age) * SurvivalRate(Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2908 com BY term F", BroodYear, Age, PSCFishery, cohrt, Cohort(BroodYear, Age), SurvivalRate(Age))
# Else
# 'total terminal landed catch + terminal shakers + terminal CNR + escapement
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2911 ShakMeth1 call TotalTerminalcatcg_Age", ShakerMethod, BroodYear, Age)
#
# cohrt = TotalTerminalCatch_Age(BroodYear, Age, pass) + Escape(BroodYear, Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2914 com BY term T", BroodYear, Age, PSCFishery, "cohort", cohrt, "totalTerminalCatch_Age", TotalTerminalCatch_Age(BroodYear, Age, pass), "Escape", Escape(BroodYear, Age))
# End If
# Else 'cohorts estimated for incomplete broods
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2917 shakerMethod1", BroodYear, ShakerMethod, "1", Age, LastAge(BroodYear), TotalVulnerableCohort)
# If ShakerMethod = "C" Or Age <= LastAge(BroodYear) Then
# cohrt = CalcEstmCohrt2(BroodYear, Age)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 incom BY shakCalcFg 1",ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt2(BroodYear, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2921 ShakerMethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt)
# Else
# cohrt = CalcEstmCohrt(BroodYear, Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_Cohort_IncompleteBroodID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2924 Shakermethod1", ShakerMethod, BroodYear, Age, PSCFishery, cohrt, CalcEstmCohrt(BroodYear, Age))
# End If
# 'for all terminal fishery ages
# If terminal(PSCFishery, Age) = True Then
# cohrt = cohrt * (1 - AveragePreTermER(Age)) * AverageMatRate(Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery And Age = traceThisAge Then WriteLine(debug_CohortID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2929 incom BY term", BroodYear, Age, PSCFishery, cohrt, AveragePreTermER(Age), AverageMatRate(Age))
# End If
# End If 'CompleteBYFlag(BroodYear) = True
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2932", BroodYear, Age, PSCFishery, TotalVulnerableCohort, "totVulnChrt before summation")
# NonVulnerableCohort(Age) = cohrt * PNV(BroodYear + Age, PSCFishery, Age)
# TotalVulnerableCohort = TotalVulnerableCohort + cohrt * (PV(BroodYear + Age, PSCFishery, Age))
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
# 'If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2937 nonVuln", ShakerMethod, BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "line 2938 totVuln", ShakerMethod, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CohortID, "line 2939 nonVuln", BroodYear, Age, PSCFishery, NonVulnerableCohort(Age), cohrt, PNV(BroodYear + Age, PSCFishery, Age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr = 1983 Then WriteLine(debug_CohortID, "line 2940 totVuln", CalYr, BroodYear, Age, PSCFishery, TotalVulnerableCohort, cohrt, PV(BroodYear + Age, PSCFishery, Age), cohrt * PV(BroodYear + Age, PSCFishery, Age))
#NxtAge:
# Next Age
# If ShakerMethod = "C" Then 'calendar year method
# TempCatch = CalendarYearLandedCatch(CalYr, PSCFishery)
# Else 'brood year method
# TempCatch = TotalLandedCatch_ByFishery(BroodYear, PSCFishery)
# End If
# For Age = OceanStartAge To MaxAge
# 'derive either brood and calendar year from age as appropriate
# If ShakerMethod = "C" Then 'CalendarYr
# BroodYear = CalYr - Age
# yr_ = CalYr
# Else 'Brood Year method
# BroodYear = CalYr - OceanStartAge
# yr_ = BroodYear + Age
# If isReplicateCohShak = True And CompleteBYFlag(BroodYear) = True Then
# yr_ = CalYr
# End If
# End If 'ShakerMethod = "C"
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_calcEstmCohrtID, "2960 calyr", yr_, "age", Age, "brood", BroodYear, "ShakerMethod", ShakerMethod, TotalVulnerableCohort)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2961", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "FirstBY", FirstBY, "ShakerMethod", ShakerMethod, "yr_", yr_, "LastIMDataYear", LastIMDataYear)
# If BroodYear < FirstBY Or yr_ > LastIMDataYear Then Exit For
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "2963", "fishery", PSCFishery, "age", Age, "brood", BroodYear, "yr_", yr_, "CNRMethod", CNRMethod(yr_, PSCFishery), "lastby", LastBY, "ShakerMethod", ShakerMethod)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2969", yr_, PSCFishery, CNRMethod(yr_, PSCFishery), TotalVulnerableCohort)
