R/func_calccohort.R
In CTCassess/ERAR: This package is a loose translation of the Chinook Technical committee ERA model
Defines functions
CalcCohort
CalcCohort_IncompleteBrood
CalcEstmCohrt2
CalcEstmCohrt
FindBY
#=======================================================
#ERA function CalcCohort
#Translated from VB ERA CIS code
#March 2019
#Author: Catarina Wor
#=======================================================
#' @title CalcCohort
#'
#' @description function where the actual ERA is done, this one is for complete cohorts only.
#'
#' @param M A list passed to StartCohortAnalysis_Click
#'
#' @param D A list containing stock specific info
#'
#' @details
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcCohort <- function(D,M){
print("enter CalcCohort")
allBY <- D$FirstBY:D$LastBY
#allCY <- (D$FirstBY + D$OceanStartAge):M$LastCalendarYear
allAge <- D$OceanStartAge:D$MaxAge
NumberOceanCohorts <- NULL
SumAEQ <- rep(0,D$MaxAge)
AverageAEQ <- NULL
SumMatRate <- rep(0,D$MaxAge)
SumPreTermER <- rep(0,D$MaxAge)
AveragePreTermER <- NULL
AverageMatRate <- NULL
PreTermER <- matrix(NA, nrow = length(allBY),ncol = 7 )
Cohort <- matrix(0, nrow = length(allBY),ncol = 7 )
MatRate <- matrix(0, nrow = length(allBY),ncol = 7 )
AEQ <- matrix(0, nrow=length(allBY),ncol = D$MaxAge + 1 )
SumAEQ <- rep(0,D$MaxAge)
SumPreTermER <- rep(0,D$MaxAge)
NumberOceanCohorts <- rep(0,D$MaxAge)
SurvivalRate <- D$survivaldf$SurvivalRate
NumberCompleteBroods<-D$NumberCompleteBroods
pass<-D$pass
RepeatPass <- FALSE
if( M$Average_Maturation_Rate == "SelectNumberCompleteBroods" ){
#This is not selecting the number of complte broods but choosing all the complete broods.
#NumAvgYears <- sum(allBY < (M$LastCalendarYear-D$MaxAge))
NumAvgYears <- M$NumAvgYears
}else{
NumAvgYears <- M$LastCompleteBroodsUsed
}
for( BYind in seq_along(allBY) ){
#'skip all missing brood years
if( !D$MissingBroodYearFlag$Flag[ BYind ] & D$CompleteBYFlag$Flag[BYind]){
#'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
TestCohortNum <- Cohort[ BYind, D$OceanStartAge ]
#'set survival rate of maxage+1 for use in AEQ equations below
SurvivalRate[ which(D$survivaldf$Age==D$MaxAge) + 1 ] <- SurvivalRate[ which(D$survivaldf$Age==D$MaxAge) ]
#'loop through each age
for( age in D$LastAge[BYind]:D$OceanStartAge ){
#'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
TotalCatch <- TotalCatch_Age(D, M, BY=BYind, age)
#'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod ){
sink("../logs/debug_terminalCatchID.log", append=TRUE)
cat(paste("2183 CalcCohort callTotalTerminalCatch_Age", M$ShakerMethod, BYind, age))
sink()
}
TotalTerminalCatch <- TotalTerminalCatch_Age(D, M, BYind, age)
#'subtract total terminal catch from total catch to get total PreTerm catch
TotalPreTermCatch <- TotalCatch - TotalTerminalCatch
if(M$isTraceCalc){
sink("../logs/debug_CohortID.log", append=TRUE)
cat(paste("line 1925","totCat", TotalCatch, "totTermCat", TotalTerminalCatch))
sink()
}
#'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
if( !D$CompleteBYFlag$Flag[BYind] & !is.na(D$CompleteBYFlag$Flag[BYind]) & age == D$LastAge[BYind] & pass > 1 ){
Cohort[BYind, age] <- CalcEstmCohrt2( D, M, BYind, age ) / D$survivaldf$SurvivalRate[ D$survivaldf$Age==age ]
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 compl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), SurvivalRate(age))
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod ){
sink("../logs/debug_Cohort_IncompleteBroodID.log", append=TRUE)
cat(paste("2158 CalcCohort", M$ShakerMethod, BYind, age, Cohort[BYind, D$OceanStartAge]))
sink()
}
}else{
Cohort[ BYind, age ] <- (Cohort[ BYind, age + 1 ] + D$Escape[ BYind, age ] + TotalCatch)/ SurvivalRate[ which(D$survivaldf$Age==age) ]
}
if( age == D$OceanStartAge & Cohort[BYind, D$OceanStartAge] == 0){
sink("../logs/debug_ERROR_noCWT.log", append=TRUE)
cat(paste("Brood Year ", allBY[BYind], " has NO CWT recoveries at all!"))
sink()
ErrCaption = paste("Brood Year ", allBY[BYind] , " has NO CWT recoveries at all! \n")
ErrMessage = paste("Hint: If the brood year has no recoveries, decrement last brood year in the .CM1 file and remove from the .CDS file.\n")
ErrMessage = paste(ErrMessage, " If intermediate brood year, treat as missing brood and remove from .CDS file.\n")
stop(paste(ErrCaption,ErrMessage))
}
CohortAfterPreTermFishery <- Cohort[ BYind, age ] * SurvivalRate[ age ] - TotalPreTermCatch
TerminalRun <- TotalTerminalCatch + D$Escape[ BYind, age ]
if( !D$ReadAvgMatRteFlg ){
#'rates not from ERA_Stock table, instead calculate from data
if( age == D$LastAge[ BYind ] & D$CompleteBYFlag$Flag[ BYind ] &!is.na(D$CompleteBYFlag$Flag[ BYind ])){
MatRate[ BYind, age ] <- 1
}else if( CohortAfterPreTermFishery <= 0 ){
MatRate[ BYind, age ] <- 0
}else{
MatRate[ BYind, age ] <- TerminalRun / CohortAfterPreTermFishery
if(M$isTraceCalc){
sink("../logs/debug_MatRteID.log", append=TRUE)
cat(paste("2189 MatRte", BYind, age, MatRate[ BYind, age ], TerminalRun, CohortAfterPreTermFishery,"\n"))
sink()
}
}
}else{
MatRate[ BYind, age ] <- D$AverageMatRate[ age-1 ]
}
# 'compute adult equivalent factor
if(age == D$LastAge[ BYind ] & !D$CompleteBYFlag$Flag[ BYind ]){
#'use average adult equivalent for incomplete brood
AEQ[ BYind, age ] <- MatRate[ BYind, age ] + ((1 - MatRate[ BYind, age ]) * SurvivalRate[ which(D$survivaldf$Age==age ) + 1 ] * AverageAEQ[age + 1])
}else{
AEQ[ BYind, age ] <- MatRate[ BYind, age ] + ((1 - MatRate[ BYind, age ]) * SurvivalRate[ which(D$survivaldf$Age==age) + 1 ] * AEQ[ BYind, age + 1 ] )
}
CohortBeforePreTermFishery <- Cohort[ BYind, age ] * SurvivalRate[ which(D$survivaldf$Age==age) ]
# 'Compute Ocean harvest rates
if(CohortBeforePreTermFishery > 0 ){
PreTermER[ BYind, age ] <- TotalPreTermCatch / CohortBeforePreTermFishery
}else{
PreTermER[ BYind, age ] <- 0
}
#parei aqui
if(M$LongTermAverage){
#ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
if(D$CompleteBYFlag$Flag[BYind]){
SumAEQ[age] <- SumAEQ[age] + AEQ[ BYind,age ]
SumPreTermER[age] <- SumPreTermER[age] + PreTermER[ BYind,age ]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
#'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
#'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
#'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
if( !D$ReadAvgMatRteFlg ){
SumMatRate[ age ] <- SumMatRate[ age ] + MatRate[ BYind, age ]
}
}
}else{
#'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average
#number of years specified BroodYear NumAvgYears
if(allBY[ BYind ] == D$LastCompleteBroodYear ){
for(BroodYearNumber in 1:NumAvgYears){
SumAEQ[age] <- SumAEQ[age] + AEQ[BYind - BroodYearNumber, age ]
SumPreTermER[age] <- sum(c(SumPreTermER[age], PreTermER[BYind - BroodYearNumber, age ]),na.rm=t)
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(!D$ReadAvgMatRteFlg){
#'rates not from .cm1 file, instead calculate from data
SumMatRate[age] <- SumMatRate[age] + MatRate[BYind - BroodYearNumber, age ]
}
}
NumberCompleteBroods <- NumAvgYears
}
}
}
ActDif <- 100 * (abs(Cohort[BYind, D$OceanStartAge] - TestCohortNum) / Cohort[BYind, D$OceanStartAge])
if( ActDif > M$TESTDIF & !RepeatPass ) RepeatPass <- TRUE
}
}
#'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
for(age in D$OceanStartAge:D$MaxAge){
if(NumberOceanCohorts[age] == 0){
#'there are never any ocean recoveries of this age
AveragePreTermER[age] <- 0
}else{
AveragePreTermER[age] <- SumPreTermER[age] / NumberOceanCohorts[age]
}
if(age != D$MaxAge){
#'rates not from ERA_Stock table, instead calculate from data
if(!D$ReadAvgMatRteFlg){
AverageMatRate[age] = SumMatRate[age] / NumberCompleteBroods
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod){
sink("../logs/debug_AvgMatRteID.log", append=TRUE)
cat(paste("2178 avgMatRte", age, AverageMatRate[age], "accum", SumMatRate[age], "numBroods", NumberCompleteBroods,"\n"))
sink()
}
}
AverageAEQ[age] = SumAEQ[age] / NumberCompleteBroods
}else{
#'rate for oldest age not from .cm1 file, instead calculate from data
if(!D$ReadAvgMatRteFlg) AverageMatRate[D$MaxAge] <- 1
AverageAEQ[D$MaxAge] <- 1
}
}
#'PUT AVERAGE VALUES INTO ARRAYS FOR INCOMPLETE BROODS
for(BYind in seq_along(allBY) ){
if(!D$CompleteBYFlag$Flag[BYind]){
for(age in D$OceanStartAge:D$MaxAge){
AEQ[BYind, age] <- AverageAEQ[age]
MatRate[BYind, age] <- AverageMatRate[age]
PreTermER[BYind, age] <- AveragePreTermER[age]
}
}
}
return(list(new=list(Cohort=Cohort,
AEQ=AEQ,
MatRate=MatRate,
PreTermER= PreTermER,
AverageAEQ=AverageAEQ,
AverageMatRate =AverageMatRate,
AveragePreTermER=AveragePreTermER,
NumberOceanCohorts =NumberOceanCohorts,
SumAEQ = SumAEQ,
SumMatRate = SumMatRate,
SumPreTermER = SumPreTermER),
old=list(NumberCompleteBroods=NumberCompleteBroods,
RepeatPass= RepeatPass)
))
#original vb code
# Dim ActDif As Single
# Dim CohortAfterPreTermFishery As Single
# Dim CohortBeforePreTermFishery As Single
# Dim TerminalRun As Single
# Dim TotalCatch, TotalTerminalCatch As Single
# Dim TotalPreTermCatch As Single
# Dim NumberOceanCohorts(MaxAge) As Integer
# Dim SumAEQ(MaxAge) As Single
# Dim SumMatRate(MaxAge) As Single
# Dim SumPreTermER(MaxAge) As Single
# ReDim PreTermER(LastBY, MaxAge)
# ReDim AveragePreTermER(MaxAge)
# NumAvgYears = MatRateNumberBroods.NumBroodsUpDown.Value
# RepeatPass = False
# For BroodYear As Integer = FirstBY To LastBY
# 'skip all missing brood years
# If MissingBroodYearFlag(BroodYear) = False Then
# 'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
# TestCohortNum = Cohort(BroodYear, OceanStartAge)
# 'set survival rate of maxage+1 for use in AEQ equations below
# SurvivalRate(MaxAge + 1) = SurvivalRate(MaxAge)
# 'loop through each age
# For age As Integer = LastAge(BroodYear) To OceanStartAge Step -1
# 'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
# TotalCatch = TotalCatch_Age(BroodYear, age, pass)
# 'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2183 CalcCohort callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
# TotalTerminalCatch = TotalTerminalCatch_Age(BroodYear, age, pass)
# 'subtract total terminal catch from total catch to get total PreTerm catch
# TotalPreTermCatch = TotalCatch - TotalTerminalCatch
# If isTraceCalc = True Then WriteLine(debug_CohortID, "line 1925", "totCat", TotalCatch, "totTermCat", TotalTerminalCatch)
# 'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
# If CompleteBYFlag(BroodYear) = False And age = LastAge(BroodYear) And pass > 1 Then
# Cohort(BroodYear, age) = CalcEstmCohrt2(BroodYear, age) / SurvivalRate(age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "2158 CalcCohort", ShakerMethod, BroodYear, age, Cohort(BroodYear, age))
# Else
# Cohort(BroodYear, age) = (Cohort(BroodYear, age + 1) + Escape(BroodYear, age) + TotalCatch) / SurvivalRate(age)
# End If
#
# If age = OceanStartAge And Cohort(BroodYear, OceanStartAge) = 0 Then
# ErrCaption = "Brood Year " & BroodYear & " has NO CWT recoveries at all!"
# ErrMessage = "Hint: If the brood year has no recoveries, decrement last brood year in the .CM1 file and remove from the .CDS file."
