R/func_CalcLandedCatchAndEscapementWithBYWeights.R
In catarinawor/ERAR: This package is a loose translation of the Chinook Technical committee ERA model
Defines functions
CalcLandedCatchAndEscapementWithBYWeights
CalcLandedCatchAndEscapement
#ERA function GetFirstAndLastBY()
#Translated from VB ERA CIS code
#October 2018
#Author: Catarina Wor
#source(utils.R)
#' @title CalcLandedCatchAndEscapementWithBYWeights
#'
#' @description
#'
#'
#'
#' @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
#'
#'
CalcLandedCatchAndEscapementWithBYWeights <- function(D,M){
#This function is not being used at the moment.
#original VB code
#=============================================================
}
#' @title CalcLandedCatchAndEscapement
#'
#' @description
#'
#'
#'
#' @param M A list passed to MainSub
#'
#' @param D A list contining the outputs of GetSizeLimitLengthVulnerable
#'
#' @details reads in catch and escapenet levels and expands them to maximum level of releases. also does a bunch of random jiggery pokery that is hard to understand.
#'
#' @return
#'
#'
#'
#' @export
#'
#' @examples
#'
#'
CalcLandedCatchAndEscapement <- function( D,M ){
#=============================================================
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' by the variable named RelRatio(BY) = MaxRelease/CWTRelease(BY)
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches) which is what is printed in the cby.out and cyr.out files
AllBY <- D$FirstBY:D$LastBY
Allages <- D$youngestAge:D$MaxAge
Escape <- matrix(0, nrow=length(AllBY), ncol=length(Allages))
tag_code <- ""
tempPSCCatch <- matrix(0, nrow=M$NumberPSCFisheries, ncol=7)
TotalLandedCatch <- matrix(0, nrow=length(AllBY), ncol=7)
TotalTerminalLandedCatch <- matrix(0, nrow=length(AllBY), ncol=7)
TotalLegalDropoffs <- matrix(0, nrow=length(AllBY), ncol=7)
LastAge <- NULL
NumberCompleteBroods <- 0
CompleteBYFlag <- data.frame(BY=AllBY, Flag=rep(FALSE, length(AllBY)))
MissingBroodYearFlag <- data.frame(BY=AllBY, Flag=rep(FALSE, length(AllBY)))
if( !M$isReplicateCohShak ){
NumFish <- M$NumberPSCFisheries
}else{
NumFish <- M$NumberERAFisheries
}
LandedCatch <- array(0, dim=c(NumFish, 7, length(AllBY)))
LegalDropoffMortality <- array(0, dim=c(NumFish, 7, length(AllBY)))
TotalLandedCatch_ByFishery <- matrix(0, nrow=length(AllBY), ncol=NumFish)
#variables created by Catarina for monitoring purposes
databasecatch<-list()
#'Loop through each PSCfishery (or ERAFishery if emulating CAS-Coshak) and escapement to obtain catch and escapement
for( Fish in seq_len(NumFish) ){
sink("../logs/CalcLandedCatchAndEscapement.log",append=T)
cat(paste0(D$CASStockString,"\n"))
cat(paste0("Get Landed Catch and Escapement for fishery " , Fish, " of ", NumFish, " fine scale fisheries\n"))
sink()
#
#'Create a list of CAS Fisheries mapped to each PSC Fishery with appropriate start and end date ranges
if( !M$isReplicateCohShak ){
d <- BuildPSCFisheryIdList( M,Fish )
ERASQL <- paste0( "SELECT wtc.BroodYear,r.Age, ",
"Sum(IIf(f.CASTerminal, r.AdjustedEstimatedNumber,IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor))) AS SumEstimatedNumber " ,
"FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) " ,
"INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode " ,
"WHERE wtc.CASStock IN ('", as.character(D$CASStockString[[1]]) ,"') AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in " , d$FisheryIdList ," ", d$DateRangeClause , " AND r.age > 1" ,
" GROUP BY r.Age,wtc.BroodYear ORDER BY wtc.BroodYear, r.Age")
}else{#'same as above except by tag code in addition to brood year and age BY ERAFishery instead of PSCFishery
#not tested
d <- BuildERAFisheryIdList( M,Fish )
ERASQL <- paste0("SELECT wtc.BroodYear,r.Age, " ,
"Sum(IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor)) AS SumEstimatedNumber, " ,
"r.TagCode ",
"FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) ",
"INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode ",
"WHERE wtc.CASStock IN ('", D$CASStockString[[1]] ,"') AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in ", d$FisheryIdList ," ", d$DateRangeClause, " AND r.age > 1 ",
" GROUP BY r.Age, wtc.BroodYear, r.TagCode ORDER BY wtc.BroodYear, r.Age")
}
#dta <- RODBC::odbcConnectAccess2007(M$datbse) #specifies the file path
EstimatedNumberdf <- RODBC::sqlQuery( M$chnl , query =ERASQL )
databasecatch[[Fish]] <- EstimatedNumberdf
BroodYear <- EstimatedNumberdf$BroodYear
RecoveryAge <- EstimatedNumberdf$Age
SumAdjustedEstimatedNumber <- EstimatedNumberdf$SumEstimatedNumber
if( M$isReplicateCohShak ){
#'reproduce CFile numbers
tag_code <- EstimatedNumberdf[,4]
#'reproduce CFile numbers
#not tested
FishName <- M$ERAFisheryName[Fish]
}else{
tag_code <- rep("",nrow(EstimatedNumberdf))
FishName <- M$PSCFisheryName[Fish]
}
#'limit data to last calendar year selected by user
if( nrow(EstimatedNumberdf)>0 ){
for( ya in 1:nrow(EstimatedNumberdf) ){
if( BroodYear[ya] + RecoveryAge[ya] <= M$LastCalendarYear ){
#print(paste(Fish,ya))
isValidAge = TRUE
#'do not use recovery records where RecoveryAge > MaxAge+2
if( RecoveryAge[ya] > D$MaxAge & RecoveryAge[ya] <= D$MaxAge + 2 ){
sink("../logs/Log_OlderThanMaxAge_ID.log", append=TRUE)
cat(paste(D$CASStockString[[1]], ShakerMethod, BroodYear[ya], RecoveryAge[ya], FishName, "assigned to age ", D$MaxAge,"\n"))
sink()
RecoveryAge[ya] <- D$MaxAge
}
if( RecoveryAge[ya] > D$MaxAge + 2 ){
isValidAge = FALSE
sink("../logs/Log_OlderThanMaxAge_ID.log", append=TRUE)
cat(paste(D$CASStockString[[1]], ShakerMethod, BroodYear[ya], RecoveryAge[ya], FishName, "will not be used in the cohort analysis\n"))
sink()
}
if( isValidAge ){
#'combine ages if requested
if( M$isCombineAge2And3[ERAStock] == TRUE & RecoveryAge[ya] == 2 ){
RecoveryAge[ya] <- 3
}else if( M$isCombineAge5And6[ERAStock] == TRUE & RecoveryAge[ya] == 6 ){
RecoveryAge[ya] <- 5
}
#'one more time, check BroodYear + RecoveryAge because of combine age
if( BroodYear[ya] + RecoveryAge[ya] <= M$LastCalendarYear ){
#'CIS multiplies fine scale fishery and tag code esc by RelRatio BEFORE combining into PSC Fishery
#'CAS-Coshak rounds fine scale fishery, then combines into PSC Fishery BEFORE multiplying by RelRatio
if( FishName == "ESCAPEMENT" | grepl("ESC",FishName) ){
if( !M$isReplicateCohShak ){
Esc <- SumAdjustedEstimatedNumber[ya] * D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear==BroodYear[ya]]
}else if( M$isReplicateCohShak ){
#'CAS round escapement before applying IDL
#'Esc = Convert.ToInt32(SumAdjustedEstimatedNumber + 0.0000001) ' 0.00000001
Esc <- SumAdjustedEstimatedNumber[ya] + 0.0001
}
if(RecoveryAge[ya] == D$OceanStartAge){
Escape[which(AllBY==BroodYear[ya]), which(Allages==RecoveryAge[ya])] <- Escape[which(AllBY==BroodYear[ya]),which(Allages==RecoveryAge[ya])] + Esc / D$InterDamSurvivaldf$JackInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear[ya] >= M$traceThisYear ){
sink("../logs/debug_EscapeID.log",append=T)
cat(paste0(D$CASStockString,"\n"))
cat(paste("1100 accum fine scale escape", BroodYear[ya], RecoveryAge[ya], tag_code[ya], Escape[which(AllBY==BroodYear[ya])&which(Allages==RecoveryAge[ya])], Esc, SumAdjustedEstimatedNumber[ya], D$InterDamSurvivaldf$JackInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]))
sink()
}
}else{
Escape[which(AllBY==BroodYear[ya]),which(Allages==RecoveryAge[ya])] <- Escape[which(AllBY==BroodYear[ya]),which(Allages==RecoveryAge[ya])] + Esc / D$InterDamSurvivaldf$AdultInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear[ya] >= M$traceThisYear) {
sink("../logs/debug_EscapeID.log",append=T)
cat(paste0(D$CASStockString,"\n"))
cat(paste("1103 accum fine scale escape", BroodYear[ya], RecoveryAge[ya], tag_code[ya], Escape[which(AllBY==BroodYear[ya])&which(Allages==RecoveryAge[ya])], Esc, SumAdjustedEstimatedNumber[ya], D$InterDamSurvivaldf$AdultInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]))
sink()
}
}
}else{ #catch
#'SQL returns fine scale fishery, this is where fine scale fishery is combined into PSC Fishery
#'WriteLine(debugID, CurrentStock, Fish, LastBY, BroodYear, RecoveryAge, BroodYear + RecoveryAge, LastCalendarYear)
if(!M$isReplicateCohShak){
LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] <- LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] + SumAdjustedEstimatedNumber[ya] * D$RelRatiodf$RelRatio[which(D$RelRatiodf$BroodYear==BroodYear[ya])]
if(RecoveryAge[ya] < D$OceanStartAge){
sink("../logs/LandedCatch.log",append=T)
cat(paste0("Youngest age = ", RecoveryAge[ya], " is less than OceanStartAge for " , BroodYear[ya] , ". Did you forget to combine age 2 and 3? Program is going to crash with an index was outside the bounds of the array error message."))
sink()
stop(" MainSub stopped check ../LandedCatch.log")
}
}else{
#multiply catch by RelRatio AFTER combining fine scale fishery into PSC Fishery
#'SQL query must returning sum by fine scale fishery, not by tag code
#'SQL must accum by fine scale fishery before rounding because if Extrapoplated = YES in CWDBRecovery table, then the fractional numbers will get lost
#'because SumAdjustedEstimatedNumber = accum fine scale catches, OK to round here
#'add 0.0000001 instead of 0.00000001 so even numbers to round up. The extra decimal place is not an issue for odd numbers.
LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] <- LandedCatch[[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])]] + SumAdjustedEstimatedNumber[ya] + 0.0001
if(RecoveryAge[ya] < D$OceanStartAge){
sink("../logs/LandedCatch.log",append=T)
cat(paste0("Youngest age = " & RecoveryAge[ya] & " is less than OceanStartAge for " & BroodYear[ya] & ". Did you forget to combine age 2 and 3? Program is going to crash with an index out of bounds error message."))
sink()
stop(" MainSub stopped check ../LandedCatch.log")
}
#'If RecoveryAge = 4 And Fish < 13 And BroodYear = 1975 Then WriteLine(debugID, "1327", ShakerMethod, Fish, RecoveryAge, BroodYear, LandedCatch(Fish, RecoveryAge, BroodYear), SumAdjustedEstimatedNumber, RelRatio(BroodYear))
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & M$isTraceByCalendarYr & (BroodYear[ya] + RecoveryAge[ya]) >= M$traceThisYear + M$traceThisAge & Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log",append=T)
cat(paste0( "line 1105 FineScaleCatch", BroodYear[ya], Fish, RecoveryAge[ya], tag_code[ya], SumAdjustedEstimatedNumber[ya], LandedCatch[Fish, RecoveryAge[ya], which(AllBY==BroodYear[ya])]))
sink()
}
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & Fish == 31 & BroodYear[ya] >= M$traceThisYear & RecoveryAge[ya] == M$traceThisAge){
sink("../logs/debug_CatchID.log",append=T)
cat(paste0("line 1106 FineScaleCatch", BroodYear[ya], Fish, RecoveryAge[ya], tag_code[ya], SumAdjustedEstimatedNumber[ya], LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])]))
sink()
}
}#'isReplicateCohShak = False
#'legal dropoff mortalities for PSCFisheries, similar code for ERAFisheries is in the next loop below.
if(!M$isReplicateCohShak){
if(D$IMdf$CNRMethod[D$IMdf$CalendarYear==BroodYear[ya] + RecoveryAge[ya] &D$IMdf$PSCFishery==Fish]!=3){
LegalDropoffMortality[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] <- LegalDropoffMortality[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]] +
LandedCatch[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]] *
D$IMdf$DropoffRate[(BroodYear[ya] + RecoveryAge[ya])==D$IMdf$CalendarYear & D$IMdf$PSCFishery==Fish]
if(is.na(LegalDropoffMortality[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]])){
LegalDropoffMortality[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]] <- 0.0
}
}
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear[ya] >= M$traceThisYear & Fish== M$traceThisFishery){
sink("../logs/debug_LegalDropoffID.log",append=T)
cat(paste("1196 L dropoff", Fish, RecoveryAge[ya], tag_code[ya], LegalDropoffMortality[Fish, RecoveryAge[ya], BroodYear[ya]], LandedCatch[Fish, RecoveryAge[ya], ya], D$DropoffRate[which((BroodYear[ya] + RecoveryAge[ya])==D$DropoffRate$CalendarYear), Fish+1]))
sink()
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_LegalDropoffID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_ShakerID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
}else{
#'to emulate CAS-Coshak, calculate dropoff after rounding ERAFishery and after combining ERAFishery into PSCFishery in the next loop below
}#sReplicateCohShak = False
}#'FishName = "ESCAPEMENT" Or FishName = "ESCAPE"
}#'BroodYear + RecoveryAge <= LastCalendarYear
}# 'isValidAge = True
} # end of if statement
}# 'BroodYear + RecoveryAge <= LastCalendarYear
}else{
LegalDropoffMortality[Fish,,] <- 0.0
LandedCatch[Fish,,] <-0.0
}
} #next Fish
if(M$isReplicateCohShak){ #'combine ERAFisheries into PSCFishery as with CMB spreadsheet
for(y in 1:length(AllBY)){
for(Fish in 1:(M$NumberPSCFisheries-1)){ #'except escapement
#initialize at the start of each PSCFishery and BroodYear
for(Age in D$OceanStartAge:D$MaxAge){
tempPSCCatch[Fish, Age] <- 0
}
D2 <- BuildERAFisheryToPSCFisheryList(Fish,M)
D$NumberERA2PSCFisheries[Fish]<-D2$NumberERA2PSCFisheries
D$ERA2PSC[[Fish]]<-D2$ERA2PSC
#'accum ERAFishery LandedCatch() into TempPSCCatch()
for(FisheryID in 1:D$NumberERA2PSCFisheries[Fish]){
ERAFish = D$ERA2PSC[[Fish]][FisheryID]
for(Age in D$OceanStartAge:D$MaxAge){
tempPSCCatch[Fish, Age] <- tempPSCCatch[Fish, Age] + LandedCatch[ERAFish, Age, y] * D$RelRatiodf$RelRatio[AllBY[y]==D$RelRatiodf$BroodYear]
if(M$isTraceCalc&M$ShakerMethod==M$traceThisShakerMethod&M$isTraceByBroodYr&BroodYear>=M$traceThisYear&Fish==M$traceThisFishery){
sink("../logs/CatchID.log",,append=T)
cat(paste("after", tempPSCCatch[Fish, Age], LandedCatch[ERAFish, Age, y], D$RelRatiodf$RelRatio[AllBY[y]==D$RelRatiodf$BroodYear]))
sink()
}
}
}
}
for(Fish in 1:(M$NumberPSCFisheries-1)){
for(Age in D$OceanStartAge:D$MaxAge){
if(AllBY[y]+Age <= M$LastCalendarYear){
LandedCatch[Fish, Age, y] <- tempPSCCatch[Fish, Age]
if(M$isTraceCalc&M$isTraceByCalendarYr&(BroodYear[y] + Age)>= M$traceThisYear& Fish==M$traceThisFishery){
sink("../logs/debug_CatchID.log", append=T)
cat(paste("line 1198 combined rounded RelRatio", Fish, BroodYear[y], Age, LandedCatch[Fish, Age, y], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]))
sink()
}
if(M$isTraceCalc&M$isTraceByBroodYr&BroodYear[y]>=M$traceThisYear&Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log")
cat(paste("line 1198 combined rounded RelRatio", Fish, BroodYear[y], Age, LandedCatch[Fish, Age, y], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]))
sink()
}
#'when emulating CAS-Coshak
#'step 1, calculate drop-off here, after rounding and combining ERAFisheries into PSCFisheries
#'step 2 use DropoffRate(BroodYear + 2, PSCFishery) instead of DropoffRate(BroodYear + Age, PSCFishery) if brood year method
#'else use DropoffRate(BroodYear + age, PSCFishery) if calendar year method
if(M$ShakerMethod == "B"){
LegalDropoffMortality[Fish, Age, y] <- LegalDropoffMortality[Fish, Age, y] + LandedCatch[Fish, Age, y] * D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + 2) & D$IMdf$PSCFishery == Fish]
}else if(M$ShakerMethod == "C"){
LegalDropoffMortality[Fish, Age, y] <- LegalDropoffMortality[Fish, Age, y] + LandedCatch[Fish, Age, y] * D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + Age) & D$IMdf$PSCFishery == Fish]
}
}else{
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & AllBY[y] >= M$traceThisYear & Fish ==M$traceThisFishery ){
sink("../logs/debug_ShakerID.log")
cat(paste("1344 L dropoff", Fish, Age, tag_code, LegalDropoffMortality[Fish, Age, y], LandedCatch[Fish, Age, y], D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + 2)& D$IMdf$PSCFishery== Fish]))
sink()
}
#'step 3 add sublegal shakers and dropoff (i.e. replicate double count) in sub ShakerMethod1
if(M$isTraceCalc & AllBY[y] >= M$traceThisYear & Fish == M$traceThisFishery){
sink("../logs/debug_LegalDropoffID.log")
cat(paste("1268 L dropofff before doubleCount", Fish, Age, tag_code, LegalDropoffMortality[Fish, Age, y], LandedCatch[PSCFishery, Age, y], D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + 2)& D$IMdf$PSCFishery== Fish]))
sink()
}
}# 'BroodYear + RecoveryAge <= LastCalendarYear
}
}
#'apply RelRatio to Escape
for(Age in 1:length(D$OceanStartAge:D$MaxAge) ){
#'limit data to last calendar year selected by user
if((BroodYear[which(BroodYear==AllBY[y])]+Age) <= M$LastCalendarYear){
Escape[y,Age] =Escape[y,Age] * D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod &AllBY[y] >= M$traceThisYear){
sink("../logs/debug_EscapeID.log")
cat(paste("1565 rounded esc * relRatio", BroodYear[BroodYear==AllBY[y]], Age, Escape[BroodYear==AllBY[y], Age], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]))
sink()
}
}
}
}
}
for(BYind in seq_along(AllBY)){
BroodYearCatch <- 0
BroodYearEscapement <- 0
for(Age in seq_along(Allages)){
if( Allages[Age] <= M$LastCalendarYear - AllBY[BYind] ){
for(Fish in seq_len(M$NumberPSCFisheries - 1)){
#print(paste(BYind,Age,Fish))
#'WriteLine(debugID, "1408", terminal(PSCFishery, Age), PSCFishery, Age)
#'total (PreTerm and terminal) landed catch BroodYear age
TotalLandedCatch[BYind, Age] = TotalLandedCatch[BYind, Age] + LandedCatch[Fish, Age, BYind]
if(M$isTraceCalc & M$isTraceByCalendarYr & (AllBY[BYind] + Allages[Age]) >= M$traceThisYear & Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log")
cat(paste("line 1127 TotalLandedcatch", AllBY[BYind], Fish, Allages[Age], TotalLandedCatch[BYind, Age], LandedCatch[Fish, Age, BYind], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[BYind]]))
sink()
}
if(M$isTraceCalc & M$isTraceByBroodYr & AllBY[BYind] >= M$traceThisYear & Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log")
cat(paste("line 1127 TotalLandedcatch", AllBY[BYind], Fish, Allages[Age], TotalLandedCatch[BYind, Age], LandedCatch[Fish, Age, BYind], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[BYind]]))
sink()
}
#'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
# 'total (PreTerm and terminal) Legal Dropoff mortalities BroodYear age
#'TotalLegalDropoffs(BroodYear, age) = TotalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
#'total (PreTerm and terminal) landed catch BroodYear fishery
TotalLandedCatch_ByFishery[BYind, Fish] = TotalLandedCatch_ByFishery[BYind, Fish] + LandedCatch[Fish , Age,BYind ]
#'total terminal landed catch BroodYear age
if(D$terminal[Fish,Age] & M$PSCFisheryGear[Fish] != "STRAY"){
TotalTerminalLandedCatch[BYind, Age] <- TotalTerminalLandedCatch[BYind, Age] + LandedCatch[Fish, Age, BYind]
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & AllBY[BYind] >= M$traceThisYear){
sink("../logs/debug_SumMatAgeCatID.log")
cat(paste("1394 sumMatCat", AllBY[BYind], Allages[Age], Fish, TotalTerminalLandedCatch[BYind, Age], LandedCatch[Fishery, Age, BYind], PSCFisheryGear[PSCFishery]))
sink()
}
#'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
#'TotalTerminalLegalDropoffs(BroodYear, age) = TotalTerminalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
}
#'If terminal(PSCFishery, Age) = True Then
#' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1289 termcatch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
#'Else
#' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1288 catch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
#'End If
}
#'sum up all catch and escapement for brood year
BroodYearCatch <- BroodYearCatch + TotalLandedCatch[BYind, Age]
BroodYearEscapement <- BroodYearEscapement + Escape[BYind, Age]
} #'age <= LastCalendarYear - BroodYear
}
#'set MissingBroodYearFlag to False if there is escapement for the brood year
#'If BroodYearEscapement > 0 Then
if( BroodYearCatch > 0 | BroodYearEscapement > 0 ){
MissingBroodYearFlag$Flag[BYind] <- FALSE
#'Get number of ages completed in a broodyear through the last calendar year
if( AllBY[BYind] + D$MaxAge <= M$LastCalendarYear ){
#'Set CompleteBYFlag and get the number of complete broods and lastCompleteBroodYear for the stock
LastAge[BYind] = D$MaxAge
NumberCompleteBroods = NumberCompleteBroods + 1
CompleteBYFlag$Flag[BYind] <- TRUE
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & AllBY[BYind] >= M$traceThisYear ){
sink("../logs/debug_EncounterRateID.log")
cat(paste("1432 completeBYFlag", AllBY[BYind], CompleteBYFlag$Flag[BYind], "max", D$MaxAge, "BY+max", AllBY[BYind] + D$MaxAge, "lastCalYr", M$LastCalendarYear))
sink()
}
LastCompleteBroodYear <- AllBY[BYind]
}else{
LastAge[BYind] <- M$LastCalendarYear - AllBY[BYind] #'last age for incomplete Brood years
}
}else{
MissingBroodYearFlag$Flag[ BYind ] <- TRUE #'set MissingBroodYearFlag to True if there is no escapement for the brood year
LastAge[BYind] <- 0
}
}
CompleteBYFlag$Flag[is.na(CompleteBYFlag$Flag)] <-FALSE
return(list(new=list(LandedCatch = LandedCatch,
TotalLandedCatch = TotalLandedCatch,
TotalLandedCatch_ByFishery = TotalLandedCatch_ByFishery,
NumberCompleteBroods = NumberCompleteBroods,
CompleteBYFlag = CompleteBYFlag,
MissingBroodYearFlag = MissingBroodYearFlag,
TotalLegalDropoffs = TotalLegalDropoffs,
TotalTerminalLandedCatch = TotalTerminalLandedCatch,
LastAge = LastAge,
Escape = Escape,
LegalDropoffMortality=LegalDropoffMortality),
old=list(LastCompleteBroodYear=LastCompleteBroodYear)))
}
#original VB code
#=============================================================
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' by the variable named RelRatio(BY) = MaxRelease/CWTRelease(BY)
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches) which is what is printed in the cby.out and cyr.out files
# ReDim CalendarYearLandedCatch(LastCalendarYear, NumberPSCFisheries)
# Dim temp(NumberPSCFisheries, 7, LastBY) 'if this is dim As Single, rounding get canceled
# Dim ERAFish, FisheryID As Integer
# Dim Esc As Single
# Dim Fish As Integer
# Dim FishName As String
# Dim NumFish As Integer
# Dim tag_code As String = ""
# Dim tempPSCCatch(NumberPSCFisheries, 7) 'if this is dim As Single, rounding get canceled
# Dim BroodYearCatch, BroodYearEscapement As Single
# Dim isValidAge As Boolean
# Dim RecoveryAge As Integer
# Dim SumAdjustedEstimatedNumber As Single
# Dim BroodYear As Integer
# If isReplicateCohShak = False Then 'reproduce CFile numbers
# NumFish = NumberPSCFisheries
# Else
# NumFish = NumberERAFisheries
# End If
# 'Loop through each PSCfishery (or ERAFishery if emulating CAS-Coshak) and escapement to obtain catch and escapement
# For Fish = 1 To NumFish
# lblStatus.Text = " Get Landed Catch and Escapement for fishery " & Fish & " of " & NumFish & " fine scale fisheries"
# lblStatus.Visible = True
# Me.Refresh()
# 'Create a list of CAS Fisheries mapped to each PSC Fishery with appropriate start and end date ranges
# If isReplicateCohShak = False Then 'reproduce CFile numbers
# Call BuildPSCFisheryIdList(Fish)
# Else
# Call BuildERAFisheryIdList(Fish)
# End If
# 'Sum up adjusted estimated numbers for a brood year and age by PSCFishery for current ERAStock
# If isReplicateCohShak = False Then
# ERASQL = "SELECT wtc.BroodYear,r.Age, " &
# "Sum(IIf(f.CASTerminal, r.AdjustedEstimatedNumber,IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor))) AS SumEstimatedNumber " &
# "FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) " &
# "INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode " &
# "WHERE wtc.CASStock IN (" & CASStockString & ") AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in " & FisheryIdList & DateRangeClause & " AND r.age > 1 " &
# " GROUP BY r.Age,wtc.BroodYear ORDER BY wtc.BroodYear, r.Age"
# Else 'same as above except by tag code in addition to brood year and age BY ERAFishery instead of PSCFishery
# ERASQL = "SELECT wtc.BroodYear,r.Age, " &
# "Sum(IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor)) AS SumEstimatedNumber, " &
# "r.TagCode " &
# "FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) " &
# "INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode " &
# "WHERE wtc.CASStock IN (" & CASStockString & ") AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in " & FisheryIdList & DateRangeClause & " AND r.age > 1 " &
# " GROUP BY r.Age, wtc.BroodYear, r.TagCode ORDER BY wtc.BroodYear, r.Age"
# End If
# ERACommand = New OleDbCommand(ERASQL, CISDBConnection)
# CISDataReader = ERACommand.ExecuteReader()
# While CISDataReader.Read()
# BroodYear = CISDataReader(0)
# RecoveryAge = CISDataReader(1)
# SumAdjustedEstimatedNumber = CISDataReader(2)
# If isReplicateCohShak = True Then 'reproduce CFile numbers
# tag_code = CISDataReader(3)
# End If
#
# If isReplicateCohShak = False Then
# FishName = PSCFisheryName(Fish)
# Else 'reproduce CFile numbers
# FishName = ERAFisheryName(Fish)
# End If
#
# 'limit data to last calendar year selected by user
# If BroodYear + RecoveryAge <= LastCalendarYear Then
# isValidAge = True
# 'do not use recovery records where RecoveryAge > MaxAge+2
# If RecoveryAge > MaxAge And RecoveryAge <= MaxAge + 2 Then
# WriteLine(Log_OlderThanMaxAge_ID, ShakerMethod, BroodYear, RecoveryAge, FishName, "assigned to age " & MaxAge)
# RecoveryAge = MaxAge
# End If
#
# If RecoveryAge > MaxAge + 2 Then
# isValidAge = False
# WriteLine(Log_OlderThanMaxAge_ID, ShakerMethod, BroodYear, RecoveryAge, FishName, "will not be used in the cohort analysis")
# End If
#
# If isValidAge = True Then
# 'combine ages if requested
# If isCombineAge2And3(ERAStock) = True And RecoveryAge = 2 Then
# RecoveryAge = 3
# End If
# If isCombineAge5And6(ERAStock) = True And RecoveryAge = 6 Then
# RecoveryAge = 5
# End If
#
# 'one more time, check BroodYear + RecoveryAge because of combine age
# If BroodYear + RecoveryAge <= LastCalendarYear Then
# 'CIS multiplies fine scale fishery and tag code esc by RelRatio BEFORE combining into PSC Fishery
# 'CAS-Coshak rounds fine scale fishery, then combines into PSC Fishery BEFORE multiplying by RelRatio
# If FishName = "ESCAPEMENT" Or FishName = "ESCAPE" Then
# If isReplicateCohShak = False Then
# Esc = SumAdjustedEstimatedNumber * RelRatio(BroodYear)
# ElseIf isReplicateCohShak = True Then
# 'CAS round escapement before applying IDL
# 'Esc = Convert.ToInt32(SumAdjustedEstimatedNumber + 0.0000001) ' 0.00000001
# Esc = SumAdjustedEstimatedNumber + 0.0001
# End If
# If RecoveryAge = OceanStartAge Then
# Escape(BroodYear, RecoveryAge) = Escape(BroodYear, RecoveryAge) + Esc / JackInterDamSurvivalRate(BroodYear + RecoveryAge)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EscapeID, "1100 accum fine scale escape", BroodYear, RecoveryAge, tag_code, Escape(BroodYear, RecoveryAge), Esc, SumAdjustedEstimatedNumber, JackInterDamSurvivalRate(BroodYear + RecoveryAge))
# Else
# Escape(BroodYear, RecoveryAge) = Escape(BroodYear, RecoveryAge) + Esc / AdultInterDamSurvivalRate(BroodYear + RecoveryAge)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EscapeID, "1103 accum fine scale escape", BroodYear, RecoveryAge, tag_code, Escape(BroodYear, RecoveryAge), Esc, SumAdjustedEstimatedNumber, AdultInterDamSurvivalRate(BroodYear + RecoveryAge))
# End If
# Else 'catch
# 'SQL returns fine scale fishery, this is where fine scale fishery is combined into PSC Fishery
# 'WriteLine(debugID, CurrentStock, Fish, LastBY, BroodYear, RecoveryAge, BroodYear + RecoveryAge, LastCalendarYear)
# If isReplicateCohShak = False Then
# Try
# LandedCatch(Fish, RecoveryAge, BroodYear) = LandedCatch(Fish, RecoveryAge, BroodYear) + SumAdjustedEstimatedNumber * RelRatio(BroodYear)
# Catch
# If (RecoveryAge < OceanStartAge) Then
# MsgBox("Youngest age = " & RecoveryAge & " is less than OceanStartAge for " & BroodYear & ". Did you forget to combine age 2 and 3? Program is going to crash with an index was outside the bounds of the array error message.")
# End If
# End Try
# Else 'multiply catch by RelRatio AFTER combining fine scale fishery into PSC Fishery
# 'SQL query must returning sum by fine scale fishery, not by tag code
# 'SQL must accum by fine scale fishery before rounding because if Extrapoplated = YES in CWDBRecovery table, then the fractional numbers will get lost
# 'because SumAdjustedEstimatedNumber = accum fine scale catches, OK to round here
# 'add 0.0000001 instead of 0.00000001 so even numbers to round up. The extra decimal place is not an issue for odd numbers.
# Try
# 'LandedCatch(Fish, RecoveryAge, BroodYear) = LandedCatch(Fish, RecoveryAge, BroodYear) + (Convert.ToInt32(SumAdjustedEstimatedNumber + 0.0000001)) '0.00000001
# LandedCatch(Fish, RecoveryAge, BroodYear) = LandedCatch(Fish, RecoveryAge, BroodYear) + (SumAdjustedEstimatedNumber + 0.0001)
# Catch
# If (RecoveryAge < OceanStartAge) Then
# MsgBox("Youngest age = " & RecoveryAge & " is less than OceanStartAge for " & BroodYear & ". Did you forget to combine age 2 and 3? Program is going to crash with an index out of bounds error message.")