# If CNRMethod(yr_, PSCFishery) <> 3 Then
# If TotalVulnerableCohort <> 0 Then
# encounterRate = 0.00001
# If NonVulnerableCohort(Age) > 0 And TotalVulnerableCohort > 0 Then
# encounterRate = NonVulnerableCohort(Age) / TotalVulnerableCohort
# End If
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_CohortID, "line 2971 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_matShakersID, "line 2972 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age), TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2970 encounterrate", BroodYear, Age, PSCFishery, encounterRate, NonVulnerableCohort(Age) / TotalVulnerableCohort, NonVulnerableCohort(Age), TotalVulnerableCohort)
# Else
# encounterRate = 0
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973 encounterRate & TotalVulnerableCohort=0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2973 encounterrate =0", BroodYear, Age, PSCFishery, encounterRate, TotalVulnerableCohort)
# End If
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_EncounterRateID, "line 2973", BroodYear, PSCFishery, Age, TotalVulnerableCohort, " totVuln after goto NxtAge and If CNRMethod(yr_, PSCFishery) <> 3")
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "2973", ShakerMethod, PSCFishery, Age, BroodYear, encounterRate, TotalVulnerableCohort)
#
# If BroodYear <= LastBY Then
# SublegalShakerMortalities(PSCFishery, Age, BroodYear) = TempCatch * SublegalIMRate(CalYr, PSCFishery) * encounterRate
# SublegalDropoffMortalities(PSCFishery, Age, BroodYear) = TempCatch * DropoffRate(CalYr, PSCFishery) * encounterRate
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2979 SL dropoff", ShakerMethod, PSCFishery, Age, BroodYear, "dropoff", SublegalDropoffMortalities(PSCFishery, Age, BroodYear), "catch", TempCatch, "dropOffRate", DropoffRate(CalYr, PSCFishery), "encRte", encounterRate, "relRatio", RelRatio(BroodYear))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_ShakerID, "line 2980 SL shaker", ShakerMethod, PSCFishery, Age, BroodYear, "shakers", SublegalShakerMortalities(PSCFishery, Age, BroodYear), "catch", TempCatch, "SublegalIMRat", SublegalIMRate(CalYr, PSCFishery), "encRte", encounterRate, "relRatio", RelRatio(BroodYear))
# 'external shaker algorithm needs more development, as is it will produce too many shakers at the older ages
# If RetentionMethod(CalYr, PSCFishery) = 1 Then 'handles external shaker estimates
# MsgBox("External Shaker algorithm is not valid. Do not trust output.")
# SublegalShakerMortalities(PSCFishery, Age, BroodYear) = ((SubLegalShakerEst(CalYr, PSCFishery) * LandedCatch(PSCFishery, Age, BroodYear)) / LandedCatchEst(CalYr, PSCFishery)) * SublegalIMRate(CalYr, PSCFishery)
# SublegalDropoffMortalities(PSCFishery, Age, BroodYear) = ((SubLegalShakerEst(CalYr, PSCFishery) * LandedCatch(PSCFishery, Age, BroodYear)) / LandedCatchEst(CalYr, PSCFishery)) * DropoffRate(CalYr, PSCFishery)
# End If
# 'total (PreTerm and terminal) sublegal shakers BroodYear age
# 'add up sublegal shakers for all fisheries and add in sublegal dropoffs
# TempSublegalShakers(BroodYear, Age) = TempSublegalShakers(BroodYear, Age) + SublegalShakerMortalities(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then WriteLine(debug_matShakersID, "2990 TempSublegalShakers", BroodYear, Age, PSCFishery, TempSublegalShakers(BroodYear, Age), TempSublegalShakers(BroodYear, Age), SublegalShakerMortalities(PSCFishery, Age, BroodYear), TempCatch, SublegalIMRate(CalYr, PSCFishery), encounterRate)
# TempSublegalShakerDropoffs(BroodYear, Age) = TempSublegalShakerDropoffs(BroodYear, Age) + SublegalDropoffMortalities(PSCFishery, Age, BroodYear)
# 'totalLegalDropoffs moved here to compare against Coshak12, remove when done testing
# TempLegalDropoffs(BroodYear, Age) = TempLegalDropoffs(BroodYear, Age) + LegalDropoffMortality(PSCFishery, Age, BroodYear)
# 'TempAgeShak(BroodYear, age) = TempAgeShak(BroodYear, age) + SublegalShakerMortalities(PSCFishery, age, BroodYear) + SublegalDropoffMortalities(PSCFishery, age, BroodYear) + LegalDropoffMortality(PSCFishery, age, BroodYear)
# If terminal(PSCFishery, Age) = True Then