# ErrMessage = ErrMessage & " If intermediate brood year, treat as missing brood and remove from .CDS file."
# Call PrintError(ErrMessage, ErrCaption)
# End If
# CohortAfterPreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age) - TotalPreTermCatch
# TerminalRun = TotalTerminalCatch + Escape(BroodYear, age)
# If ReadAvgMatRteFlg = False Then
# 'rates not from ERA_Stock table, instead calculate from data
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = True Then 'And CohortAfterPreTermFishery > 0 Then
# MatRate(BroodYear, age) = 1
# ElseIf CohortAfterPreTermFishery <= 0 Then
# MatRate(BroodYear, age) = 0
# Else
# MatRate(BroodYear, age) = TerminalRun / CohortAfterPreTermFishery
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2189 MatRte ", BroodYear, age, MatRate(BroodYear, age), TerminalRun, CohortAfterPreTermFishery)
# End If
# 'WriteLine(debugID, "calcCohort", BroodYear, age, ShakerMethod, MatRate(BroodYear, age))
# Else
# 'average mat. rates from ERA_Stock table
# MatRate(BroodYear, age) = AverageMatRate(age)
# End If
# 'compute adult equivalent factor
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = False Then 'use average adult equivalent for incomplete brood
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AverageAEQ(age + 1))
# Else
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AEQ(BroodYear, age + 1))
# End If
# CohortBeforePreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age)
# 'Compute Ocean harvest rates
# If CohortBeforePreTermFishery > 0 Then
# PreTermER(BroodYear, age) = TotalPreTermCatch / CohortBeforePreTermFishery
# Else
# PreTermER(BroodYear, age) = 0
# End If
# If LongTermAverage.Checked = True Then
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
# If CompleteBYFlag(BroodYear) = True Then
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# 'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
# 'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
# 'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
# If ReadAvgMatRteFlg = False Then 'rates not from ERA_Stock table, instead calculate from data
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear, age)
# End If
# End If
# Else
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average number of years specified BroodYear NumAvgYears
# If BroodYear = LastCompleteBroodYear Then
# For BroodYearNumber As Integer = 0 To NumAvgYears - 1
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear - BroodYearNumber, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear - BroodYearNumber, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = False Then 'rates not from .cm1 file, instead calculate from data
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear - BroodYearNumber, age)
# End If
# Next BroodYearNumber
# NumberCompleteBroods = NumAvgYears
# End If
# End If
# Next age
# ActDif = 100 * (System.Math.Abs(Cohort(BroodYear, OceanStartAge) - TestCohortNum) / Cohort(BroodYear, OceanStartAge))
# If ActDif > TESTDIF And RepeatPass = False Then RepeatPass = True
# End If
# Next BroodYear
# 'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
# For Age = OceanStartAge To MaxAge
# If NumberOceanCohorts(Age) = 0 Then
# 'there are never any ocean recoveries of this age
# AveragePreTermER(Age) = 0
# Else
# AveragePreTermER(Age) = SumPreTermER(Age) / NumberOceanCohorts(Age)
# End If
# If Age <> MaxAge Then
# 'rates not from ERA_Stock table, instead calculate from data
# If ReadAvgMatRteFlg = False Then
# AverageMatRate(Age) = SumMatRate(Age) / NumberCompleteBroods
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2178 avgMatRte", Age, AverageMatRate(Age), "accum", SumMatRate(Age), "numBroods", NumberCompleteBroods)
# End If
# AverageAEQ(Age) = SumAEQ(Age) / NumberCompleteBroods
# Else
# 'rate for oldest age not from .cm1 file, instead calculate from data
# If ReadAvgMatRteFlg = False Then AverageMatRate(MaxAge) = 1
# AverageAEQ(MaxAge) = 1
# End If
# Next Age
# 'PUT AVERAGE VALUES INTO ARRAYS FOR INCOMPLETE BROODS
# For BY = FirstBY To LastBY
# If CompleteBYFlag(BY) = False Then
# For Age = OceanStartAge To MaxAge
# AEQ(BY, Age) = AverageAEQ(Age)
# MatRate(BY, Age) = AverageMatRate(Age)
# PreTermER(BY, Age) = AveragePreTermER(Age)
# Next Age
# End If
# Next BY
}
#' @title CalcCohort_IncompleteBrood
#'
#' @description function where the actual ERA is done, this one is for incomplete cohorts only.
#'
#' @param M A list passed to StartCohortAnalysis_Click
#'
#' @param D A list containing stock specific info
#'
#' @details
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcCohort_IncompleteBrood <- function(D,M){
allBY <- D$FirstBY:D$LastBY
NumberOceanCohorts <- rep(0,D$MaxAge)
AvgAdltEqv <- rep(0,D$MaxAge)
SumAEQ <- rep(0,D$MaxAge)
#AverageAEQ <- NULL
SumMatRate <- rep(0,D$MaxAge)
SumPreTermER <- rep(0,D$MaxAge)
#AveragePreTermER <- NULL
AverageMatRate <- NULL
#PreTermER <- matrix(NA, nrow = length(allBY),ncol = 7 )
if("Cohort" %in% names(D)){
Cohort <- D$Cohort
}else{
Cohort <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("MatRate" %in% names(D)){
MatRate <- D$MatRate
}else{
MatRate <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("AEQ" %in% names(D)){
AEQ <- D$AEQ
}else{
AEQ <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("AEQ" %in% names(D)){
PreTermER <- D$PreTermER
}else{
PreTermER <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("AEQ" %in% names(D)){
AveragePreTermER <- D$AveragePreTermER
}else{
AveragePreTermER <- matrix(0, nrow = length(allBY),ncol = 7 )
}
#
#AEQ <- matrix(0, nrow=length(allBY),ncol = D$MaxAge + 1 )
#SumAEQ <- rep(0,D$MaxAge)
#SumPreTermER <- rep(0,D$MaxAge)
#NumberOceanCohorts <- rep(0,D$MaxAge)
#'determine the last complete brood year
LastCompleteBroodYear<-max(D$CompleteBYFlag$BY[D$CompleteBYFlag$Flag])
# 'Set AEQ, Mat rate, and ocean HR totals to 1 prior to calculating the products for use in a geometric mean, this eliminates multiplication by zero for the first BY in the avg. calcs.
if(!M$ArithmeticMeanFlag){
for(age in D$OceanStartAge:D$MaxAge){
SumAEQ[age] <- 1
SumPreTermER[age] <- 1
SumMatRate[age] <- 1
}
}
for(BroodYear in seq_along(allBY)){
#'if missing brood year, then skip to next brood year that is not missing
if(D$MissingBroodYearFlag$Flag[BroodYear]){
next
}
# 'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
TestCohortNum <- Cohort[BroodYear, OceanStartAge]
for(age in D$LastAge[BroodYear]:D$OceanStartAge){
#'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
TotalCatch <- TotalCatch_Age(D, M, BY=BroodYear, age)
#'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2340 CalcCohrt_inc callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
TotalTerminalCatch <- TotalTerminalCatch_Age(D, M, BY=BroodYear, age)
#'subtract total terminal catch from total catch to get total PreTerm catch
TotalPreTermCatch <- TotalCatch - TotalTerminalCatch
#'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "2078 CaclCohortinCompl BY", ShakerMethod, BroodYear, age, "totCat", TotalCatch, "totTermCat", TotalTerminalCatch)
if(!D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]] & age == D$LastAge[BroodYear] & pass > 1){
Cohort[BroodYear,age] <- CalcEstmCohrt2(D, M, BroodYear, age) / D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 compl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), SurvivalRate(age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 CalcCohortincompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age))
}else{
Cohort[BroodYear, age] <- (Cohort[BroodYear, age + 1] + D$Escape[BroodYear, age] + TotalCatch) / D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1821 CalcCohortinCompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), Cohort(BroodYear, age + 1), Escape(BroodYear, age), TotalCatch, SurvivalRate(age))
}
if(age == D$OceanStartAge & Cohort[BroodYear, D$OceanStartAge] == 0){
ErrCaption <- paste("Brood Year", BroodYear, "has NO CWT recoveries at all! \n")
ErrMessage <- paste("Hint: If the brood year has no recoveries, decrement last brood year")# in the .CM1 file and remove from the .CDS file."
ErrMessage <- paste(ErrMessage,"If intermediate brood year, treat as missing brood")# and remove from .CDS file."