# End If
# End Try
# 'If RecoveryAge = 4 And Fish < 13 And BroodYear = 1975 Then WriteLine(debugID, "1327", ShakerMethod, Fish, RecoveryAge, BroodYear, LandedCatch(Fish, RecoveryAge, BroodYear), SumAdjustedEstimatedNumber, RelRatio(BroodYear))
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And isTraceByCalendarYr = True And (BroodYear + RecoveryAge) >= traceThisYear + traceThisAge And Fish = traceThisFishery Then WriteLine(debug_CatchID, "line 1105 FineScaleCatch", BroodYear, Fish, RecoveryAge, tag_code, SumAdjustedEstimatedNumber, LandedCatch(Fish, RecoveryAge, BroodYear))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And Fish = 31 And BroodYear >= traceThisYear And RecoveryAge = traceThisAge Then WriteLine(debug_CatchID, "line 1106 FineScaleCatch", BroodYear, Fish, RecoveryAge, tag_code, SumAdjustedEstimatedNumber, LandedCatch(Fish, RecoveryAge, BroodYear))
# End If 'isReplicateCohShak = False
# 'legal dropoff mortalities for PSCFisheries, similar code for ERAFisheries is in the next loop below.
# If isReplicateCohShak = False Then
# If CNRMethod(BroodYear + RecoveryAge, Fish) <> 3 Then
# LegalDropoffMortality(Fish, RecoveryAge, BroodYear) = LegalDropoffMortality(Fish, RecoveryAge, BroodYear) + LandedCatch(Fish, RecoveryAge, BroodYear) * DropoffRate(BroodYear + RecoveryAge, Fish)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_LegalDropoffID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_ShakerID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
# End If
# Else
# 'to emulate CAS-Coshak, calculate dropoff after rounding ERAFishery and after combining ERAFishery into PSCFishery in the next loop below
# End If 'sReplicateCohShak = False
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# End If 'FishName = "ESCAPEMENT" Or FishName = "ESCAPE"
# End If 'isValidAge = True
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# End While 'loop thru tag codes, brood years, and ages
# CISDataReader.Close()
# ProgressBar1.PerformStep()
# Next Fish
#
# If isReplicateCohShak = True Then 'combine ERAFisheries into PSCFishery as with CMB spreadsheet
# For BroodYear = FirstBY To LastBY
# For PSCFishery = 1 To NumberPSCFisheries - 1 'except escapement
# 'initialize at the start of each PSCFishery and BroodYear
# For Age = OceanStartAge To MaxAge
# tempPSCCatch(PSCFishery, Age) = 0
# Next Age
# BuildERAFisheryToPSCFisheryList(PSCFishery)
# For FisheryID = 1 To NumberERA2PSCFisheries
# 'accum ERAFishery LandedCatch() into TempPSCCatch()
# ERAFish = ERA2PSC(FisheryID)
# For Age = OceanStartAge To MaxAge
# 'limit data to last calendar year selected by user
# If BroodYear + Age <= LastCalendarYear Then
# 'apply relRatio after combine ERAFisheries into PSCFishery
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then Write(debug_CatchID, "line 1259 collapse fisheries RelRatio", PSCFishery, ERAFish, BroodYear, Age, "before", tempPSCCatch(PSCFishery, Age))
# tempPSCCatch(PSCFishery, Age) = tempPSCCatch(PSCFishery, Age) + LandedCatch(ERAFish, Age, BroodYear) * RelRatio(BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "after", tempPSCCatch(PSCFishery, Age), LandedCatch(ERAFish, Age, BroodYear), RelRatio(BroodYear))
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# 'If Age = 4 And PSCFishery = 1 And BroodYear = 1975 Then WriteLine(debugID, "1371", ShakerMethod, ERAFish, PSCFishery, Age, BroodYear, tempPSCCatch(PSCFishery, Age), LandedCatch(ERAFish, Age, BroodYear), RelRatio(BroodYear))
# Next Age
# Next FisheryID
# Next PSCFishery
#
#
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
# If isreplicate2016URBdata = True Then
# 'for test only -- manually add fish that are missing in the CAS database
# 'so differences related to with missing records in CAS database go away
# 'and therefore isolate differences that have nothing to do with missing records in CAS database
# If BroodYear = 2009 And CurrentStock = "URB" Then
# tempPSCCatch(67, 4) = tempPSCCatch(67, 4) + 150 * RelRatio(BroodYear)
# tempPSCCatch(4, 5) = tempPSCCatch(4, 5) + 3 * RelRatio(BroodYear)
# tempPSCCatch(12, 5) = tempPSCCatch(12, 5) + 2 * RelRatio(BroodYear)
# End If
# If BroodYear = 2010 And CurrentStock = "URB" Then
# tempPSCCatch(67, 3) = tempPSCCatch(67, 3) + 277 * RelRatio(BroodYear)
# End If
# If BroodYear = 2011 And CurrentStock = "URB" Then
# tempPSCCatch(67, 2) = tempPSCCatch(67, 2) + 13 * RelRatio(BroodYear)
# End If
# End If
# 'when done testing delete the code above that adds fish missing in the database
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
#
# For PSCFishery = 1 To NumberPSCFisheries - 1 'except escapement
# 'when all ERAfisheries are combined into PSCFisheries, then copy TempPSCCatch() to LandedCatch()
# For Age = OceanStartAge To MaxAge
# 'limit data to last calendar year selected by user
# If BroodYear + Age <= LastCalendarYear Then
# LandedCatch(PSCFishery, Age, BroodYear) = tempPSCCatch(PSCFishery, Age)
# If isTraceCalc = True And isTraceByCalendarYr = True And (BroodYear + Age) >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1198 combined rounded RelRatio", PSCFishery, BroodYear, Age, LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# If isTraceCalc = True And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1198 combined rounded RelRatio", PSCFishery, BroodYear, Age, LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# 'when emulating CAS-Coshak
# 'step 1, calculate drop-off here, after rounding and combining ERAFisheries into PSCFisheries
# 'step 2 use DropoffRate(BroodYear + 2, PSCFishery) instead of DropoffRate(BroodYear + Age, PSCFishery) if brood year method
# 'else use DropoffRate(BroodYear + age, PSCFishery) if calendar year method
# If ShakerMethod = "B" Then
# LegalDropoffMortality(PSCFishery, Age, BroodYear) = LegalDropoffMortality(PSCFishery, Age, BroodYear) + LandedCatch(PSCFishery, Age, BroodYear) * DropoffRate(BroodYear + 2, PSCFishery)
# ElseIf ShakerMethod = "C" Then
# LegalDropoffMortality(PSCFishery, Age, BroodYear) = LegalDropoffMortality(PSCFishery, Age, BroodYear) + LandedCatch(PSCFishery, Age, BroodYear) * DropoffRate(BroodYear + Age, PSCFishery)
# End If
# Else
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "1344 L dropoff", PSCFishery, Age, tag_code, LegalDropoffMortality(PSCFishery, Age, BroodYear), LandedCatch(PSCFishery, Age, BroodYear), DropoffRate(BroodYear + 2, PSCFishery))
# 'step 3 add sublegal shakers and dropoff (i.e. replicate double count) in sub ShakerMethod1
# If isTraceCalc = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_LegalDropoffID, "1268 L dropofff before doubleCount", PSCFishery, Age, tag_code, LegalDropoffMortality(PSCFishery, Age, BroodYear), LandedCatch(PSCFishery, Age, BroodYear), DropoffRate(BroodYear + 2, PSCFishery))
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# Next Age
# Next PSCFishery
#
# 'apply RelRatio to Escape
# For Age = OceanStartAge To MaxAge
# 'limit data to last calendar year selected by user
# If BroodYear + Age <= LastCalendarYear Then
# Escape(BroodYear, Age) = Escape(BroodYear, Age) * RelRatio(BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EscapeID, "1565 rounded esc * relRatio", BroodYear, Age, Escape(BroodYear, Age), RelRatio(BroodYear))
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# Next Age
# Next BroodYear
# End If 'isReplicateCohShak = True
#
# 'Sum up totals
# For BroodYear = FirstBY To LastBY
# BroodYearCatch = 0
# BroodYearEscapement = 0
# For Age = OceanStartAge To MaxAge
# If Age <= LastCalendarYear - BroodYear Then
# For PSCFishery = 1 To NumberPSCFisheries - 1 'except escapement
# 'WriteLine(debugID, "1408", terminal(PSCFishery, Age), PSCFishery, Age)
# 'total (PreTerm and terminal) landed catch BroodYear age
# TotalLandedCatch(BroodYear, Age) = TotalLandedCatch(BroodYear, Age) + LandedCatch(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And isTraceByCalendarYr = True And (BroodYear + Age) >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1127 TotalLandedcatch", BroodYear, PSCFishery, Age, TotalLandedCatch(BroodYear, Age), LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# If isTraceCalc = True And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1127 TotalLandedcatch", BroodYear, PSCFishery, Age, TotalLandedCatch(BroodYear, Age), LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# 'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
# 'total (PreTerm and terminal) Legal Dropoff mortalities BroodYear age
# 'TotalLegalDropoffs(BroodYear, age) = TotalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
# 'total (PreTerm and terminal) landed catch BroodYear fishery
# TotalLandedCatch_ByFishery(BroodYear, PSCFishery) = TotalLandedCatch_ByFishery(BroodYear, PSCFishery) + LandedCatch(PSCFishery, Age, BroodYear)
# 'total terminal landed catch BroodYear age
# If terminal(PSCFishery, Age) = True And PSCFisheryGear(PSCFishery) <> "STRAY" Then
# TotalTerminalLandedCatch(BroodYear, Age) = TotalTerminalLandedCatch(BroodYear, Age) + LandedCatch(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_SumMatAgeCatID, "1394 sumMatCat", BroodYear, Age, PSCFishery, TotalTerminalLandedCatch(BroodYear, Age), LandedCatch(PSCFishery, Age, BroodYear), PSCFisheryGear(PSCFishery))
# 'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
# 'TotalTerminalLegalDropoffs(BroodYear, age) = TotalTerminalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
# End If
# 'If terminal(PSCFishery, Age) = True Then
# ' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1289 termcatch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
# 'Else
# ' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1288 catch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
# 'End If
# Next PSCFishery
# 'sum up all catch and escapement for brood year
# BroodYearCatch += TotalLandedCatch(BroodYear, Age)
# BroodYearEscapement += Escape(BroodYear, Age)
# End If 'age <= LastCalendarYear - BroodYear
# Next Age
# 'set MissingBroodYearFlag to False if there is escapement for the brood year
# 'If BroodYearEscapement > 0 Then
# If BroodYearCatch > 0 Or BroodYearEscapement > 0 Then
# MissingBroodYearFlag(BroodYear) = False
# 'Get number of ages completed in a broodyear through the last calendar year
# If BroodYear + MaxAge <= LastCalendarYear Then 'complete brood years
# 'Set CompleteBYFlag and get the number of complete broods and lastCompleteBroodYear for the stock
# LastAge(BroodYear) = MaxAge
# NumberCompleteBroods = NumberCompleteBroods + 1
# CompleteBYFlag(BroodYear) = True
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EncounterRateID, "1432 completeBYFlag", BroodYear, CompleteBYFlag(BroodYear), "max", MaxAge, "BY+max", BroodYear + MaxAge, "lastCalYr", LastCalendarYear)
# LastCompleteBroodYear = BroodYear
# Else
# LastAge(BroodYear) = LastCalendarYear - BroodYear 'last age for incomplete Brood years
# End If
# Else
# MissingBroodYearFlag(BroodYear) = True 'set MissingBroodYearFlag to True if there is no escapement for the brood year
# End If
# Next BroodYear
#End Sub
catarinawor/ERAR documentation built on Sept. 21, 2019, 8:25 a.m.
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Defines functions CalcLandedCatchAndEscapementWithBYWeights CalcLandedCatchAndEscapement
#ERA function GetFirstAndLastBY()
#Translated from VB ERA CIS code
#October 2018
#Author: Catarina Wor
#source(utils.R)
#' @title CalcLandedCatchAndEscapementWithBYWeights
#'
#' @description
#'
#'
#'
#' @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
#'
#'
CalcLandedCatchAndEscapementWithBYWeights <- function(D,M){
#This function is not being used at the moment.
#original VB code
#=============================================================
}
#' @title CalcLandedCatchAndEscapement
#'
#' @description
#'
#'
#'
#' @param M A list passed to MainSub
#'
#' @param D A list contining the outputs of GetSizeLimitLengthVulnerable
#'
#' @details reads in catch and escapenet levels and expands them to maximum level of releases. also does a bunch of random jiggery pokery that is hard to understand.