# TempTerminalShakers(BroodYear, Age) = TempTerminalShakers(BroodYear, Age) + SublegalShakerMortalities(PSCFishery, Age, BroodYear)
# TempTerminalShakerDropoffs(BroodYear, Age) = TempTerminalShakerDropoffs(BroodYear, Age) + SublegalDropoffMortalities(PSCFishery, Age, BroodYear)
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And Age = traceThisAge Then WriteLine(debug_matShakersID, "2999 term shakers", BroodYear, Age, PSCFishery, TempSublegalShakers(BroodYear, Age), TempTerminalShakers(BroodYear, Age), SublegalShakerMortalities(PSCFishery, Age, BroodYear), "calYr", CalYr, "catch", TempCatch, "endRte", encounterRate, "shakerRate", SublegalIMRate(CalYr, PSCFishery), "dropoffRate", DropoffRate(CalYr, PSCFishery))
# 'moved to ShakerMethod1 to compare against Coshak12, remove from ShakerMethod1 when done testing
# TempTerminalLegalDropoffs(BroodYear, Age) = TempTerminalLegalDropoffs(BroodYear, Age) + LegalDropoffMortality(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear Then WriteLine(debug_terminalCatchID, "3011 ShakerMethod`", BroodYear, Age, PSCFishery, "TerminalLegalDropoffs", TempTerminalLegalDropoffs(BroodYear, Age), "dropoff", LegalDropoffMortality(PSCFishery, Age, BroodYear))
# End If
# End If 'BroodYear <= LastBY
# End If 'CNRMethod(yr_, PSCFishery) <> 3
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, Age, PSCFishery, TotalVulnerableCohort, " totVulnChrt before next age")
# Next Age
#SkipYR:
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear = traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_EncounterRateID, "line 3011", BroodYear, PSCFishery, TotalVulnerableCohort, "totVulnChrt before next yr")
# Next CalYr
# Next PSCFishery
# 'code below is necessary outside of loop above so that function TotalCatch_Age works correctly
# For BroodYear = FirstBY To LastBY
# For Age = OceanStartAge To MaxAge
# 'total (PreTerm and terminal) sublegal shakers by age
# 'add up sublegal shakers for all fisheries and add in sublegal dropoffs
# TotalSublegalShakers(BroodYear, Age) = TempSublegalShakers(BroodYear, Age)
# TotalSublegalShakerDropoffs(BroodYear, Age) = TempSublegalShakerDropoffs(BroodYear, Age)
# 'totalLegalDropoffs moved here to compare against Coshak12, remove when done testing
# TotalLegalDropoffs(BroodYear, Age) = TempLegalDropoffs(BroodYear, Age)
# TotalTerminalShakers(BroodYear, Age) = TempTerminalShakers(BroodYear, Age)
# TotalTerminalShakerDropoffs(BroodYear, Age) = TempTerminalShakerDropoffs(BroodYear, Age)
# 'moved to ShakerMethod1 to compare against Coshak12, remove from ShakerMethod1 when done testing
# TotalTerminalLegalDropoffs(BroodYear, Age) = TempTerminalLegalDropoffs(BroodYear, Age)
# Next Age
# Next BroodYear
#
# 'calculate shakers for each calendar year and fishery
# 'old code errantly added legal dropoffs to shakers so I have added them for now to allow testing against old code output
# '************legal dropoffs should be removed from here for final code
# For CalYr As Integer = FirstBY + OceanStartAge To LastCalendarYear
# For PSCFishery As Integer = 1 To NumberPSCFisheries
# isOK = True
# If PSCFisheryGear(PSCFishery) = "STRAY" Then isOK = False
# If PSCFisheryGear(PSCFishery) = "ESC" Then isOK = False
# If isOK = True Then
# For Age = OceanStartAge To MaxAge
# If CalYr - Age >= FirstBY And CalYr - Age <= LastBY Then
# CalendarYearShakers(CalYr, PSCFishery) += SublegalShakerMortalities(PSCFishery, Age, CalYr - Age) + SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age) + LegalDropoffMortality(PSCFishery, Age, CalYr - Age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And CalYr - Age >= traceThisYear And PSCFishery = 8 Then WriteLine(debug_CalYrShakersID, "3038 CalYrShakers", CalYr, PSCFishery, Age, "accum by fishery", CalendarYearShakers(CalYr, PSCFishery), "shaker+dropoff", (SublegalShakerMortalities(PSCFishery, Age, CalYr - Age) + SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age) + LegalDropoffMortality(PSCFishery, Age, CalYr - Age)), "shaker", SublegalShakerMortalities(PSCFishery, Age, CalYr - Age), "SL dropoff", SublegalDropoffMortalities(PSCFishery, Age, CalYr - Age), "L dropoff", LegalDropoffMortality(PSCFishery, Age, CalYr - Age))
# End If
# Next Age
# End If
# Next PSCFishery
# Next CalYr
}
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