error(paste(ErrCaption,ErrMessage))
}
CohortAfterPreTermFishery <- Cohort[BroodYear, age] * D$survivaldf$SurvivalRate[age] - TotalPreTermCatch
TerminalRun <- TotalTerminalCatch + D$Escape[BroodYear, age]
if(!D$ReadAvgMatRteFlg){
#'rates not from ERA_Stock table, instead calculate from data
if(age == D$LastAge[BroodYear] & D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]] & CohortAfterPreTermFishery > 0 ){
MatRate[BroodYear, age] <- 1
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2587 MatRte ", MatRate(BroodYear, age))
}else if(CohortAfterPreTermFishery <= 0){
MatRate[BroodYear, age] <- 0
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2590 MatRte ", MatRate(BroodYear, age))
}else{
MatRate[BroodYear, age] <- TerminalRun / CohortAfterPreTermFishery
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2591 MatRte ", CohortAfterPreTermFishery, Cohort(BroodYear, age), SurvivalRate(age), TotalPreTermCatch)
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2592 MatRte ", TerminalRun, TotalTerminalCatch, Escape(BroodYear, age))
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2593 MatRte ", ShakerMethod, BroodYear, age, MatRate(BroodYear, age), TerminalRun / RelRatio(BroodYear), CohortAfterPreTermFishery / RelRatio(BroodYear), TotalTerminalCatch / RelRatio(BroodYear), Escape(BroodYear, age) / RelRatio(BroodYear), Cohort(BroodYear, age) / RelRatio(BroodYear), SurvivalRate(age), TotalPreTermCatch / RelRatio(BroodYear), RelRatio(BroodYear))
}
#'If isTraceCalc = True And shakermethod = traceThisShakerMethod Then WriteLine(debugID, "incompleteBrood", BroodYear, age, ShakerMethod, MatRate(BroodYear, age))
}else{
#'average mat. rates from ERA_Stock table
MatRate[BroodYear, age] <- D$AverageMatRate[age]
}
#'compute adult equivalent factor
if(age == D$LastAge[BroodYear] & !D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==BroodYear]){
#'use average adult equivalent for incomplete brood
AEQ[BroodYear, age] <- MatRate[BroodYear, age] + ((1 - MatRate[BroodYear, age]) * D$survivaldf$SurvivalRate[D$survivaldf$Age==(age+1)] * AverageAEQ[age + 1])
}else{
AEQ[BroodYear, age] <- MatRate[BroodYear, age] + ((1 - MatRate[BroodYear, age]) * D$survivaldf$SurvivalRate[D$survivaldf$Age==(age+1)] * AEQ[BroodYear, age + 1])
}
CohortBeforePreTermFishery = Cohort[BroodYear, age] * D$survivaldf$SurvivalRate[D$survivaldf$Age == age]
#'Compute Ocean harvest rates
if(CohortBeforePreTermFishery > 0){
PreTermER[BroodYear, age] <- TotalPreTermCatch / CohortBeforePreTermFishery
}else{
PreTermER[BroodYear, age] <- 0
}
if(M$ArithmeticMeanFlag){
#'Summation of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in arithmetic mean
if(M$LongTermAverage){
#'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
if(D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]]){
SumAEQ[age] <- SumAEQ[age] + AEQ[BroodYear, age]
SumPreTermER[age] <- SumPreTermER[age] + PreTermER[BroodYear, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
#'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
#'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
#'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
if(!D$ReadAvgMatRteFlg){
#'rates not from ERA_Stock table, instead calculate from data
if(MatRate[BroodYear, age] == 0){
MatRate[BroodYear, age] <- 0.0000001
#'prevents SumMatRte = 0
}
SumMatRate[age] <- SumMatRate[age] + MatRate[BroodYear, age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2625 avgMatRte LTA", BroodYear, age, SumMatRate(age), MatRate(BroodYear, age))
}
}
}else{
#'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average number of years specified BroodYear NumAvgYears
if(allBY[BroodYear] == D$LastCompleteBroodYear){
for(BroodYearNumber in 0:(M$NumAvgYears - 1)){
SumAEQ[age] <- SumAEQ[age] + AEQ[BroodYear - BroodYearNumber, age]
SumPreTermER[age] <- SumPreTermER[age] + PreTermER[BroodYear - BroodYearNumber, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(!D$ReadAvgMatRteFlg){
if(MatRate[BroodYear - BroodYearNumber, age] == 0 ){
#'prevents SumMatRte = 0
MatRate[BroodYear - BroodYearNumber, age] = 0.0000001
}
SumMatRate[age] = SumMatRate[age] + MatRate[BroodYear - BroodYearNumber, age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2638 avgMatRte", BroodYear - BroodYearNumber, age, SumMatRate(age), MatRate(BroodYear - BroodYearNumber, age))
}
}
#NumberCompleteBroods = NumAvgYears
}
}
}else{
#'Product of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in geometric mean
if(M$LongTermAverage){
#'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using longterm average
if(D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]]){
SumAEQ[age] <- SumAEQ[age] * AEQ[BroodYear, age]
if(PreTermER[BroodYear, age] == 0){
PreTermER[BroodYear, age] <- 0.0000001
}
SumPreTermER[age] <- SumPreTermER[age] * PreTermER[BroodYear, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(D$ReadAvgMatRteFlg == 0){
#'rates not from .cm1 file, instead calculate from data
if( MatRate[BroodYear, age] == 0){
#'prevents SumMatRte = 0
MatRate(BroodYear, age) <- 0.0000001
}
SumMatRate[age] = SumMatRate[age] * MatRate[BroodYear, age]
}
}
}else{
#'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using average number of years specified by NumAvgYears
if(BroodYear == D$LastCompleteBroodYear){
for(BY in 0:(M$NumAvgYears-1)){
SumAEQ[age] = SumAEQ[age] * AEQ[BroodYear - BY, age]
if(PreTermER[BroodYear, age] == 0){
PreTermER[BroodYear, age] <- 0.0000001
}
SumPreTermER[age] <- SumPreTermER[age] * PreTermER[BroodYear - BY, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(D$ReadAvgMatRteFlg ==0 ){
#'rates not from .cm1 file, instead calculate from data
if(MatRate[BroodYear- BY,age] == 0){
#'prevents a TotMatRate of 0
MatRate[BroodYear - BY, age] <- 0.0000001
}
SumMatRate[age] <- SumMatRate[age] * MatRate[BroodYear - BY, age]
}
}
NumberCompleteBroods = NumAvgYears
}
}
}
}
ActDif = 100 * (abs(Cohort[BroodYear, OceanStartAge] - TestCohortNum)/ Cohort[BroodYear, OceanStartAge])
if(ActDif > TESTDIF & !D$RepeatPass ){
RepeatPass = True
}
}
#'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
for(age in D$OceanStartAge:D$MaxAge){
if(M$ArithmeticMeanFlag){
if(D$NumberOceanCohorts[age]==0){
#'there are never any ocean recoveries of this age
AveragePreTermER[age] <- 0
}else{
AverageMatRate[age] <- SumMatRate[age] / NumberCompleteBroods
}
if(age != D$MaxAge){
#'rates not from ERA_Stock table, instead calculate from data
if(!D$ReadAvgMatRteFlg){
AverageMatRate[age] <- SumMatRate[age] / NumberCompleteBroods
}
AverageAEQ[age] <- SumAEQ[age] / NumberCompleteBroods
}else{
#'rate for oldest age not from .cm1 file, instead calculate from data
if(!D$ReadAvgMatRteFlg){
AverageMatRate[D$MaxAge] <- 1
}
AverageAEQ[D$MaxAge] <- 1
}
}else{
#'if you want to use the geometric mean
if(D$NumberOceanCohorts[age]==0){
#'there are never any ocean recoveries of this age
AveragePreTermER[age] <- 0
}else{
AveragePreTermER[age] = SumPreTermER[age]^(1 / NumberOceanCohorts[age])
}
if(age != D$MaxAge){
if(D$ReadAvgMatRteFlg == 0){
#'rates not from .cm1 file, instead calculate from data
AverageMatRate[age] = SumMatRate[age] ^ (1 / D$NumberCompleteBroods)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2379 avgMatRte", BroodYear, Age, AverageMatRate(Age), "accum", SumMatRate(Age), "numBroods", NumberCompleteBroods)
}
AverageAEQ[age] <- SumAEQ[age] ^ (1 / D$NumberCompleteBroods)
}else{
if(D$ReadAvgMatRteFlg){
#'rate for oldest age not from .cm1 file, instead calculate from data
AverageMatRate[MaxAge] <- 1
}
AverageAEQ[MaxAge] = 1
}
} #'ArithmeticMeanFlag = True
}
return(list(NumberOceanCohorts=NumberOceanCohorts,
SumAEQ=SumAEQ,
SumMatRate=SumMatRate,
SumPreTermER=SumPreTermER,
PreTermER=PreTermER,
AveragePreTermER=AveragePreTermER,
Cohort= Cohort,
MatRate=MatRate,
AEQ=AEQ,
))
#==========================================================
#Original VB code
# Dim ActDif As Single
# Dim AvgAdltEqv(MaxAge) As Single
# Dim BroodYear As Integer
# Dim CohortAfterPreTermFishery As Single
# Dim CohortBeforePreTermFishery As Single
# Dim LastCompleteBroodYear As Integer
# Dim TerminalRun As Single
# Dim TotalCatch, TotalTerminalCatch As Single
# Dim TotalPreTermCatch As Single
# Dim NumberOceanCohorts(MaxAge) As Integer
# Dim SumAEQ(MaxAge) As Single
# Dim SumMatRate(MaxAge) As Single
# Dim SumPreTermER(MaxAge) As Single
# ReDim PreTermER(LastBY, MaxAge)
# ReDim AveragePreTermER(MaxAge)
# NumAvgYears = MatRateNumberBroods.NumBroodsUpDown.Value
# RepeatPass = False
#
# 'determine the last complete brood year
# For BY = FirstBY To LastBY
# 'skip over missing brood years,
# If MissingBroodYearFlag(BY) = True Then BY = FindBY(BY)
# If CompleteBYFlag(BY) = True Then
# LastCompleteBroodYear = BY
# End If
# Next BY
# 'Set AEQ, Mat rate, and ocean HR totals to 1 prior to calculating the products for use in a geometric mean, this eliminates multiplication by zero for the first BY in the avg. calcs.
# If ArithmeticMeanFlag = False Then
# For Age = OceanStartAge To MaxAge
# SumAEQ(Age) = 1
# SumPreTermER(Age) = 1
# SumMatRate(Age) = 1
# Next Age
# End If
#
# For BroodYear = FirstBY To LastBY
# 'if missing brood year, then skip to next brood year that is not missing
# If MissingBroodYearFlag(BroodYear) = True Then BroodYear = FindBY(BroodYear)
# 'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
# TestCohortNum = Cohort(BroodYear, OceanStartAge)
# 'loop through each age
# For age = LastAge(BroodYear) To OceanStartAge Step -1
# 'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
# TotalCatch = TotalCatch_Age(BroodYear, age, pass)
# 'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2340 CalcCohrt_inc callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
# TotalTerminalCatch = TotalTerminalCatch_Age(BroodYear, age, pass)
# 'subtract total terminal catch from total catch to get total PreTerm catch
# TotalPreTermCatch = TotalCatch - TotalTerminalCatch
# 'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "2078 CaclCohortinCompl BY", ShakerMethod, BroodYear, age, "totCat", TotalCatch, "totTermCat", TotalTerminalCatch)
# If CompleteBYFlag(BroodYear) = False And age = LastAge(BroodYear) And pass > 1 Then
# Cohort(BroodYear, age) = CalcEstmCohrt2(BroodYear, age) / SurvivalRate(age)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 compl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), SurvivalRate(age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 CalcCohortincompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age))
# Else
# Cohort(BroodYear, age) = (Cohort(BroodYear, age + 1) + Escape(BroodYear, age) + TotalCatch) / SurvivalRate(age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1821 CalcCohortinCompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), Cohort(BroodYear, age + 1), Escape(BroodYear, age), TotalCatch, SurvivalRate(age))
# End If
#
# If age = OceanStartAge And Cohort(BroodYear, OceanStartAge) = 0 Then
# ErrCaption = "Brood Year " & BroodYear & " has NO CWT recoveries at all!"
# ErrMessage = "Hint: If the brood year has no recoveries, decrement last brood year in the .CM1 file and remove from the .CDS file."