#'
#' @return
#'
#'
#'
#' @export
#'
#' @examples
#'
#'
CalcLandedCatchAndEscapement <- function( D,M ){
#=============================================================
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' by the variable named RelRatio(BY) = MaxRelease/CWTRelease(BY)
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches) which is what is printed in the cby.out and cyr.out files
AllBY <- D$FirstBY:D$LastBY
Allages <- D$youngestAge:D$MaxAge
Escape <- matrix(0, nrow=length(AllBY), ncol=length(Allages))
tag_code <- ""
tempPSCCatch <- matrix(0, nrow=M$NumberPSCFisheries, ncol=7)
TotalLandedCatch <- matrix(0, nrow=length(AllBY), ncol=7)
TotalTerminalLandedCatch <- matrix(0, nrow=length(AllBY), ncol=7)
TotalLegalDropoffs <- matrix(0, nrow=length(AllBY), ncol=7)
LastAge <- NULL
NumberCompleteBroods <- 0
CompleteBYFlag <- data.frame(BY=AllBY, Flag=rep(FALSE, length(AllBY)))
MissingBroodYearFlag <- data.frame(BY=AllBY, Flag=rep(FALSE, length(AllBY)))
if( !M$isReplicateCohShak ){
NumFish <- M$NumberPSCFisheries
}else{
NumFish <- M$NumberERAFisheries
}
LandedCatch <- array(0, dim=c(NumFish, 7, length(AllBY)))
LegalDropoffMortality <- array(0, dim=c(NumFish, 7, length(AllBY)))
TotalLandedCatch_ByFishery <- matrix(0, nrow=length(AllBY), ncol=NumFish)
#variables created by Catarina for monitoring purposes
databasecatch<-list()
#'Loop through each PSCfishery (or ERAFishery if emulating CAS-Coshak) and escapement to obtain catch and escapement
for( Fish in seq_len(NumFish) ){
sink("../logs/CalcLandedCatchAndEscapement.log",append=T)
cat(paste0(D$CASStockString,"\n"))
cat(paste0("Get Landed Catch and Escapement for fishery " , Fish, " of ", NumFish, " fine scale fisheries\n"))
sink()
#
#'Create a list of CAS Fisheries mapped to each PSC Fishery with appropriate start and end date ranges
if( !M$isReplicateCohShak ){
d <- BuildPSCFisheryIdList( M,Fish )
ERASQL <- paste0( "SELECT wtc.BroodYear,r.Age, ",
"Sum(IIf(f.CASTerminal, r.AdjustedEstimatedNumber,IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor))) AS SumEstimatedNumber " ,
"FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) " ,
"INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode " ,
"WHERE wtc.CASStock IN ('", as.character(D$CASStockString[[1]]) ,"') AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in " , d$FisheryIdList ," ", d$DateRangeClause , " AND r.age > 1" ,
" GROUP BY r.Age,wtc.BroodYear ORDER BY wtc.BroodYear, r.Age")
}else{#'same as above except by tag code in addition to brood year and age BY ERAFishery instead of PSCFishery
#not tested
d <- BuildERAFisheryIdList( M,Fish )
ERASQL <- paste0("SELECT wtc.BroodYear,r.Age, " ,
"Sum(IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor)) AS SumEstimatedNumber, " ,
"r.TagCode ",
"FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) ",
"INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode ",
"WHERE wtc.CASStock IN ('", D$CASStockString[[1]] ,"') AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in ", d$FisheryIdList ," ", d$DateRangeClause, " AND r.age > 1 ",
" GROUP BY r.Age, wtc.BroodYear, r.TagCode ORDER BY wtc.BroodYear, r.Age")
}
#dta <- RODBC::odbcConnectAccess2007(M$datbse) #specifies the file path
EstimatedNumberdf <- RODBC::sqlQuery( M$chnl , query =ERASQL )
databasecatch[[Fish]] <- EstimatedNumberdf
BroodYear <- EstimatedNumberdf$BroodYear
RecoveryAge <- EstimatedNumberdf$Age
SumAdjustedEstimatedNumber <- EstimatedNumberdf$SumEstimatedNumber
if( M$isReplicateCohShak ){
#'reproduce CFile numbers
tag_code <- EstimatedNumberdf[,4]
#'reproduce CFile numbers
#not tested
FishName <- M$ERAFisheryName[Fish]
}else{
tag_code <- rep("",nrow(EstimatedNumberdf))
FishName <- M$PSCFisheryName[Fish]
}
#'limit data to last calendar year selected by user
if( nrow(EstimatedNumberdf)>0 ){
for( ya in 1:nrow(EstimatedNumberdf) ){
if( BroodYear[ya] + RecoveryAge[ya] <= M$LastCalendarYear ){
#print(paste(Fish,ya))
isValidAge = TRUE
#'do not use recovery records where RecoveryAge > MaxAge+2
if( RecoveryAge[ya] > D$MaxAge & RecoveryAge[ya] <= D$MaxAge + 2 ){
sink("../logs/Log_OlderThanMaxAge_ID.log", append=TRUE)
cat(paste(D$CASStockString[[1]], ShakerMethod, BroodYear[ya], RecoveryAge[ya], FishName, "assigned to age ", D$MaxAge,"\n"))
sink()
RecoveryAge[ya] <- D$MaxAge
}
if( RecoveryAge[ya] > D$MaxAge + 2 ){
isValidAge = FALSE
sink("../logs/Log_OlderThanMaxAge_ID.log", append=TRUE)
cat(paste(D$CASStockString[[1]], ShakerMethod, BroodYear[ya], RecoveryAge[ya], FishName, "will not be used in the cohort analysis\n"))
sink()
}
if( isValidAge ){
#'combine ages if requested
if( M$isCombineAge2And3[ERAStock] == TRUE & RecoveryAge[ya] == 2 ){
RecoveryAge[ya] <- 3
}else if( M$isCombineAge5And6[ERAStock] == TRUE & RecoveryAge[ya] == 6 ){
RecoveryAge[ya] <- 5
}
#'one more time, check BroodYear + RecoveryAge because of combine age
if( BroodYear[ya] + RecoveryAge[ya] <= M$LastCalendarYear ){
#'CIS multiplies fine scale fishery and tag code esc by RelRatio BEFORE combining into PSC Fishery
#'CAS-Coshak rounds fine scale fishery, then combines into PSC Fishery BEFORE multiplying by RelRatio
if( FishName == "ESCAPEMENT" | grepl("ESC",FishName) ){
if( !M$isReplicateCohShak ){
Esc <- SumAdjustedEstimatedNumber[ya] * D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear==BroodYear[ya]]
}else if( M$isReplicateCohShak ){
#'CAS round escapement before applying IDL
#'Esc = Convert.ToInt32(SumAdjustedEstimatedNumber + 0.0000001) ' 0.00000001
Esc <- SumAdjustedEstimatedNumber[ya] + 0.0001
}
if(RecoveryAge[ya] == D$OceanStartAge){
Escape[which(AllBY==BroodYear[ya]), which(Allages==RecoveryAge[ya])] <- Escape[which(AllBY==BroodYear[ya]),which(Allages==RecoveryAge[ya])] + Esc / D$InterDamSurvivaldf$JackInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear[ya] >= M$traceThisYear ){
sink("../logs/debug_EscapeID.log",append=T)
cat(paste0(D$CASStockString,"\n"))
cat(paste("1100 accum fine scale escape", BroodYear[ya], RecoveryAge[ya], tag_code[ya], Escape[which(AllBY==BroodYear[ya])&which(Allages==RecoveryAge[ya])], Esc, SumAdjustedEstimatedNumber[ya], D$InterDamSurvivaldf$JackInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]))
sink()
}
}else{
Escape[which(AllBY==BroodYear[ya]),which(Allages==RecoveryAge[ya])] <- Escape[which(AllBY==BroodYear[ya]),which(Allages==RecoveryAge[ya])] + Esc / D$InterDamSurvivaldf$AdultInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear[ya] >= M$traceThisYear) {
sink("../logs/debug_EscapeID.log",append=T)
cat(paste0(D$CASStockString,"\n"))
cat(paste("1103 accum fine scale escape", BroodYear[ya], RecoveryAge[ya], tag_code[ya], Escape[which(AllBY==BroodYear[ya])&which(Allages==RecoveryAge[ya])], Esc, SumAdjustedEstimatedNumber[ya], D$InterDamSurvivaldf$AdultInterDamSurvivalRate[which(D$InterDamSurvivaldf$InterDamSurvival_CalendarYear==(BroodYear[ya] + RecoveryAge[ya]))]))
sink()
}
}
}else{ #catch
#'SQL returns fine scale fishery, this is where fine scale fishery is combined into PSC Fishery
#'WriteLine(debugID, CurrentStock, Fish, LastBY, BroodYear, RecoveryAge, BroodYear + RecoveryAge, LastCalendarYear)
if(!M$isReplicateCohShak){
LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] <- LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] + SumAdjustedEstimatedNumber[ya] * D$RelRatiodf$RelRatio[which(D$RelRatiodf$BroodYear==BroodYear[ya])]
if(RecoveryAge[ya] < D$OceanStartAge){
sink("../logs/LandedCatch.log",append=T)
cat(paste0("Youngest age = ", RecoveryAge[ya], " is less than OceanStartAge for " , BroodYear[ya] , ". Did you forget to combine age 2 and 3? Program is going to crash with an index was outside the bounds of the array error message."))
sink()
stop(" MainSub stopped check ../LandedCatch.log")
}
}else{
#multiply catch by RelRatio AFTER combining fine scale fishery into PSC Fishery
#'SQL query must returning sum by fine scale fishery, not by tag code
#'SQL must accum by fine scale fishery before rounding because if Extrapoplated = YES in CWDBRecovery table, then the fractional numbers will get lost
#'because SumAdjustedEstimatedNumber = accum fine scale catches, OK to round here
#'add 0.0000001 instead of 0.00000001 so even numbers to round up. The extra decimal place is not an issue for odd numbers.
LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] <- LandedCatch[[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])]] + SumAdjustedEstimatedNumber[ya] + 0.0001
if(RecoveryAge[ya] < D$OceanStartAge){
sink("../logs/LandedCatch.log",append=T)
cat(paste0("Youngest age = " & RecoveryAge[ya] & " is less than OceanStartAge for " & BroodYear[ya] & ". Did you forget to combine age 2 and 3? Program is going to crash with an index out of bounds error message."))
sink()
stop(" MainSub stopped check ../LandedCatch.log")
}
#'If RecoveryAge = 4 And Fish < 13 And BroodYear = 1975 Then WriteLine(debugID, "1327", ShakerMethod, Fish, RecoveryAge, BroodYear, LandedCatch(Fish, RecoveryAge, BroodYear), SumAdjustedEstimatedNumber, RelRatio(BroodYear))
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & M$isTraceByCalendarYr & (BroodYear[ya] + RecoveryAge[ya]) >= M$traceThisYear + M$traceThisAge & Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log",append=T)
cat(paste0( "line 1105 FineScaleCatch", BroodYear[ya], Fish, RecoveryAge[ya], tag_code[ya], SumAdjustedEstimatedNumber[ya], LandedCatch[Fish, RecoveryAge[ya], which(AllBY==BroodYear[ya])]))
sink()
}
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & Fish == 31 & BroodYear[ya] >= M$traceThisYear & RecoveryAge[ya] == M$traceThisAge){
sink("../logs/debug_CatchID.log",append=T)
cat(paste0("line 1106 FineScaleCatch", BroodYear[ya], Fish, RecoveryAge[ya], tag_code[ya], SumAdjustedEstimatedNumber[ya], LandedCatch[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])]))
sink()
}
}#'isReplicateCohShak = False
#'legal dropoff mortalities for PSCFisheries, similar code for ERAFisheries is in the next loop below.