# ErrMessage = ErrMessage & " If intermediate brood year, treat as missing brood and remove from .CDS file."
# Call PrintError(ErrMessage, ErrCaption)
# End If
# CohortAfterPreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age) - TotalPreTermCatch
# TerminalRun = TotalTerminalCatch + Escape(BroodYear, age)
# If ReadAvgMatRteFlg = False Then
# 'rates not from ERA_Stock table, instead calculate from data
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = True And CohortAfterPreTermFishery > 0 Then
# MatRate(BroodYear, age) = 1
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2587 MatRte ", MatRate(BroodYear, age))
# ElseIf CohortAfterPreTermFishery <= 0 Then
# MatRate(BroodYear, age) = 0
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2590 MatRte ", MatRate(BroodYear, age))
# Else
# MatRate(BroodYear, age) = TerminalRun / CohortAfterPreTermFishery
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2591 MatRte ", CohortAfterPreTermFishery, Cohort(BroodYear, age), SurvivalRate(age), TotalPreTermCatch)
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2592 MatRte ", TerminalRun, TotalTerminalCatch, Escape(BroodYear, age))
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2593 MatRte ", ShakerMethod, BroodYear, age, MatRate(BroodYear, age), TerminalRun / RelRatio(BroodYear), CohortAfterPreTermFishery / RelRatio(BroodYear), TotalTerminalCatch / RelRatio(BroodYear), Escape(BroodYear, age) / RelRatio(BroodYear), Cohort(BroodYear, age) / RelRatio(BroodYear), SurvivalRate(age), TotalPreTermCatch / RelRatio(BroodYear), RelRatio(BroodYear))
# End If
# 'If isTraceCalc = True And shakermethod = traceThisShakerMethod Then WriteLine(debugID, "incompleteBrood", BroodYear, age, ShakerMethod, MatRate(BroodYear, age))
# Else
# 'average mat. rates from ERA_Stock table
# MatRate(BroodYear, age) = AverageMatRate(age)
# End If
#
# 'compute adult equivalent factor
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = False Then 'use average adult equivalent for incomplete brood
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AverageAEQ(age + 1))
# Else
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AEQ(BroodYear, age + 1))
# End If
# CohortBeforePreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age)
# 'Compute Ocean harvest rates
# If CohortBeforePreTermFishery > 0 Then
# PreTermER(BroodYear, age) = TotalPreTermCatch / CohortBeforePreTermFishery
# Else
# PreTermER(BroodYear, age) = 0
# End If
# If ArithmeticMeanFlag = True Then 'Summation of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in arithmetic mean
# If LongTermAverage.Checked = True Then
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
# If CompleteBYFlag(BroodYear) = True Then
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# 'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
# 'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
# 'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
# If ReadAvgMatRteFlg = False Then 'rates not from ERA_Stock table, instead calculate from data
# If MatRate(BroodYear, age) = 0 Then MatRate(BroodYear, age) = 0.0000001 'prevents SumMatRte = 0
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear, age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2625 avgMatRte LTA", BroodYear, age, SumMatRate(age), MatRate(BroodYear, age))
# End If
# End If
# Else
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average number of years specified BroodYear NumAvgYears
# If BroodYear = LastCompleteBroodYear Then
# For BroodYearNumber = 0 To NumAvgYears - 1
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear - BroodYearNumber, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear - BroodYearNumber, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = False Then 'rates not from .cm1 file, instead calculate from data
# If MatRate(BroodYear - BroodYearNumber, age) = 0 Then MatRate(BroodYear - BroodYearNumber, age) = 0.0000001 'prevents SumMatRte = 0
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear - BroodYearNumber, age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2638 avgMatRte", BroodYear - BroodYearNumber, age, SumMatRate(age), MatRate(BroodYear - BroodYearNumber, age))
# End If
# Next BroodYearNumber
# NumberCompleteBroods = NumAvgYears
# End If
# End If
# Else 'Product of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in geometric mean
# If LongTermAverage.Checked = True Then 'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using longterm average
# If CompleteBYFlag(BroodYear) = True Then
# SumAEQ(age) = SumAEQ(age) * AEQ(BroodYear, age)
# If PreTermER(BroodYear, age) = 0 Then PreTermER(BroodYear, age) = 0.0000001
# SumPreTermER(age) = SumPreTermER(age) * PreTermER(BroodYear, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = 0 Then 'rates not from .cm1 file, instead calculate from data
# If MatRate(BroodYear, age) = 0 Then MatRate(BroodYear, age) = 0.0000001 'prevents SumMatRte = 0
# SumMatRate(age) = SumMatRate(age) * MatRate(BroodYear, age)
# End If
# End If
# Else 'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using average number of years specified by NumAvgYears
# If BroodYear = LastCompleteBroodYear Then
# For BY = 0 To NumAvgYears - 1
# SumAEQ(age) = SumAEQ(age) * AEQ(BroodYear - BY, age)
# If PreTermER(BroodYear, age) = 0 Then PreTermER(BroodYear, age) = 0.0000001
# SumPreTermER(age) = SumPreTermER(age) * PreTermER(BroodYear - BY, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = 0 Then 'rates not from .cm1 file, instead calculate from data
# If MatRate(BroodYear - BY, age) = 0 Then MatRate(BroodYear - BY, age) = 0.0000001 'prevents a TotMatRate of 0
# SumMatRate(age) = SumMatRate(age) * MatRate(BroodYear - BY, age)
# End If
# Next BY
# NumberCompleteBroods = NumAvgYears
# End If
# End If
# End If
# Next age
# ActDif = 100 * (System.Math.Abs(Cohort(BroodYear, OceanStartAge) - TestCohortNum) / Cohort(BroodYear, OceanStartAge))
# If ActDif > TESTDIF And RepeatPass = False Then RepeatPass = True
# Next BroodYear
# 'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
# For Age = OceanStartAge To MaxAge
# If ArithmeticMeanFlag = True Then
# If NumberOceanCohorts(Age) = 0 Then
# 'there are never any ocean recoveries of this age
# AveragePreTermER(Age) = 0
# Else
# AveragePreTermER(Age) = SumPreTermER(Age) / NumberOceanCohorts(Age)
# End If
# If Age <> MaxAge Then
# 'rates not from ERA_Stock table, instead calculate from data
# If ReadAvgMatRteFlg = False Then
# AverageMatRate(Age) = SumMatRate(Age) / NumberCompleteBroods
# End If
# AverageAEQ(Age) = SumAEQ(Age) / NumberCompleteBroods
# Else
# 'rate for oldest age not from .cm1 file, instead calculate from data
# If ReadAvgMatRteFlg = False Then AverageMatRate(MaxAge) = 1
# AverageAEQ(MaxAge) = 1
# End If
# Else 'if you want to use the geometric mean
# If NumberOceanCohorts(Age) = 0 Then
# 'there are never any ocean recoveries of this age
# AveragePreTermER(Age) = 0
# Else
# AveragePreTermER(Age) = SumPreTermER(Age) ^ (1 / NumberOceanCohorts(Age))
# End If
# If Age <> MaxAge Then
# If ReadAvgMatRteFlg = 0 Then 'rates not from .cm1 file, instead calculate from data
# AverageMatRate(Age) = SumMatRate(Age) ^ (1 / NumberCompleteBroods)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2379 avgMatRte", BroodYear, Age, AverageMatRate(Age), "accum", SumMatRate(Age), "numBroods", NumberCompleteBroods)
# End If
# AverageAEQ(Age) = SumAEQ(Age) ^ (1 / NumberCompleteBroods)
# Else
# If ReadAvgMatRteFlg = 0 Then AverageMatRate(MaxAge) = 1 'rate for oldest age not from .cm1 file, instead calculate from data
# AverageAEQ(MaxAge) = 1
# End If
# End If 'ArithmeticMeanFlag = True
# Next Age
#
# }
#
#}
}
#' @title CalcEstmCohrt2
#'
#' @description .
#'
#' @param BroodYear integer indicating brood year
#'
#' @param Age integer indicating age
#'
#' @details
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcEstmCohrt2 <- function( D, M, BroodYear,Age ){
#print("Enter CalcEstmCohrt2")
#'This subroutine increases current age cohort sizes to correct for the lack of
#'recoveries in older age classes in incomplete brood years (used by Calendar Year shaker
#'option and Brood Year shaker option with oldest age and in final calculation of harvest rates).
#'local variables
#BroodYear<-BYind
#Age<-age
if( D$MissingBroodYearFlag$Flag[BroodYear] ){
return(NULL)
}else{
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod ){
sink("../logs/debug_terminalCatchID.log", append=TRUE)
cat(paste("2522 CalcEstmCohrt2 call TotalTerminalCatch_age",M$ShakerMethod,BroodYear, Age, "\n"))
sink()
}
TerminalRun <- TotalTerminalCatch_Age(D, M, BroodYear, D$LastAge[BroodYear]) + D$Escape[BroodYear, D$LastAge[BroodYear]]
#'USE AVERAGE MATURATION RATE TO ESTIMATE COHORT SIZE AFTER MATURATION FOR INCOMPLETE BROOD
Chort <- (1 - D$AverageMatRate[D$LastAge[BroodYear]]) * TerminalRun / D$AverageMatRate[D$LastAge[BroodYear]]
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear >= M$traceThisYear ){
sink("../logs/debug_Cohort_IncompleteBroodID.log", append=TRUE)
cat(paste("1991 calcestmcohrt2",M$ShakerMethod,BroodYear, Age,
Chort, "avgMatRte", D$AverageMatRate[D$LastAge[BroodYear]], "termRun", TerminalRun, "\n"))
sink()
}
#'RECONSTRUCT COHORT SIZES BroodYear ADDING CATCH, ESCAPEMENT, AND NATURAL MORTALITY
for( A in D$LastAge[BroodYear]:Age ){
Chort <- Chort + D$Escape[BroodYear, A] + TotalCatch_Age( D, M, BroodYear, A )
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear >= M$traceThisYear ){
sink("../logs/debug_Cohort_IncompleteBroodID.log", append=TRUE)
cat(paste("1996 calcestmcohrt2",M$ShakerMethod,BroodYear, A, "accum", Chort, "escape",
D$Escape[BroodYear, A], "totCat", TotalCatch_Age(D, M, BroodYear, A), "surv",
D$survivaldf$SurvivalRate[D$survivaldf$Age==A], "\n"))
sink()
}
if( A != Age ){ Chort = Chort/ D$survivaldf$SurvivalRate[D$survivaldf$Age==A] }
}
#'COHORT SIZE AFTER NATURAL MORTALITY
if( is.na(Chort) ){
return(0.0)
}else{
return(Chort)
}
}
#Function CalcEstmCohrt2(ByRef BroodYear As Integer, ByRef Age As Integer) As Single
#'This subroutine increases current age cohort sizes to correct for the lack of
#'recoveries in older age classes in incomplete brood years (used by Calendar Year shaker
#'option and Brood Year shaker option with oldest age and in final calculation of harvest rates).
#'local variables
#Dim Chort, TerminalRun As Single
#If MissingBroodYearFlag(BroodYear) = True Then Exit Function
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2522 CalcEstmCohrt2 call TotalTerminalCatch_age", ShakerMethod, BroodYear, Age)
#
#TerminalRun = TotalTerminalCatch_Age(BroodYear, LastAge(BroodYear), pass) + Escape(BroodYear, LastAge(BroodYear))
#'USE AVERAGE MATURATION RATE TO ESTIMATE COHORT SIZE AFTER MATURATION FOR INCOMPLETE BROOD
#Chort = (1 - AverageMatRate(LastAge(BroodYear))) * TerminalRun / AverageMatRate(LastAge(BroodYear))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1991 calcestmcohrt2", ShakerMethod, BroodYear, Age, Chort, "avgMatRte", AverageMatRate(LastAge(BroodYear)), "termRun", TerminalRun)
#'RECONSTRUCT COHORT SIZES BroodYear ADDING CATCH, ESCAPEMENT, AND NATURAL MORTALITY
#For A As Integer = LastAge(BroodYear) To Age Step -1
# Chort = Chort + Escape(BroodYear, A) + TotalCatch_Age(BroodYear, A, pass)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1996 calcestmcohrt2", ShakerMethod, BroodYear, A, "accum", Chort, "escape", Escape(BroodYear, A), "totCat", TotalCatch_Age(BroodYear, A, pass), "surv", SurvivalRate(A))
# If A <> Age Then Chort = Chort / SurvivalRate(A)
#Next A
#'COHORT SIZE AFTER NATURAL MORTALITY
#If Single.IsNaN(Chort) Then
# CalcEstmCohrt2 = 0.0
#
#Else
# CalcEstmCohrt2 = Chort
#
#End If
#End Function
}
#' @title CalcEstmCohrt
#'
#' @description .
#'
#' @param BroodYear integer indicating brood year
#'
#' @param Age integer indicating age
#'
#' @details This subroutine estimates future age cohort sizes so that shakers can be
#' calculated for incomplete brood years (Brood Year shaker option only).
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcEstmCohrt <- function( D, M, BY,Age ){
#print("Enter CalcEstmCohrt")
stopifnot(!D$MissingBroodYearFlag$Flag[BY])
for(CurrAge in (D$LastAge[BY]+1):Age){
PrevAge <- CurrAge - 1
if(PrevAge == D$LastAge[BY]){
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2501 CalcEstmCohrt call TotalTerminalCatch_Age", ShakerMethod, BroodYear, Age)
MatRun <- TotalTerminalCatch_Age(D, M, BY, PrevAge, D$pass) + D$Escape[BY, PrevAge]
}else{
#'Use Average Ocean Harvest Rate at current age and Avg Maturity Rate to
#'estimate mature run
MatRun <- cohrt * (1 - D$AveragePreTermER[CurrAge]) * D$AverageMatRate[PrevAge]
}
#'Use Avg Mat Rate to estimate incomplete cohort
cohrt <- (1 - D$AverageMatRate[PrevAge]) * MatRun / D$AverageMatRate[PrevAge]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1974 calcestmcohrt", ShakerMethod, BroodYear, CurrAge, cohrt, (1 - AverageMatRate(PrevAge)), MatRun, AverageMatRate(PrevAge))
cohrt <- cohrt * D$survivaldf$SurvivalRate[D$survivaldf$Age==CurrAge]
}
if(is.na(cohrt)){
CalcEstmCohrt <- 0
}else{
CalcEstmCohrt <- cohrt
}
return(CalcEstmCohrt)
#========================================================================
#Original vb code
#========================================================================
#'This subroutine estimates future age cohort sizes so that shakers can be
# 'calculated for incomplete brood years (Brood Year shaker option only).
# Dim cohrt, MatRun As Single
# Dim CurrAge, PrevAge As Integer
# If MissingBroodYearFlag(BroodYear) = True Then Exit Function
# For CurrAge = LastAge(BroodYear) + 1 To Age
# PrevAge = CurrAge - 1
# If PrevAge = LastAge(BroodYear) Then
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2501 CalcEstmCohrt call TotalTerminalCatch_Age", ShakerMethod, BroodYear, Age)
#
# MatRun = TotalTerminalCatch_Age(BroodYear, PrevAge, pass) + Escape(BroodYear, PrevAge)
# Else
# 'Use Average Ocean Harvest Rate at current age and Avg Maturity Rate to
# 'estimate mature run
# MatRun = cohrt * (1 - AveragePreTermER(CurrAge)) * AverageMatRate(PrevAge)
# End If
# 'Use Avg Mat Rate to estimate incomplete cohort
# cohrt = (1 - AverageMatRate(PrevAge)) * MatRun / AverageMatRate(PrevAge)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1974 calcestmcohrt", ShakerMethod, BroodYear, CurrAge, cohrt, (1 - AverageMatRate(PrevAge)), MatRun, AverageMatRate(PrevAge))
# cohrt = cohrt * SurvivalRate(CurrAge)
# Next CurrAge
# If Single.IsNaN(cohrt) Then
# CalcEstmCohrt = 0.0
# Else
#
# CalcEstmCohrt = cohrt
# End If
}
#' @title FindBY
#'
#' @description .
#'
#' @param BY integer indicating brood year
#'
#' @details 'give a brood year where Brood(BY%).MissingByFlg = true
#' 'return the next brood year where Brood(BY%).MissingByFlg = false
#'
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
FindBY <- function(BY, D){
#'give a brood year where Brood(BY%).MissingByFlg = true
#'return the next brood year where Brood(BY%).MissingByFlg = false
BY <- BY + 1
while(D$MissingBroodYearFlag$Flag[BY]){
if(BY > D$LastBY){
BY <- D$LastBY
break
}else{
BY <- BY + 1
}
}
return(BY)
#-------------------------------------
#Original VB code
#'give a brood year where Brood(BY%).MissingByFlg = true
# 'return the next brood year where Brood(BY%).MissingByFlg = false
# Do
# by = by + 1
# If by > LastBY Then
# by = LastBY
# Exit Do
# End If
# Loop Until MissingBroodYearFlag(by) = False
# FindBY = by
}
CTCassess/ERAR documentation built on Sept. 22, 2019, 10:18 p.m.
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Defines functions CalcCohort CalcCohort_IncompleteBrood CalcEstmCohrt2 CalcEstmCohrt FindBY
#=======================================================
#ERA function CalcCohort
#Translated from VB ERA CIS code
#March 2019
#Author: Catarina Wor
#=======================================================
#' @title CalcCohort
#'
#' @description function where the actual ERA is done, this one is for complete cohorts only.
#'
#' @param M A list passed to StartCohortAnalysis_Click
#'
#' @param D A list containing stock specific info
#'
#' @details
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcCohort <- function(D,M){
print("enter CalcCohort")
allBY <- D$FirstBY:D$LastBY
#allCY <- (D$FirstBY + D$OceanStartAge):M$LastCalendarYear
allAge <- D$OceanStartAge:D$MaxAge
NumberOceanCohorts <- NULL
SumAEQ <- rep(0,D$MaxAge)
AverageAEQ <- NULL
SumMatRate <- rep(0,D$MaxAge)
SumPreTermER <- rep(0,D$MaxAge)
AveragePreTermER <- NULL
AverageMatRate <- NULL
PreTermER <- matrix(NA, nrow = length(allBY),ncol = 7 )
Cohort <- matrix(0, nrow = length(allBY),ncol = 7 )
MatRate <- matrix(0, nrow = length(allBY),ncol = 7 )
AEQ <- matrix(0, nrow=length(allBY),ncol = D$MaxAge + 1 )
SumAEQ <- rep(0,D$MaxAge)
SumPreTermER <- rep(0,D$MaxAge)
NumberOceanCohorts <- rep(0,D$MaxAge)
SurvivalRate <- D$survivaldf$SurvivalRate
NumberCompleteBroods<-D$NumberCompleteBroods
pass<-D$pass
RepeatPass <- FALSE
if( M$Average_Maturation_Rate == "SelectNumberCompleteBroods" ){
#This is not selecting the number of complte broods but choosing all the complete broods.
#NumAvgYears <- sum(allBY < (M$LastCalendarYear-D$MaxAge))
NumAvgYears <- M$NumAvgYears
}else{
NumAvgYears <- M$LastCompleteBroodsUsed
}
for( BYind in seq_along(allBY) ){
#'skip all missing brood years
if( !D$MissingBroodYearFlag$Flag[ BYind ] & D$CompleteBYFlag$Flag[BYind]){
#'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
TestCohortNum <- Cohort[ BYind, D$OceanStartAge ]
#'set survival rate of maxage+1 for use in AEQ equations below
SurvivalRate[ which(D$survivaldf$Age==D$MaxAge) + 1 ] <- SurvivalRate[ which(D$survivaldf$Age==D$MaxAge) ]
#'loop through each age
for( age in D$LastAge[BYind]:D$OceanStartAge ){
#'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
TotalCatch <- TotalCatch_Age(D, M, BY=BYind, age)
#'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod ){
sink("../logs/debug_terminalCatchID.log", append=TRUE)
cat(paste("2183 CalcCohort callTotalTerminalCatch_Age", M$ShakerMethod, BYind, age))
sink()
}
TotalTerminalCatch <- TotalTerminalCatch_Age(D, M, BYind, age)
#'subtract total terminal catch from total catch to get total PreTerm catch
TotalPreTermCatch <- TotalCatch - TotalTerminalCatch
if(M$isTraceCalc){
sink("../logs/debug_CohortID.log", append=TRUE)
cat(paste("line 1925","totCat", TotalCatch, "totTermCat", TotalTerminalCatch))
sink()
}
#'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
if( !D$CompleteBYFlag$Flag[BYind] & !is.na(D$CompleteBYFlag$Flag[BYind]) & age == D$LastAge[BYind] & pass > 1 ){
Cohort[BYind, age] <- CalcEstmCohrt2( D, M, BYind, age ) / D$survivaldf$SurvivalRate[ D$survivaldf$Age==age ]
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 compl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), SurvivalRate(age))
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod ){
sink("../logs/debug_Cohort_IncompleteBroodID.log", append=TRUE)
cat(paste("2158 CalcCohort", M$ShakerMethod, BYind, age, Cohort[BYind, D$OceanStartAge]))
sink()
}
}else{
Cohort[ BYind, age ] <- (Cohort[ BYind, age + 1 ] + D$Escape[ BYind, age ] + TotalCatch)/ SurvivalRate[ which(D$survivaldf$Age==age) ]
}
if( age == D$OceanStartAge & Cohort[BYind, D$OceanStartAge] == 0){
sink("../logs/debug_ERROR_noCWT.log", append=TRUE)
cat(paste("Brood Year ", allBY[BYind], " has NO CWT recoveries at all!"))
sink()
ErrCaption = paste("Brood Year ", allBY[BYind] , " has NO CWT recoveries at all! \n")
ErrMessage = paste("Hint: If the brood year has no recoveries, decrement last brood year in the .CM1 file and remove from the .CDS file.\n")
ErrMessage = paste(ErrMessage, " If intermediate brood year, treat as missing brood and remove from .CDS file.\n")
stop(paste(ErrCaption,ErrMessage))
}
CohortAfterPreTermFishery <- Cohort[ BYind, age ] * SurvivalRate[ age ] - TotalPreTermCatch
TerminalRun <- TotalTerminalCatch + D$Escape[ BYind, age ]
if( !D$ReadAvgMatRteFlg ){
#'rates not from ERA_Stock table, instead calculate from data
if( age == D$LastAge[ BYind ] & D$CompleteBYFlag$Flag[ BYind ] &!is.na(D$CompleteBYFlag$Flag[ BYind ])){
MatRate[ BYind, age ] <- 1
}else if( CohortAfterPreTermFishery <= 0 ){
MatRate[ BYind, age ] <- 0
}else{
MatRate[ BYind, age ] <- TerminalRun / CohortAfterPreTermFishery
if(M$isTraceCalc){
sink("../logs/debug_MatRteID.log", append=TRUE)
cat(paste("2189 MatRte", BYind, age, MatRate[ BYind, age ], TerminalRun, CohortAfterPreTermFishery,"\n"))
sink()
}
}
}else{
MatRate[ BYind, age ] <- D$AverageMatRate[ age-1 ]
}
# 'compute adult equivalent factor
if(age == D$LastAge[ BYind ] & !D$CompleteBYFlag$Flag[ BYind ]){
#'use average adult equivalent for incomplete brood
AEQ[ BYind, age ] <- MatRate[ BYind, age ] + ((1 - MatRate[ BYind, age ]) * SurvivalRate[ which(D$survivaldf$Age==age ) + 1 ] * AverageAEQ[age + 1])
}else{
AEQ[ BYind, age ] <- MatRate[ BYind, age ] + ((1 - MatRate[ BYind, age ]) * SurvivalRate[ which(D$survivaldf$Age==age) + 1 ] * AEQ[ BYind, age + 1 ] )
}
CohortBeforePreTermFishery <- Cohort[ BYind, age ] * SurvivalRate[ which(D$survivaldf$Age==age) ]
# 'Compute Ocean harvest rates
if(CohortBeforePreTermFishery > 0 ){
PreTermER[ BYind, age ] <- TotalPreTermCatch / CohortBeforePreTermFishery
}else{
PreTermER[ BYind, age ] <- 0
}
#parei aqui
if(M$LongTermAverage){
#ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
if(D$CompleteBYFlag$Flag[BYind]){
SumAEQ[age] <- SumAEQ[age] + AEQ[ BYind,age ]
SumPreTermER[age] <- SumPreTermER[age] + PreTermER[ BYind,age ]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
#'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
#'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
#'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
if( !D$ReadAvgMatRteFlg ){
SumMatRate[ age ] <- SumMatRate[ age ] + MatRate[ BYind, age ]
}
}
}else{
#'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average
#number of years specified BroodYear NumAvgYears
if(allBY[ BYind ] == D$LastCompleteBroodYear ){
for(BroodYearNumber in 1:NumAvgYears){
SumAEQ[age] <- SumAEQ[age] + AEQ[BYind - BroodYearNumber, age ]
SumPreTermER[age] <- sum(c(SumPreTermER[age], PreTermER[BYind - BroodYearNumber, age ]),na.rm=t)
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(!D$ReadAvgMatRteFlg){
#'rates not from .cm1 file, instead calculate from data
SumMatRate[age] <- SumMatRate[age] + MatRate[BYind - BroodYearNumber, age ]
}
}
NumberCompleteBroods <- NumAvgYears
}
}
}
ActDif <- 100 * (abs(Cohort[BYind, D$OceanStartAge] - TestCohortNum) / Cohort[BYind, D$OceanStartAge])
if( ActDif > M$TESTDIF & !RepeatPass ) RepeatPass <- TRUE
}
}
#'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
for(age in D$OceanStartAge:D$MaxAge){
if(NumberOceanCohorts[age] == 0){
#'there are never any ocean recoveries of this age
AveragePreTermER[age] <- 0
}else{
AveragePreTermER[age] <- SumPreTermER[age] / NumberOceanCohorts[age]
}
if(age != D$MaxAge){
#'rates not from ERA_Stock table, instead calculate from data
if(!D$ReadAvgMatRteFlg){
AverageMatRate[age] = SumMatRate[age] / NumberCompleteBroods
if(M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod){
sink("../logs/debug_AvgMatRteID.log", append=TRUE)
cat(paste("2178 avgMatRte", age, AverageMatRate[age], "accum", SumMatRate[age], "numBroods", NumberCompleteBroods,"\n"))
sink()
}
}
AverageAEQ[age] = SumAEQ[age] / NumberCompleteBroods