if(!M$isReplicateCohShak){
if(D$IMdf$CNRMethod[D$IMdf$CalendarYear==BroodYear[ya] + RecoveryAge[ya] &D$IMdf$PSCFishery==Fish]!=3){
LegalDropoffMortality[Fish,RecoveryAge[ya],which(AllBY==BroodYear[ya])] <- LegalDropoffMortality[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]] +
LandedCatch[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]] *
D$IMdf$DropoffRate[(BroodYear[ya] + RecoveryAge[ya])==D$IMdf$CalendarYear & D$IMdf$PSCFishery==Fish]
if(is.na(LegalDropoffMortality[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]])){
LegalDropoffMortality[Fish,RecoveryAge[ya],AllBY==BroodYear[ya]] <- 0.0
}
}
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear[ya] >= M$traceThisYear & Fish== M$traceThisFishery){
sink("../logs/debug_LegalDropoffID.log",append=T)
cat(paste("1196 L dropoff", Fish, RecoveryAge[ya], tag_code[ya], LegalDropoffMortality[Fish, RecoveryAge[ya], BroodYear[ya]], LandedCatch[Fish, RecoveryAge[ya], ya], D$DropoffRate[which((BroodYear[ya] + RecoveryAge[ya])==D$DropoffRate$CalendarYear), Fish+1]))
sink()
}
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_LegalDropoffID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_ShakerID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
}else{
#'to emulate CAS-Coshak, calculate dropoff after rounding ERAFishery and after combining ERAFishery into PSCFishery in the next loop below
}#sReplicateCohShak = False
}#'FishName = "ESCAPEMENT" Or FishName = "ESCAPE"
}#'BroodYear + RecoveryAge <= LastCalendarYear
}# 'isValidAge = True
} # end of if statement
}# 'BroodYear + RecoveryAge <= LastCalendarYear
}else{
LegalDropoffMortality[Fish,,] <- 0.0
LandedCatch[Fish,,] <-0.0
}
} #next Fish
if(M$isReplicateCohShak){ #'combine ERAFisheries into PSCFishery as with CMB spreadsheet
for(y in 1:length(AllBY)){
for(Fish in 1:(M$NumberPSCFisheries-1)){ #'except escapement
#initialize at the start of each PSCFishery and BroodYear
for(Age in D$OceanStartAge:D$MaxAge){
tempPSCCatch[Fish, Age] <- 0
}
D2 <- BuildERAFisheryToPSCFisheryList(Fish,M)
D$NumberERA2PSCFisheries[Fish]<-D2$NumberERA2PSCFisheries
D$ERA2PSC[[Fish]]<-D2$ERA2PSC
#'accum ERAFishery LandedCatch() into TempPSCCatch()
for(FisheryID in 1:D$NumberERA2PSCFisheries[Fish]){
ERAFish = D$ERA2PSC[[Fish]][FisheryID]
for(Age in D$OceanStartAge:D$MaxAge){
tempPSCCatch[Fish, Age] <- tempPSCCatch[Fish, Age] + LandedCatch[ERAFish, Age, y] * D$RelRatiodf$RelRatio[AllBY[y]==D$RelRatiodf$BroodYear]
if(M$isTraceCalc&M$ShakerMethod==M$traceThisShakerMethod&M$isTraceByBroodYr&BroodYear>=M$traceThisYear&Fish==M$traceThisFishery){
sink("../logs/CatchID.log",,append=T)
cat(paste("after", tempPSCCatch[Fish, Age], LandedCatch[ERAFish, Age, y], D$RelRatiodf$RelRatio[AllBY[y]==D$RelRatiodf$BroodYear]))
sink()
}
}
}
}
for(Fish in 1:(M$NumberPSCFisheries-1)){
for(Age in D$OceanStartAge:D$MaxAge){
if(AllBY[y]+Age <= M$LastCalendarYear){
LandedCatch[Fish, Age, y] <- tempPSCCatch[Fish, Age]
if(M$isTraceCalc&M$isTraceByCalendarYr&(BroodYear[y] + Age)>= M$traceThisYear& Fish==M$traceThisFishery){
sink("../logs/debug_CatchID.log", append=T)
cat(paste("line 1198 combined rounded RelRatio", Fish, BroodYear[y], Age, LandedCatch[Fish, Age, y], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]))
sink()
}
if(M$isTraceCalc&M$isTraceByBroodYr&BroodYear[y]>=M$traceThisYear&Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log")
cat(paste("line 1198 combined rounded RelRatio", Fish, BroodYear[y], Age, LandedCatch[Fish, Age, y], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]))
sink()
}
#'when emulating CAS-Coshak
#'step 1, calculate drop-off here, after rounding and combining ERAFisheries into PSCFisheries
#'step 2 use DropoffRate(BroodYear + 2, PSCFishery) instead of DropoffRate(BroodYear + Age, PSCFishery) if brood year method
#'else use DropoffRate(BroodYear + age, PSCFishery) if calendar year method
if(M$ShakerMethod == "B"){
LegalDropoffMortality[Fish, Age, y] <- LegalDropoffMortality[Fish, Age, y] + LandedCatch[Fish, Age, y] * D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + 2) & D$IMdf$PSCFishery == Fish]
}else if(M$ShakerMethod == "C"){
LegalDropoffMortality[Fish, Age, y] <- LegalDropoffMortality[Fish, Age, y] + LandedCatch[Fish, Age, y] * D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + Age) & D$IMdf$PSCFishery == Fish]
}
}else{
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & AllBY[y] >= M$traceThisYear & Fish ==M$traceThisFishery ){
sink("../logs/debug_ShakerID.log")
cat(paste("1344 L dropoff", Fish, Age, tag_code, LegalDropoffMortality[Fish, Age, y], LandedCatch[Fish, Age, y], D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + 2)& D$IMdf$PSCFishery== Fish]))
sink()
}
#'step 3 add sublegal shakers and dropoff (i.e. replicate double count) in sub ShakerMethod1
if(M$isTraceCalc & AllBY[y] >= M$traceThisYear & Fish == M$traceThisFishery){
sink("../logs/debug_LegalDropoffID.log")
cat(paste("1268 L dropofff before doubleCount", Fish, Age, tag_code, LegalDropoffMortality[Fish, Age, y], LandedCatch[PSCFishery, Age, y], D$IMdf$DropoffRate[D$IMdf$CalendarYear==(AllBY[y] + 2)& D$IMdf$PSCFishery== Fish]))
sink()
}
}# 'BroodYear + RecoveryAge <= LastCalendarYear
}
}
#'apply RelRatio to Escape
for(Age in 1:length(D$OceanStartAge:D$MaxAge) ){
#'limit data to last calendar year selected by user
if((BroodYear[which(BroodYear==AllBY[y])]+Age) <= M$LastCalendarYear){
Escape[y,Age] =Escape[y,Age] * D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod &AllBY[y] >= M$traceThisYear){
sink("../logs/debug_EscapeID.log")
cat(paste("1565 rounded esc * relRatio", BroodYear[BroodYear==AllBY[y]], Age, Escape[BroodYear==AllBY[y], Age], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[y]]))
sink()
}
}
}
}
}
for(BYind in seq_along(AllBY)){
BroodYearCatch <- 0
BroodYearEscapement <- 0
for(Age in seq_along(Allages)){
if( Allages[Age] <= M$LastCalendarYear - AllBY[BYind] ){
for(Fish in seq_len(M$NumberPSCFisheries - 1)){
#print(paste(BYind,Age,Fish))
#'WriteLine(debugID, "1408", terminal(PSCFishery, Age), PSCFishery, Age)
#'total (PreTerm and terminal) landed catch BroodYear age
TotalLandedCatch[BYind, Age] = TotalLandedCatch[BYind, Age] + LandedCatch[Fish, Age, BYind]
if(M$isTraceCalc & M$isTraceByCalendarYr & (AllBY[BYind] + Allages[Age]) >= M$traceThisYear & Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log")
cat(paste("line 1127 TotalLandedcatch", AllBY[BYind], Fish, Allages[Age], TotalLandedCatch[BYind, Age], LandedCatch[Fish, Age, BYind], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[BYind]]))
sink()
}
if(M$isTraceCalc & M$isTraceByBroodYr & AllBY[BYind] >= M$traceThisYear & Fish == M$traceThisFishery){
sink("../logs/debug_CatchID.log")
cat(paste("line 1127 TotalLandedcatch", AllBY[BYind], Fish, Allages[Age], TotalLandedCatch[BYind, Age], LandedCatch[Fish, Age, BYind], D$RelRatiodf$RelRatio[D$RelRatiodf$BroodYear ==AllBY[BYind]]))
sink()
}
#'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
# 'total (PreTerm and terminal) Legal Dropoff mortalities BroodYear age
#'TotalLegalDropoffs(BroodYear, age) = TotalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
#'total (PreTerm and terminal) landed catch BroodYear fishery
TotalLandedCatch_ByFishery[BYind, Fish] = TotalLandedCatch_ByFishery[BYind, Fish] + LandedCatch[Fish , Age,BYind ]
#'total terminal landed catch BroodYear age
if(D$terminal[Fish,Age] & M$PSCFisheryGear[Fish] != "STRAY"){
TotalTerminalLandedCatch[BYind, Age] <- TotalTerminalLandedCatch[BYind, Age] + LandedCatch[Fish, Age, BYind]
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & AllBY[BYind] >= M$traceThisYear){
sink("../logs/debug_SumMatAgeCatID.log")
cat(paste("1394 sumMatCat", AllBY[BYind], Allages[Age], Fish, TotalTerminalLandedCatch[BYind, Age], LandedCatch[Fishery, Age, BYind], PSCFisheryGear[PSCFishery]))
sink()
}
#'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
#'TotalTerminalLegalDropoffs(BroodYear, age) = TotalTerminalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
}
#'If terminal(PSCFishery, Age) = True Then
#' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1289 termcatch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
#'Else
#' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1288 catch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
#'End If
}
#'sum up all catch and escapement for brood year
BroodYearCatch <- BroodYearCatch + TotalLandedCatch[BYind, Age]
BroodYearEscapement <- BroodYearEscapement + Escape[BYind, Age]
} #'age <= LastCalendarYear - BroodYear
}
#'set MissingBroodYearFlag to False if there is escapement for the brood year
#'If BroodYearEscapement > 0 Then
if( BroodYearCatch > 0 | BroodYearEscapement > 0 ){
MissingBroodYearFlag$Flag[BYind] <- FALSE
#'Get number of ages completed in a broodyear through the last calendar year
if( AllBY[BYind] + D$MaxAge <= M$LastCalendarYear ){
#'Set CompleteBYFlag and get the number of complete broods and lastCompleteBroodYear for the stock
LastAge[BYind] = D$MaxAge
NumberCompleteBroods = NumberCompleteBroods + 1
CompleteBYFlag$Flag[BYind] <- TRUE
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & AllBY[BYind] >= M$traceThisYear ){
sink("../logs/debug_EncounterRateID.log")