}else{
#'rate for oldest age not from .cm1 file, instead calculate from data
if(!D$ReadAvgMatRteFlg) AverageMatRate[D$MaxAge] <- 1
AverageAEQ[D$MaxAge] <- 1
}
}
#'PUT AVERAGE VALUES INTO ARRAYS FOR INCOMPLETE BROODS
for(BYind in seq_along(allBY) ){
if(!D$CompleteBYFlag$Flag[BYind]){
for(age in D$OceanStartAge:D$MaxAge){
AEQ[BYind, age] <- AverageAEQ[age]
MatRate[BYind, age] <- AverageMatRate[age]
PreTermER[BYind, age] <- AveragePreTermER[age]
}
}
}
return(list(new=list(Cohort=Cohort,
AEQ=AEQ,
MatRate=MatRate,
PreTermER= PreTermER,
AverageAEQ=AverageAEQ,
AverageMatRate =AverageMatRate,
AveragePreTermER=AveragePreTermER,
NumberOceanCohorts =NumberOceanCohorts,
SumAEQ = SumAEQ,
SumMatRate = SumMatRate,
SumPreTermER = SumPreTermER),
old=list(NumberCompleteBroods=NumberCompleteBroods,
RepeatPass= RepeatPass)
))
#original vb code
# Dim ActDif As Single
# Dim CohortAfterPreTermFishery As Single
# Dim CohortBeforePreTermFishery As Single
# Dim TerminalRun As Single
# Dim TotalCatch, TotalTerminalCatch As Single
# Dim TotalPreTermCatch As Single
# Dim NumberOceanCohorts(MaxAge) As Integer
# Dim SumAEQ(MaxAge) As Single
# Dim SumMatRate(MaxAge) As Single
# Dim SumPreTermER(MaxAge) As Single
# ReDim PreTermER(LastBY, MaxAge)
# ReDim AveragePreTermER(MaxAge)
# NumAvgYears = MatRateNumberBroods.NumBroodsUpDown.Value
# RepeatPass = False
# For BroodYear As Integer = FirstBY To LastBY
# 'skip all missing brood years
# If MissingBroodYearFlag(BroodYear) = False Then
# 'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
# TestCohortNum = Cohort(BroodYear, OceanStartAge)
# 'set survival rate of maxage+1 for use in AEQ equations below
# SurvivalRate(MaxAge + 1) = SurvivalRate(MaxAge)
# 'loop through each age
# For age As Integer = LastAge(BroodYear) To OceanStartAge Step -1
# 'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
# TotalCatch = TotalCatch_Age(BroodYear, age, pass)
# 'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2183 CalcCohort callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
# TotalTerminalCatch = TotalTerminalCatch_Age(BroodYear, age, pass)
# 'subtract total terminal catch from total catch to get total PreTerm catch
# TotalPreTermCatch = TotalCatch - TotalTerminalCatch
# If isTraceCalc = True Then WriteLine(debug_CohortID, "line 1925", "totCat", TotalCatch, "totTermCat", TotalTerminalCatch)
# 'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
# If CompleteBYFlag(BroodYear) = False And age = LastAge(BroodYear) And pass > 1 Then
# Cohort(BroodYear, age) = CalcEstmCohrt2(BroodYear, age) / SurvivalRate(age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "2158 CalcCohort", ShakerMethod, BroodYear, age, Cohort(BroodYear, age))
# Else
# Cohort(BroodYear, age) = (Cohort(BroodYear, age + 1) + Escape(BroodYear, age) + TotalCatch) / SurvivalRate(age)
# End If
#
# If age = OceanStartAge And Cohort(BroodYear, OceanStartAge) = 0 Then
# ErrCaption = "Brood Year " & BroodYear & " has NO CWT recoveries at all!"
# ErrMessage = "Hint: If the brood year has no recoveries, decrement last brood year in the .CM1 file and remove from the .CDS file."
# ErrMessage = ErrMessage & " If intermediate brood year, treat as missing brood and remove from .CDS file."
# Call PrintError(ErrMessage, ErrCaption)
# End If
# CohortAfterPreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age) - TotalPreTermCatch
# TerminalRun = TotalTerminalCatch + Escape(BroodYear, age)
# If ReadAvgMatRteFlg = False Then
# 'rates not from ERA_Stock table, instead calculate from data
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = True Then 'And CohortAfterPreTermFishery > 0 Then
# MatRate(BroodYear, age) = 1
# ElseIf CohortAfterPreTermFishery <= 0 Then
# MatRate(BroodYear, age) = 0
# Else
# MatRate(BroodYear, age) = TerminalRun / CohortAfterPreTermFishery
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2189 MatRte ", BroodYear, age, MatRate(BroodYear, age), TerminalRun, CohortAfterPreTermFishery)
# End If
# 'WriteLine(debugID, "calcCohort", BroodYear, age, ShakerMethod, MatRate(BroodYear, age))
# Else
# 'average mat. rates from ERA_Stock table
# MatRate(BroodYear, age) = AverageMatRate(age)
# End If
# 'compute adult equivalent factor
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = False Then 'use average adult equivalent for incomplete brood
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AverageAEQ(age + 1))
# Else
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AEQ(BroodYear, age + 1))
# End If
# CohortBeforePreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age)
# 'Compute Ocean harvest rates
# If CohortBeforePreTermFishery > 0 Then
# PreTermER(BroodYear, age) = TotalPreTermCatch / CohortBeforePreTermFishery
# Else
# PreTermER(BroodYear, age) = 0
# End If
# If LongTermAverage.Checked = True Then
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
# If CompleteBYFlag(BroodYear) = True Then
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# 'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
# 'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
# 'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
# If ReadAvgMatRteFlg = False Then 'rates not from ERA_Stock table, instead calculate from data
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear, age)
# End If
# End If
# Else
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average number of years specified BroodYear NumAvgYears
# If BroodYear = LastCompleteBroodYear Then
# For BroodYearNumber As Integer = 0 To NumAvgYears - 1
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear - BroodYearNumber, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear - BroodYearNumber, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = False Then 'rates not from .cm1 file, instead calculate from data
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear - BroodYearNumber, age)
# End If
# Next BroodYearNumber
# NumberCompleteBroods = NumAvgYears
# End If
# End If
# Next age
# ActDif = 100 * (System.Math.Abs(Cohort(BroodYear, OceanStartAge) - TestCohortNum) / Cohort(BroodYear, OceanStartAge))
# If ActDif > TESTDIF And RepeatPass = False Then RepeatPass = True
# End If
# Next BroodYear
# 'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
# For Age = OceanStartAge To MaxAge
# If NumberOceanCohorts(Age) = 0 Then
# 'there are never any ocean recoveries of this age
# AveragePreTermER(Age) = 0
# Else
# AveragePreTermER(Age) = SumPreTermER(Age) / NumberOceanCohorts(Age)
# End If
# If Age <> MaxAge Then
# 'rates not from ERA_Stock table, instead calculate from data
# If ReadAvgMatRteFlg = False Then
# AverageMatRate(Age) = SumMatRate(Age) / NumberCompleteBroods
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2178 avgMatRte", Age, AverageMatRate(Age), "accum", SumMatRate(Age), "numBroods", NumberCompleteBroods)
# End If
# AverageAEQ(Age) = SumAEQ(Age) / NumberCompleteBroods
# Else
# 'rate for oldest age not from .cm1 file, instead calculate from data
# If ReadAvgMatRteFlg = False Then AverageMatRate(MaxAge) = 1
# AverageAEQ(MaxAge) = 1
# End If
# Next Age
# 'PUT AVERAGE VALUES INTO ARRAYS FOR INCOMPLETE BROODS
# For BY = FirstBY To LastBY
# If CompleteBYFlag(BY) = False Then
# For Age = OceanStartAge To MaxAge
# AEQ(BY, Age) = AverageAEQ(Age)
# MatRate(BY, Age) = AverageMatRate(Age)
# PreTermER(BY, Age) = AveragePreTermER(Age)
# Next Age
# End If
# Next BY
}
#' @title CalcCohort_IncompleteBrood
#'
#' @description function where the actual ERA is done, this one is for incomplete cohorts only.
#'
#' @param M A list passed to StartCohortAnalysis_Click
#'
#' @param D A list containing stock specific info
#'
#' @details
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcCohort_IncompleteBrood <- function(D,M){
allBY <- D$FirstBY:D$LastBY
NumberOceanCohorts <- rep(0,D$MaxAge)
AvgAdltEqv <- rep(0,D$MaxAge)
SumAEQ <- rep(0,D$MaxAge)
#AverageAEQ <- NULL
SumMatRate <- rep(0,D$MaxAge)
SumPreTermER <- rep(0,D$MaxAge)
#AveragePreTermER <- NULL
AverageMatRate <- NULL
#PreTermER <- matrix(NA, nrow = length(allBY),ncol = 7 )
if("Cohort" %in% names(D)){
Cohort <- D$Cohort
}else{
Cohort <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("MatRate" %in% names(D)){
MatRate <- D$MatRate
}else{
MatRate <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("AEQ" %in% names(D)){
AEQ <- D$AEQ
}else{
AEQ <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("AEQ" %in% names(D)){
PreTermER <- D$PreTermER
}else{
PreTermER <- matrix(0, nrow = length(allBY),ncol = 7 )
}
if("AEQ" %in% names(D)){
AveragePreTermER <- D$AveragePreTermER
}else{
AveragePreTermER <- matrix(0, nrow = length(allBY),ncol = 7 )
}
#
#AEQ <- matrix(0, nrow=length(allBY),ncol = D$MaxAge + 1 )
#SumAEQ <- rep(0,D$MaxAge)
#SumPreTermER <- rep(0,D$MaxAge)
#NumberOceanCohorts <- rep(0,D$MaxAge)
#'determine the last complete brood year
LastCompleteBroodYear<-max(D$CompleteBYFlag$BY[D$CompleteBYFlag$Flag])
# 'Set AEQ, Mat rate, and ocean HR totals to 1 prior to calculating the products for use in a geometric mean, this eliminates multiplication by zero for the first BY in the avg. calcs.
if(!M$ArithmeticMeanFlag){
for(age in D$OceanStartAge:D$MaxAge){
SumAEQ[age] <- 1
SumPreTermER[age] <- 1
SumMatRate[age] <- 1
}
}
for(BroodYear in seq_along(allBY)){
#'if missing brood year, then skip to next brood year that is not missing
if(D$MissingBroodYearFlag$Flag[BroodYear]){
next
}
# 'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
TestCohortNum <- Cohort[BroodYear, OceanStartAge]
for(age in D$LastAge[BroodYear]:D$OceanStartAge){
#'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
TotalCatch <- TotalCatch_Age(D, M, BY=BroodYear, age)
#'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2340 CalcCohrt_inc callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
TotalTerminalCatch <- TotalTerminalCatch_Age(D, M, BY=BroodYear, age)
#'subtract total terminal catch from total catch to get total PreTerm catch
TotalPreTermCatch <- TotalCatch - TotalTerminalCatch
#'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "2078 CaclCohortinCompl BY", ShakerMethod, BroodYear, age, "totCat", TotalCatch, "totTermCat", TotalTerminalCatch)
if(!D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]] & age == D$LastAge[BroodYear] & pass > 1){
Cohort[BroodYear,age] <- CalcEstmCohrt2(D, M, BroodYear, age) / D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
#'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 compl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), SurvivalRate(age))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 CalcCohortincompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age))
}else{
Cohort[BroodYear, age] <- (Cohort[BroodYear, age + 1] + D$Escape[BroodYear, age] + TotalCatch) / D$survivaldf$SurvivalRate[D$survivaldf$Age==age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1821 CalcCohortinCompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), Cohort(BroodYear, age + 1), Escape(BroodYear, age), TotalCatch, SurvivalRate(age))
}
if(age == D$OceanStartAge & Cohort[BroodYear, D$OceanStartAge] == 0){
ErrCaption <- paste("Brood Year", BroodYear, "has NO CWT recoveries at all! \n")
ErrMessage <- paste("Hint: If the brood year has no recoveries, decrement last brood year")# in the .CM1 file and remove from the .CDS file."
ErrMessage <- paste(ErrMessage,"If intermediate brood year, treat as missing brood")# and remove from .CDS file."
error(paste(ErrCaption,ErrMessage))
}
CohortAfterPreTermFishery <- Cohort[BroodYear, age] * D$survivaldf$SurvivalRate[age] - TotalPreTermCatch
TerminalRun <- TotalTerminalCatch + D$Escape[BroodYear, age]
if(!D$ReadAvgMatRteFlg){
#'rates not from ERA_Stock table, instead calculate from data
if(age == D$LastAge[BroodYear] & D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]] & CohortAfterPreTermFishery > 0 ){
MatRate[BroodYear, age] <- 1
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2587 MatRte ", MatRate(BroodYear, age))
}else if(CohortAfterPreTermFishery <= 0){
MatRate[BroodYear, age] <- 0
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2590 MatRte ", MatRate(BroodYear, age))
}else{
MatRate[BroodYear, age] <- TerminalRun / CohortAfterPreTermFishery
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2591 MatRte ", CohortAfterPreTermFishery, Cohort(BroodYear, age), SurvivalRate(age), TotalPreTermCatch)
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2592 MatRte ", TerminalRun, TotalTerminalCatch, Escape(BroodYear, age))
#If isTraceCalc = True Then WriteLine(debug_MatRteID, "2593 MatRte ", ShakerMethod, BroodYear, age, MatRate(BroodYear, age), TerminalRun / RelRatio(BroodYear), CohortAfterPreTermFishery / RelRatio(BroodYear), TotalTerminalCatch / RelRatio(BroodYear), Escape(BroodYear, age) / RelRatio(BroodYear), Cohort(BroodYear, age) / RelRatio(BroodYear), SurvivalRate(age), TotalPreTermCatch / RelRatio(BroodYear), RelRatio(BroodYear))
}
#'If isTraceCalc = True And shakermethod = traceThisShakerMethod Then WriteLine(debugID, "incompleteBrood", BroodYear, age, ShakerMethod, MatRate(BroodYear, age))
}else{
#'average mat. rates from ERA_Stock table
MatRate[BroodYear, age] <- D$AverageMatRate[age]
}
#'compute adult equivalent factor
if(age == D$LastAge[BroodYear] & !D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==BroodYear]){
#'use average adult equivalent for incomplete brood
AEQ[BroodYear, age] <- MatRate[BroodYear, age] + ((1 - MatRate[BroodYear, age]) * D$survivaldf$SurvivalRate[D$survivaldf$Age==(age+1)] * AverageAEQ[age + 1])
}else{
AEQ[BroodYear, age] <- MatRate[BroodYear, age] + ((1 - MatRate[BroodYear, age]) * D$survivaldf$SurvivalRate[D$survivaldf$Age==(age+1)] * AEQ[BroodYear, age + 1])
}
CohortBeforePreTermFishery = Cohort[BroodYear, age] * D$survivaldf$SurvivalRate[D$survivaldf$Age == age]
#'Compute Ocean harvest rates
if(CohortBeforePreTermFishery > 0){
PreTermER[BroodYear, age] <- TotalPreTermCatch / CohortBeforePreTermFishery
}else{
PreTermER[BroodYear, age] <- 0
}
if(M$ArithmeticMeanFlag){
#'Summation of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in arithmetic mean
if(M$LongTermAverage){
#'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
if(D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]]){
SumAEQ[age] <- SumAEQ[age] + AEQ[BroodYear, age]
SumPreTermER[age] <- SumPreTermER[age] + PreTermER[BroodYear, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
#'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
#'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
#'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
if(!D$ReadAvgMatRteFlg){
#'rates not from ERA_Stock table, instead calculate from data
if(MatRate[BroodYear, age] == 0){
MatRate[BroodYear, age] <- 0.0000001
#'prevents SumMatRte = 0
}
SumMatRate[age] <- SumMatRate[age] + MatRate[BroodYear, age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2625 avgMatRte LTA", BroodYear, age, SumMatRate(age), MatRate(BroodYear, age))
}
}
}else{
#'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average number of years specified BroodYear NumAvgYears
if(allBY[BroodYear] == D$LastCompleteBroodYear){
for(BroodYearNumber in 0:(M$NumAvgYears - 1)){
SumAEQ[age] <- SumAEQ[age] + AEQ[BroodYear - BroodYearNumber, age]
SumPreTermER[age] <- SumPreTermER[age] + PreTermER[BroodYear - BroodYearNumber, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(!D$ReadAvgMatRteFlg){
if(MatRate[BroodYear - BroodYearNumber, age] == 0 ){
#'prevents SumMatRte = 0
MatRate[BroodYear - BroodYearNumber, age] = 0.0000001
}
SumMatRate[age] = SumMatRate[age] + MatRate[BroodYear - BroodYearNumber, age]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2638 avgMatRte", BroodYear - BroodYearNumber, age, SumMatRate(age), MatRate(BroodYear - BroodYearNumber, age))
}
}
#NumberCompleteBroods = NumAvgYears
}
}
}else{
#'Product of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in geometric mean
if(M$LongTermAverage){
#'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using longterm average
if(D$CompleteBYFlag$Flag[D$CompleteBYFlag$BY==allBY[BroodYear]]){
SumAEQ[age] <- SumAEQ[age] * AEQ[BroodYear, age]
if(PreTermER[BroodYear, age] == 0){
PreTermER[BroodYear, age] <- 0.0000001
}
SumPreTermER[age] <- SumPreTermER[age] * PreTermER[BroodYear, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(D$ReadAvgMatRteFlg == 0){
#'rates not from .cm1 file, instead calculate from data
if( MatRate[BroodYear, age] == 0){
#'prevents SumMatRte = 0
MatRate(BroodYear, age) <- 0.0000001
}
SumMatRate[age] = SumMatRate[age] * MatRate[BroodYear, age]
}
}
}else{
#'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using average number of years specified by NumAvgYears
if(BroodYear == D$LastCompleteBroodYear){
for(BY in 0:(M$NumAvgYears-1)){
SumAEQ[age] = SumAEQ[age] * AEQ[BroodYear - BY, age]
if(PreTermER[BroodYear, age] == 0){
PreTermER[BroodYear, age] <- 0.0000001
}
SumPreTermER[age] <- SumPreTermER[age] * PreTermER[BroodYear - BY, age]
NumberOceanCohorts[age] <- NumberOceanCohorts[age] + 1
if(D$ReadAvgMatRteFlg ==0 ){
#'rates not from .cm1 file, instead calculate from data
if(MatRate[BroodYear- BY,age] == 0){
#'prevents a TotMatRate of 0
MatRate[BroodYear - BY, age] <- 0.0000001
}
SumMatRate[age] <- SumMatRate[age] * MatRate[BroodYear - BY, age]
}
}
NumberCompleteBroods = NumAvgYears
}
}
}
}
ActDif = 100 * (abs(Cohort[BroodYear, OceanStartAge] - TestCohortNum)/ Cohort[BroodYear, OceanStartAge])
if(ActDif > TESTDIF & !D$RepeatPass ){
RepeatPass = True
}
}
#'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
for(age in D$OceanStartAge:D$MaxAge){
if(M$ArithmeticMeanFlag){
if(D$NumberOceanCohorts[age]==0){
#'there are never any ocean recoveries of this age
AveragePreTermER[age] <- 0
}else{
AverageMatRate[age] <- SumMatRate[age] / NumberCompleteBroods
}
if(age != D$MaxAge){
#'rates not from ERA_Stock table, instead calculate from data
if(!D$ReadAvgMatRteFlg){
AverageMatRate[age] <- SumMatRate[age] / NumberCompleteBroods
}
AverageAEQ[age] <- SumAEQ[age] / NumberCompleteBroods
}else{
#'rate for oldest age not from .cm1 file, instead calculate from data
if(!D$ReadAvgMatRteFlg){
AverageMatRate[D$MaxAge] <- 1
}
AverageAEQ[D$MaxAge] <- 1
}
}else{
#'if you want to use the geometric mean
if(D$NumberOceanCohorts[age]==0){
#'there are never any ocean recoveries of this age
AveragePreTermER[age] <- 0
}else{
AveragePreTermER[age] = SumPreTermER[age]^(1 / NumberOceanCohorts[age])
}
if(age != D$MaxAge){
if(D$ReadAvgMatRteFlg == 0){
#'rates not from .cm1 file, instead calculate from data
AverageMatRate[age] = SumMatRate[age] ^ (1 / D$NumberCompleteBroods)
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2379 avgMatRte", BroodYear, Age, AverageMatRate(Age), "accum", SumMatRate(Age), "numBroods", NumberCompleteBroods)
}
AverageAEQ[age] <- SumAEQ[age] ^ (1 / D$NumberCompleteBroods)
}else{
if(D$ReadAvgMatRteFlg){
#'rate for oldest age not from .cm1 file, instead calculate from data
AverageMatRate[MaxAge] <- 1
}
AverageAEQ[MaxAge] = 1
}
} #'ArithmeticMeanFlag = True
}
return(list(NumberOceanCohorts=NumberOceanCohorts,
SumAEQ=SumAEQ,
SumMatRate=SumMatRate,
SumPreTermER=SumPreTermER,
PreTermER=PreTermER,
AveragePreTermER=AveragePreTermER,
Cohort= Cohort,
MatRate=MatRate,
AEQ=AEQ,
))
#==========================================================
#Original VB code
# Dim ActDif As Single
# Dim AvgAdltEqv(MaxAge) As Single
# Dim BroodYear As Integer
# Dim CohortAfterPreTermFishery As Single
# Dim CohortBeforePreTermFishery As Single
# Dim LastCompleteBroodYear As Integer
# Dim TerminalRun As Single
# Dim TotalCatch, TotalTerminalCatch As Single
# Dim TotalPreTermCatch As Single
# Dim NumberOceanCohorts(MaxAge) As Integer
# Dim SumAEQ(MaxAge) As Single
# Dim SumMatRate(MaxAge) As Single
# Dim SumPreTermER(MaxAge) As Single
# ReDim PreTermER(LastBY, MaxAge)
# ReDim AveragePreTermER(MaxAge)
# NumAvgYears = MatRateNumberBroods.NumBroodsUpDown.Value
# RepeatPass = False
#
# 'determine the last complete brood year
# For BY = FirstBY To LastBY
# 'skip over missing brood years,
# If MissingBroodYearFlag(BY) = True Then BY = FindBY(BY)
# If CompleteBYFlag(BY) = True Then
# LastCompleteBroodYear = BY
# End If
# Next BY
# 'Set AEQ, Mat rate, and ocean HR totals to 1 prior to calculating the products for use in a geometric mean, this eliminates multiplication by zero for the first BY in the avg. calcs.