cat(paste("1432 completeBYFlag", AllBY[BYind], CompleteBYFlag$Flag[BYind], "max", D$MaxAge, "BY+max", AllBY[BYind] + D$MaxAge, "lastCalYr", M$LastCalendarYear))
sink()
}
LastCompleteBroodYear <- AllBY[BYind]
}else{
LastAge[BYind] <- M$LastCalendarYear - AllBY[BYind] #'last age for incomplete Brood years
}
}else{
MissingBroodYearFlag$Flag[ BYind ] <- TRUE #'set MissingBroodYearFlag to True if there is no escapement for the brood year
LastAge[BYind] <- 0
}
}
CompleteBYFlag$Flag[is.na(CompleteBYFlag$Flag)] <-FALSE
return(list(new=list(LandedCatch = LandedCatch,
TotalLandedCatch = TotalLandedCatch,
TotalLandedCatch_ByFishery = TotalLandedCatch_ByFishery,
NumberCompleteBroods = NumberCompleteBroods,
CompleteBYFlag = CompleteBYFlag,
MissingBroodYearFlag = MissingBroodYearFlag,
TotalLegalDropoffs = TotalLegalDropoffs,
TotalTerminalLandedCatch = TotalTerminalLandedCatch,
LastAge = LastAge,
Escape = Escape,
LegalDropoffMortality=LegalDropoffMortality),
old=list(LastCompleteBroodYear=LastCompleteBroodYear)))
}
#original VB code
#=============================================================
# 'NOTE: All catches and escapements are expanded to the maximum level of release found for all brood years
# ' by the variable named RelRatio(BY) = MaxRelease/CWTRelease(BY)
# ' This is done so that when the calculations for sub-legal CNR mortalities are done, there is no bias
# ' introduced resulting from differential levels of marking between brood years. This is because
# ' CWT catch is compared to Actual Catch to calculate the proportion of the total catch assigned to the
# ' CWT stock. If one brood year is under- or over- represented, it will bias the over-all assignment of
# ' sub-legal mortalities. The catches are set back to the original values after the cohort analysis
# ' (see SUB ResetCatches) which is what is printed in the cby.out and cyr.out files
# ReDim CalendarYearLandedCatch(LastCalendarYear, NumberPSCFisheries)
# Dim temp(NumberPSCFisheries, 7, LastBY) 'if this is dim As Single, rounding get canceled
# Dim ERAFish, FisheryID As Integer
# Dim Esc As Single
# Dim Fish As Integer
# Dim FishName As String
# Dim NumFish As Integer
# Dim tag_code As String = ""
# Dim tempPSCCatch(NumberPSCFisheries, 7) 'if this is dim As Single, rounding get canceled
# Dim BroodYearCatch, BroodYearEscapement As Single
# Dim isValidAge As Boolean
# Dim RecoveryAge As Integer
# Dim SumAdjustedEstimatedNumber As Single
# Dim BroodYear As Integer
# If isReplicateCohShak = False Then 'reproduce CFile numbers
# NumFish = NumberPSCFisheries
# Else
# NumFish = NumberERAFisheries
# End If
# 'Loop through each PSCfishery (or ERAFishery if emulating CAS-Coshak) and escapement to obtain catch and escapement
# For Fish = 1 To NumFish
# lblStatus.Text = " Get Landed Catch and Escapement for fishery " & Fish & " of " & NumFish & " fine scale fisheries"
# lblStatus.Visible = True
# Me.Refresh()
# 'Create a list of CAS Fisheries mapped to each PSC Fishery with appropriate start and end date ranges
# If isReplicateCohShak = False Then 'reproduce CFile numbers
# Call BuildPSCFisheryIdList(Fish)
# Else
# Call BuildERAFisheryIdList(Fish)
# End If
# 'Sum up adjusted estimated numbers for a brood year and age by PSCFishery for current ERAStock
# If isReplicateCohShak = False Then
# ERASQL = "SELECT wtc.BroodYear,r.Age, " &
# "Sum(IIf(f.CASTerminal, r.AdjustedEstimatedNumber,IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor))) AS SumEstimatedNumber " &
# "FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) " &
# "INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode " &
# "WHERE wtc.CASStock IN (" & CASStockString & ") AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in " & FisheryIdList & DateRangeClause & " AND r.age > 1 " &
# " GROUP BY r.Age,wtc.BroodYear ORDER BY wtc.BroodYear, r.Age"
# Else 'same as above except by tag code in addition to brood year and age BY ERAFishery instead of PSCFishery
# ERASQL = "SELECT wtc.BroodYear,r.Age, " &
# "Sum(IIf(IsNull(c.ExpansionFactor), r.AdjustedEstimatedNumber, r.AdjustedEstimatedNumber * c.ExpansionFactor)) AS SumEstimatedNumber, " &
# "r.TagCode " &
# "FROM ((ERA_CWDBRecovery AS r LEFT JOIN ERA_CWDBCatchSample AS c ON (r.Agency = c.Agency) AND (r.RunYear = c.CatchYear) AND (r.CatchSampleId = c.CatchSampleId)) " &
# "INNER JOIN ERA_Fishery AS f ON r.Fishery = f.Id) INNER JOIN ERA_WireTagCode AS wtc ON r.TagCode = wtc.TagCode " &
# "WHERE wtc.CASStock IN (" & CASStockString & ") AND Not wtc.ExcludeTagCodeFromERA = -1 AND r.Fishery in " & FisheryIdList & DateRangeClause & " AND r.age > 1 " &
# " GROUP BY r.Age, wtc.BroodYear, r.TagCode ORDER BY wtc.BroodYear, r.Age"
# End If
# ERACommand = New OleDbCommand(ERASQL, CISDBConnection)
# CISDataReader = ERACommand.ExecuteReader()
# While CISDataReader.Read()
# BroodYear = CISDataReader(0)
# RecoveryAge = CISDataReader(1)
# SumAdjustedEstimatedNumber = CISDataReader(2)
# If isReplicateCohShak = True Then 'reproduce CFile numbers
# tag_code = CISDataReader(3)
# End If
#
# If isReplicateCohShak = False Then
# FishName = PSCFisheryName(Fish)
# Else 'reproduce CFile numbers
# FishName = ERAFisheryName(Fish)
# End If
#
# 'limit data to last calendar year selected by user
# If BroodYear + RecoveryAge <= LastCalendarYear Then
# isValidAge = True
# 'do not use recovery records where RecoveryAge > MaxAge+2
# If RecoveryAge > MaxAge And RecoveryAge <= MaxAge + 2 Then
# WriteLine(Log_OlderThanMaxAge_ID, ShakerMethod, BroodYear, RecoveryAge, FishName, "assigned to age " & MaxAge)
# RecoveryAge = MaxAge
# End If
#
# If RecoveryAge > MaxAge + 2 Then
# isValidAge = False
# WriteLine(Log_OlderThanMaxAge_ID, ShakerMethod, BroodYear, RecoveryAge, FishName, "will not be used in the cohort analysis")
# End If
#
# If isValidAge = True Then
# 'combine ages if requested
# If isCombineAge2And3(ERAStock) = True And RecoveryAge = 2 Then
# RecoveryAge = 3
# End If
# If isCombineAge5And6(ERAStock) = True And RecoveryAge = 6 Then
# RecoveryAge = 5
# End If
#
# 'one more time, check BroodYear + RecoveryAge because of combine age
# If BroodYear + RecoveryAge <= LastCalendarYear Then
# 'CIS multiplies fine scale fishery and tag code esc by RelRatio BEFORE combining into PSC Fishery
# 'CAS-Coshak rounds fine scale fishery, then combines into PSC Fishery BEFORE multiplying by RelRatio
# If FishName = "ESCAPEMENT" Or FishName = "ESCAPE" Then
# If isReplicateCohShak = False Then
# Esc = SumAdjustedEstimatedNumber * RelRatio(BroodYear)
# ElseIf isReplicateCohShak = True Then
# 'CAS round escapement before applying IDL
# 'Esc = Convert.ToInt32(SumAdjustedEstimatedNumber + 0.0000001) ' 0.00000001
# Esc = SumAdjustedEstimatedNumber + 0.0001
# End If
# If RecoveryAge = OceanStartAge Then
# Escape(BroodYear, RecoveryAge) = Escape(BroodYear, RecoveryAge) + Esc / JackInterDamSurvivalRate(BroodYear + RecoveryAge)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EscapeID, "1100 accum fine scale escape", BroodYear, RecoveryAge, tag_code, Escape(BroodYear, RecoveryAge), Esc, SumAdjustedEstimatedNumber, JackInterDamSurvivalRate(BroodYear + RecoveryAge))
# Else
# Escape(BroodYear, RecoveryAge) = Escape(BroodYear, RecoveryAge) + Esc / AdultInterDamSurvivalRate(BroodYear + RecoveryAge)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EscapeID, "1103 accum fine scale escape", BroodYear, RecoveryAge, tag_code, Escape(BroodYear, RecoveryAge), Esc, SumAdjustedEstimatedNumber, AdultInterDamSurvivalRate(BroodYear + RecoveryAge))
# End If
# Else 'catch
# 'SQL returns fine scale fishery, this is where fine scale fishery is combined into PSC Fishery
# 'WriteLine(debugID, CurrentStock, Fish, LastBY, BroodYear, RecoveryAge, BroodYear + RecoveryAge, LastCalendarYear)
# If isReplicateCohShak = False Then
# Try
# LandedCatch(Fish, RecoveryAge, BroodYear) = LandedCatch(Fish, RecoveryAge, BroodYear) + SumAdjustedEstimatedNumber * RelRatio(BroodYear)
# Catch
# If (RecoveryAge < OceanStartAge) Then
# MsgBox("Youngest age = " & RecoveryAge & " is less than OceanStartAge for " & BroodYear & ". Did you forget to combine age 2 and 3? Program is going to crash with an index was outside the bounds of the array error message.")
# End If
# End Try
# Else 'multiply catch by RelRatio AFTER combining fine scale fishery into PSC Fishery
# 'SQL query must returning sum by fine scale fishery, not by tag code
# 'SQL must accum by fine scale fishery before rounding because if Extrapoplated = YES in CWDBRecovery table, then the fractional numbers will get lost
# 'because SumAdjustedEstimatedNumber = accum fine scale catches, OK to round here
# 'add 0.0000001 instead of 0.00000001 so even numbers to round up. The extra decimal place is not an issue for odd numbers.
# Try
# 'LandedCatch(Fish, RecoveryAge, BroodYear) = LandedCatch(Fish, RecoveryAge, BroodYear) + (Convert.ToInt32(SumAdjustedEstimatedNumber + 0.0000001)) '0.00000001
# LandedCatch(Fish, RecoveryAge, BroodYear) = LandedCatch(Fish, RecoveryAge, BroodYear) + (SumAdjustedEstimatedNumber + 0.0001)
# Catch
# If (RecoveryAge < OceanStartAge) Then
# MsgBox("Youngest age = " & RecoveryAge & " is less than OceanStartAge for " & BroodYear & ". Did you forget to combine age 2 and 3? Program is going to crash with an index out of bounds error message.")
# End If
# End Try
# 'If RecoveryAge = 4 And Fish < 13 And BroodYear = 1975 Then WriteLine(debugID, "1327", ShakerMethod, Fish, RecoveryAge, BroodYear, LandedCatch(Fish, RecoveryAge, BroodYear), SumAdjustedEstimatedNumber, RelRatio(BroodYear))
#
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And isTraceByCalendarYr = True And (BroodYear + RecoveryAge) >= traceThisYear + traceThisAge And Fish = traceThisFishery Then WriteLine(debug_CatchID, "line 1105 FineScaleCatch", BroodYear, Fish, RecoveryAge, tag_code, SumAdjustedEstimatedNumber, LandedCatch(Fish, RecoveryAge, BroodYear))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And Fish = 31 And BroodYear >= traceThisYear And RecoveryAge = traceThisAge Then WriteLine(debug_CatchID, "line 1106 FineScaleCatch", BroodYear, Fish, RecoveryAge, tag_code, SumAdjustedEstimatedNumber, LandedCatch(Fish, RecoveryAge, BroodYear))
# End If 'isReplicateCohShak = False
# 'legal dropoff mortalities for PSCFisheries, similar code for ERAFisheries is in the next loop below.
# If isReplicateCohShak = False Then
# If CNRMethod(BroodYear + RecoveryAge, Fish) <> 3 Then
# LegalDropoffMortality(Fish, RecoveryAge, BroodYear) = LegalDropoffMortality(Fish, RecoveryAge, BroodYear) + LandedCatch(Fish, RecoveryAge, BroodYear) * DropoffRate(BroodYear + RecoveryAge, Fish)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_LegalDropoffID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And Fish = traceThisFishery Then WriteLine(debug_ShakerID, "1196 L dropoff", Fish, RecoveryAge, tag_code, LegalDropoffMortality(Fish, RecoveryAge, BroodYear), LandedCatch(Fish, RecoveryAge, BroodYear), DropoffRate(BroodYear + RecoveryAge, Fish))
# End If
# Else
# 'to emulate CAS-Coshak, calculate dropoff after rounding ERAFishery and after combining ERAFishery into PSCFishery in the next loop below
# End If 'sReplicateCohShak = False
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# End If 'FishName = "ESCAPEMENT" Or FishName = "ESCAPE"
# End If 'isValidAge = True
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# End While 'loop thru tag codes, brood years, and ages
# CISDataReader.Close()
# ProgressBar1.PerformStep()
# Next Fish
#
# If isReplicateCohShak = True Then 'combine ERAFisheries into PSCFishery as with CMB spreadsheet
# For BroodYear = FirstBY To LastBY
# For PSCFishery = 1 To NumberPSCFisheries - 1 'except escapement
# 'initialize at the start of each PSCFishery and BroodYear
# For Age = OceanStartAge To MaxAge
# tempPSCCatch(PSCFishery, Age) = 0
# Next Age
# BuildERAFisheryToPSCFisheryList(PSCFishery)
# For FisheryID = 1 To NumberERA2PSCFisheries
# 'accum ERAFishery LandedCatch() into TempPSCCatch()
# ERAFish = ERA2PSC(FisheryID)
# For Age = OceanStartAge To MaxAge
# 'limit data to last calendar year selected by user
# If BroodYear + Age <= LastCalendarYear Then
# 'apply relRatio after combine ERAFisheries into PSCFishery
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then Write(debug_CatchID, "line 1259 collapse fisheries RelRatio", PSCFishery, ERAFish, BroodYear, Age, "before", tempPSCCatch(PSCFishery, Age))
# tempPSCCatch(PSCFishery, Age) = tempPSCCatch(PSCFishery, Age) + LandedCatch(ERAFish, Age, BroodYear) * RelRatio(BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "after", tempPSCCatch(PSCFishery, Age), LandedCatch(ERAFish, Age, BroodYear), RelRatio(BroodYear))
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# 'If Age = 4 And PSCFishery = 1 And BroodYear = 1975 Then WriteLine(debugID, "1371", ShakerMethod, ERAFish, PSCFishery, Age, BroodYear, tempPSCCatch(PSCFishery, Age), LandedCatch(ERAFish, Age, BroodYear), RelRatio(BroodYear))
# Next Age
# Next FisheryID
# Next PSCFishery
#
#
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
# If isreplicate2016URBdata = True Then
# 'for test only -- manually add fish that are missing in the CAS database
# 'so differences related to with missing records in CAS database go away
# 'and therefore isolate differences that have nothing to do with missing records in CAS database
# If BroodYear = 2009 And CurrentStock = "URB" Then
# tempPSCCatch(67, 4) = tempPSCCatch(67, 4) + 150 * RelRatio(BroodYear)
# tempPSCCatch(4, 5) = tempPSCCatch(4, 5) + 3 * RelRatio(BroodYear)
# tempPSCCatch(12, 5) = tempPSCCatch(12, 5) + 2 * RelRatio(BroodYear)
# End If
# If BroodYear = 2010 And CurrentStock = "URB" Then
# tempPSCCatch(67, 3) = tempPSCCatch(67, 3) + 277 * RelRatio(BroodYear)
# End If
# If BroodYear = 2011 And CurrentStock = "URB" Then
# tempPSCCatch(67, 2) = tempPSCCatch(67, 2) + 13 * RelRatio(BroodYear)
# End If
# End If
# 'when done testing delete the code above that adds fish missing in the database
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
# '*************************************************************************
#
# For PSCFishery = 1 To NumberPSCFisheries - 1 'except escapement
# 'when all ERAfisheries are combined into PSCFisheries, then copy TempPSCCatch() to LandedCatch()
# For Age = OceanStartAge To MaxAge
# 'limit data to last calendar year selected by user
# If BroodYear + Age <= LastCalendarYear Then
# LandedCatch(PSCFishery, Age, BroodYear) = tempPSCCatch(PSCFishery, Age)
# If isTraceCalc = True And isTraceByCalendarYr = True And (BroodYear + Age) >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1198 combined rounded RelRatio", PSCFishery, BroodYear, Age, LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# If isTraceCalc = True And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1198 combined rounded RelRatio", PSCFishery, BroodYear, Age, LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# 'when emulating CAS-Coshak
# 'step 1, calculate drop-off here, after rounding and combining ERAFisheries into PSCFisheries
# 'step 2 use DropoffRate(BroodYear + 2, PSCFishery) instead of DropoffRate(BroodYear + Age, PSCFishery) if brood year method
# 'else use DropoffRate(BroodYear + age, PSCFishery) if calendar year method
# If ShakerMethod = "B" Then
# LegalDropoffMortality(PSCFishery, Age, BroodYear) = LegalDropoffMortality(PSCFishery, Age, BroodYear) + LandedCatch(PSCFishery, Age, BroodYear) * DropoffRate(BroodYear + 2, PSCFishery)
# ElseIf ShakerMethod = "C" Then
# LegalDropoffMortality(PSCFishery, Age, BroodYear) = LegalDropoffMortality(PSCFishery, Age, BroodYear) + LandedCatch(PSCFishery, Age, BroodYear) * DropoffRate(BroodYear + Age, PSCFishery)
# End If
# Else
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_ShakerID, "1344 L dropoff", PSCFishery, Age, tag_code, LegalDropoffMortality(PSCFishery, Age, BroodYear), LandedCatch(PSCFishery, Age, BroodYear), DropoffRate(BroodYear + 2, PSCFishery))
# 'step 3 add sublegal shakers and dropoff (i.e. replicate double count) in sub ShakerMethod1
# If isTraceCalc = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_LegalDropoffID, "1268 L dropofff before doubleCount", PSCFishery, Age, tag_code, LegalDropoffMortality(PSCFishery, Age, BroodYear), LandedCatch(PSCFishery, Age, BroodYear), DropoffRate(BroodYear + 2, PSCFishery))
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# Next Age
# Next PSCFishery
#
# 'apply RelRatio to Escape
# For Age = OceanStartAge To MaxAge
# 'limit data to last calendar year selected by user
# If BroodYear + Age <= LastCalendarYear Then
# Escape(BroodYear, Age) = Escape(BroodYear, Age) * RelRatio(BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EscapeID, "1565 rounded esc * relRatio", BroodYear, Age, Escape(BroodYear, Age), RelRatio(BroodYear))
# End If 'BroodYear + RecoveryAge <= LastCalendarYear
# Next Age
# Next BroodYear
# End If 'isReplicateCohShak = True
#
# 'Sum up totals
# For BroodYear = FirstBY To LastBY
# BroodYearCatch = 0
# BroodYearEscapement = 0
# For Age = OceanStartAge To MaxAge
# If Age <= LastCalendarYear - BroodYear Then
# For PSCFishery = 1 To NumberPSCFisheries - 1 'except escapement
# 'WriteLine(debugID, "1408", terminal(PSCFishery, Age), PSCFishery, Age)
# 'total (PreTerm and terminal) landed catch BroodYear age
# TotalLandedCatch(BroodYear, Age) = TotalLandedCatch(BroodYear, Age) + LandedCatch(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And isTraceByCalendarYr = True And (BroodYear + Age) >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1127 TotalLandedcatch", BroodYear, PSCFishery, Age, TotalLandedCatch(BroodYear, Age), LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# If isTraceCalc = True And isTraceByBroodYr = True And BroodYear >= traceThisYear And PSCFishery = traceThisFishery Then WriteLine(debug_CatchID, "line 1127 TotalLandedcatch", BroodYear, PSCFishery, Age, TotalLandedCatch(BroodYear, Age), LandedCatch(PSCFishery, Age, BroodYear), RelRatio(BroodYear))
# 'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
# 'total (PreTerm and terminal) Legal Dropoff mortalities BroodYear age
# 'TotalLegalDropoffs(BroodYear, age) = TotalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
# 'total (PreTerm and terminal) landed catch BroodYear fishery
# TotalLandedCatch_ByFishery(BroodYear, PSCFishery) = TotalLandedCatch_ByFishery(BroodYear, PSCFishery) + LandedCatch(PSCFishery, Age, BroodYear)
# 'total terminal landed catch BroodYear age
# If terminal(PSCFishery, Age) = True And PSCFisheryGear(PSCFishery) <> "STRAY" Then
# TotalTerminalLandedCatch(BroodYear, Age) = TotalTerminalLandedCatch(BroodYear, Age) + LandedCatch(PSCFishery, Age, BroodYear)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_SumMatAgeCatID, "1394 sumMatCat", BroodYear, Age, PSCFishery, TotalTerminalLandedCatch(BroodYear, Age), LandedCatch(PSCFishery, Age, BroodYear), PSCFisheryGear(PSCFishery))
# 'moved to ShakerMethod1 to compare against Coshak12, uncomment here and remove from ShakerMethod1 when done testing
# 'TotalTerminalLegalDropoffs(BroodYear, age) = TotalTerminalLegalDropoffs(BroodYear, age) + LegalDropoffMortality(PSCFishery, age, BroodYear)
# End If
# 'If terminal(PSCFishery, Age) = True Then
# ' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1289 termcatch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
# 'Else
# ' If isTraceCalc = True and shakermethod = traceThisShakerMethod Then WriteLine(debugID, "1288 catch", PSCFishery, Age, BroodYear, LandedCatch(PSCFishery, Age, BroodYear))
# 'End If
# Next PSCFishery
# 'sum up all catch and escapement for brood year
# BroodYearCatch += TotalLandedCatch(BroodYear, Age)
# BroodYearEscapement += Escape(BroodYear, Age)
# End If 'age <= LastCalendarYear - BroodYear
# Next Age
# 'set MissingBroodYearFlag to False if there is escapement for the brood year
# 'If BroodYearEscapement > 0 Then
# If BroodYearCatch > 0 Or BroodYearEscapement > 0 Then
# MissingBroodYearFlag(BroodYear) = False
# 'Get number of ages completed in a broodyear through the last calendar year
# If BroodYear + MaxAge <= LastCalendarYear Then 'complete brood years
# 'Set CompleteBYFlag and get the number of complete broods and lastCompleteBroodYear for the stock
# LastAge(BroodYear) = MaxAge
# NumberCompleteBroods = NumberCompleteBroods + 1
# CompleteBYFlag(BroodYear) = True
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_EncounterRateID, "1432 completeBYFlag", BroodYear, CompleteBYFlag(BroodYear), "max", MaxAge, "BY+max", BroodYear + MaxAge, "lastCalYr", LastCalendarYear)
# LastCompleteBroodYear = BroodYear
# Else
# LastAge(BroodYear) = LastCalendarYear - BroodYear 'last age for incomplete Brood years
# End If
# Else
# MissingBroodYearFlag(BroodYear) = True 'set MissingBroodYearFlag to True if there is no escapement for the brood year
# End If
# Next BroodYear
#End Sub
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