# If ArithmeticMeanFlag = False Then
# For Age = OceanStartAge To MaxAge
# SumAEQ(Age) = 1
# SumPreTermER(Age) = 1
# SumMatRate(Age) = 1
# Next Age
# End If
#
# For BroodYear = FirstBY To LastBY
# 'if missing brood year, then skip to next brood year that is not missing
# If MissingBroodYearFlag(BroodYear) = True Then BroodYear = FindBY(BroodYear)
# 'the first time, this sub is called then Cohort(BroodYear, OceanStartAge) is empty or zero
# TestCohortNum = Cohort(BroodYear, OceanStartAge)
# 'loop through each age
# For age = LastAge(BroodYear) To OceanStartAge Step -1
# 'sum up total catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff), first time through will just be landed catch
# TotalCatch = TotalCatch_Age(BroodYear, age, pass)
# 'sum up total terminal catch BroodYear age (landed catch + legal dropoff+ shakers + shakerdropoffs + legalCNR + sublegalCNR + legalCNRdropoff + sublegalCNRdropoff)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2340 CalcCohrt_inc callTotalTerminalCatch_Age", ShakerMethod, BroodYear, age)
# TotalTerminalCatch = TotalTerminalCatch_Age(BroodYear, age, pass)
# 'subtract total terminal catch from total catch to get total PreTerm catch
# TotalPreTermCatch = TotalCatch - TotalTerminalCatch
# 'estimate cohort size for last available age of an incomplete cohort, otherwise estimate cohort size from backwards cohort analysis
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "2078 CaclCohortinCompl BY", ShakerMethod, BroodYear, age, "totCat", TotalCatch, "totTermCat", TotalTerminalCatch)
# If CompleteBYFlag(BroodYear) = False And age = LastAge(BroodYear) And pass > 1 Then
# Cohort(BroodYear, age) = CalcEstmCohrt2(BroodYear, age) / SurvivalRate(age)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod And BroodYear>= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 compl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), SurvivalRate(age))
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_Cohort_IncompleteBroodID, "1818 CalcCohortincompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age))
# Else
# Cohort(BroodYear, age) = (Cohort(BroodYear, age + 1) + Escape(BroodYear, age) + TotalCatch) / SurvivalRate(age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1821 CalcCohortinCompl BY", ShakerMethod, BroodYear, age, Cohort(BroodYear, age), Cohort(BroodYear, age + 1), Escape(BroodYear, age), TotalCatch, SurvivalRate(age))
# End If
#
# If age = OceanStartAge And Cohort(BroodYear, OceanStartAge) = 0 Then
# ErrCaption = "Brood Year " & BroodYear & " has NO CWT recoveries at all!"
# ErrMessage = "Hint: If the brood year has no recoveries, decrement last brood year in the .CM1 file and remove from the .CDS file."
# ErrMessage = ErrMessage & " If intermediate brood year, treat as missing brood and remove from .CDS file."
# Call PrintError(ErrMessage, ErrCaption)
# End If
# CohortAfterPreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age) - TotalPreTermCatch
# TerminalRun = TotalTerminalCatch + Escape(BroodYear, age)
# If ReadAvgMatRteFlg = False Then
# 'rates not from ERA_Stock table, instead calculate from data
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = True And CohortAfterPreTermFishery > 0 Then
# MatRate(BroodYear, age) = 1
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2587 MatRte ", MatRate(BroodYear, age))
# ElseIf CohortAfterPreTermFishery <= 0 Then
# MatRate(BroodYear, age) = 0
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2590 MatRte ", MatRate(BroodYear, age))
# Else
# MatRate(BroodYear, age) = TerminalRun / CohortAfterPreTermFishery
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2591 MatRte ", CohortAfterPreTermFishery, Cohort(BroodYear, age), SurvivalRate(age), TotalPreTermCatch)
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2592 MatRte ", TerminalRun, TotalTerminalCatch, Escape(BroodYear, age))
# If isTraceCalc = True Then WriteLine(debug_MatRteID, "2593 MatRte ", ShakerMethod, BroodYear, age, MatRate(BroodYear, age), TerminalRun / RelRatio(BroodYear), CohortAfterPreTermFishery / RelRatio(BroodYear), TotalTerminalCatch / RelRatio(BroodYear), Escape(BroodYear, age) / RelRatio(BroodYear), Cohort(BroodYear, age) / RelRatio(BroodYear), SurvivalRate(age), TotalPreTermCatch / RelRatio(BroodYear), RelRatio(BroodYear))
# End If
# 'If isTraceCalc = True And shakermethod = traceThisShakerMethod Then WriteLine(debugID, "incompleteBrood", BroodYear, age, ShakerMethod, MatRate(BroodYear, age))
# Else
# 'average mat. rates from ERA_Stock table
# MatRate(BroodYear, age) = AverageMatRate(age)
# End If
#
# 'compute adult equivalent factor
# If age = LastAge(BroodYear) And CompleteBYFlag(BroodYear) = False Then 'use average adult equivalent for incomplete brood
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AverageAEQ(age + 1))
# Else
# AEQ(BroodYear, age) = MatRate(BroodYear, age) + ((1 - MatRate(BroodYear, age)) * SurvivalRate(age + 1) * AEQ(BroodYear, age + 1))
# End If
# CohortBeforePreTermFishery = Cohort(BroodYear, age) * SurvivalRate(age)
# 'Compute Ocean harvest rates
# If CohortBeforePreTermFishery > 0 Then
# PreTermER(BroodYear, age) = TotalPreTermCatch / CohortBeforePreTermFishery
# Else
# PreTermER(BroodYear, age) = 0
# End If
# If ArithmeticMeanFlag = True Then 'Summation of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in arithmetic mean
# If LongTermAverage.Checked = True Then
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using longterm average
# If CompleteBYFlag(BroodYear) = True Then
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# 'ACCUMULATE MATURATION RATES IF NOT USING INPUT AVERAGE
# 'note: because AverageMatRate(age) = SumMatRate(age) / NumberCompleteBroods%
# 'therefore SumMatRate(age) is not needed or used if ReadAvgMatRteFlg% = 1
# If ReadAvgMatRteFlg = False Then 'rates not from ERA_Stock table, instead calculate from data
# If MatRate(BroodYear, age) = 0 Then MatRate(BroodYear, age) = 0.0000001 'prevents SumMatRte = 0
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear, age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2625 avgMatRte LTA", BroodYear, age, SumMatRate(age), MatRate(BroodYear, age))
# End If
# End If
# Else
# 'ACCUMULATE ADULT EQUIVALENTS AND MATURATION RATES FOR COMPLETE BROODS using average number of years specified BroodYear NumAvgYears
# If BroodYear = LastCompleteBroodYear Then
# For BroodYearNumber = 0 To NumAvgYears - 1
# SumAEQ(age) = SumAEQ(age) + AEQ(BroodYear - BroodYearNumber, age)
# SumPreTermER(age) = SumPreTermER(age) + PreTermER(BroodYear - BroodYearNumber, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = False Then 'rates not from .cm1 file, instead calculate from data
# If MatRate(BroodYear - BroodYearNumber, age) = 0 Then MatRate(BroodYear - BroodYearNumber, age) = 0.0000001 'prevents SumMatRte = 0
# SumMatRate(age) = SumMatRate(age) + MatRate(BroodYear - BroodYearNumber, age)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2638 avgMatRte", BroodYear - BroodYearNumber, age, SumMatRate(age), MatRate(BroodYear - BroodYearNumber, age))
# End If
# Next BroodYearNumber
# NumberCompleteBroods = NumAvgYears
# End If
# End If
# Else 'Product of ADULT EQUIVALENTS,MATURATION RATES, and Ocean HRs FOR COMPLETE BROODS, for use in geometric mean
# If LongTermAverage.Checked = True Then 'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using longterm average
# If CompleteBYFlag(BroodYear) = True Then
# SumAEQ(age) = SumAEQ(age) * AEQ(BroodYear, age)
# If PreTermER(BroodYear, age) = 0 Then PreTermER(BroodYear, age) = 0.0000001
# SumPreTermER(age) = SumPreTermER(age) * PreTermER(BroodYear, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = 0 Then 'rates not from .cm1 file, instead calculate from data
# If MatRate(BroodYear, age) = 0 Then MatRate(BroodYear, age) = 0.0000001 'prevents SumMatRte = 0
# SumMatRate(age) = SumMatRate(age) * MatRate(BroodYear, age)
# End If
# End If
# Else 'Product of ADULT EQUIVALENTS AND MATURATION RATES and Ocean HRs FOR COMPLETE BROODS using average number of years specified by NumAvgYears
# If BroodYear = LastCompleteBroodYear Then
# For BY = 0 To NumAvgYears - 1
# SumAEQ(age) = SumAEQ(age) * AEQ(BroodYear - BY, age)
# If PreTermER(BroodYear, age) = 0 Then PreTermER(BroodYear, age) = 0.0000001
# SumPreTermER(age) = SumPreTermER(age) * PreTermER(BroodYear - BY, age)
# NumberOceanCohorts(age) = NumberOceanCohorts(age) + 1
# If ReadAvgMatRteFlg = 0 Then 'rates not from .cm1 file, instead calculate from data
# If MatRate(BroodYear - BY, age) = 0 Then MatRate(BroodYear - BY, age) = 0.0000001 'prevents a TotMatRate of 0
# SumMatRate(age) = SumMatRate(age) * MatRate(BroodYear - BY, age)
# End If
# Next BY
# NumberCompleteBroods = NumAvgYears
# End If
# End If
# End If
# Next age
# ActDif = 100 * (System.Math.Abs(Cohort(BroodYear, OceanStartAge) - TestCohortNum) / Cohort(BroodYear, OceanStartAge))
# If ActDif > TESTDIF And RepeatPass = False Then RepeatPass = True
# Next BroodYear
# 'COMPUTE AVERAGE MATURATION RATES, OCEAN HARVEST RATES, AND ADULT EQUIVALENTS
# For Age = OceanStartAge To MaxAge
# If ArithmeticMeanFlag = True Then
# If NumberOceanCohorts(Age) = 0 Then
# 'there are never any ocean recoveries of this age
# AveragePreTermER(Age) = 0
# Else
# AveragePreTermER(Age) = SumPreTermER(Age) / NumberOceanCohorts(Age)
# End If
# If Age <> MaxAge Then
# 'rates not from ERA_Stock table, instead calculate from data
# If ReadAvgMatRteFlg = False Then
# AverageMatRate(Age) = SumMatRate(Age) / NumberCompleteBroods
# End If
# AverageAEQ(Age) = SumAEQ(Age) / NumberCompleteBroods
# Else
# 'rate for oldest age not from .cm1 file, instead calculate from data
# If ReadAvgMatRteFlg = False Then AverageMatRate(MaxAge) = 1
# AverageAEQ(MaxAge) = 1
# End If
# Else 'if you want to use the geometric mean
# If NumberOceanCohorts(Age) = 0 Then
# 'there are never any ocean recoveries of this age
# AveragePreTermER(Age) = 0
# Else
# AveragePreTermER(Age) = SumPreTermER(Age) ^ (1 / NumberOceanCohorts(Age))
# End If
# If Age <> MaxAge Then
# If ReadAvgMatRteFlg = 0 Then 'rates not from .cm1 file, instead calculate from data
# AverageMatRate(Age) = SumMatRate(Age) ^ (1 / NumberCompleteBroods)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_AvgMatRteID, "2379 avgMatRte", BroodYear, Age, AverageMatRate(Age), "accum", SumMatRate(Age), "numBroods", NumberCompleteBroods)
# End If
# AverageAEQ(Age) = SumAEQ(Age) ^ (1 / NumberCompleteBroods)
# Else
# If ReadAvgMatRteFlg = 0 Then AverageMatRate(MaxAge) = 1 'rate for oldest age not from .cm1 file, instead calculate from data
# AverageAEQ(MaxAge) = 1
# End If
# End If 'ArithmeticMeanFlag = True
# Next Age
#
# }
#
#}
}
#' @title CalcEstmCohrt2
#'
#' @description .
#'
#' @param BroodYear integer indicating brood year
#'
#' @param Age integer indicating age
#'
#' @details
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcEstmCohrt2 <- function( D, M, BroodYear,Age ){
#print("Enter CalcEstmCohrt2")
#'This subroutine increases current age cohort sizes to correct for the lack of
#'recoveries in older age classes in incomplete brood years (used by Calendar Year shaker
#'option and Brood Year shaker option with oldest age and in final calculation of harvest rates).
#'local variables
#BroodYear<-BYind
#Age<-age
if( D$MissingBroodYearFlag$Flag[BroodYear] ){
return(NULL)
}else{
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod ){
sink("../logs/debug_terminalCatchID.log", append=TRUE)
cat(paste("2522 CalcEstmCohrt2 call TotalTerminalCatch_age",M$ShakerMethod,BroodYear, Age, "\n"))
sink()
}
TerminalRun <- TotalTerminalCatch_Age(D, M, BroodYear, D$LastAge[BroodYear]) + D$Escape[BroodYear, D$LastAge[BroodYear]]
#'USE AVERAGE MATURATION RATE TO ESTIMATE COHORT SIZE AFTER MATURATION FOR INCOMPLETE BROOD
Chort <- (1 - D$AverageMatRate[D$LastAge[BroodYear]]) * TerminalRun / D$AverageMatRate[D$LastAge[BroodYear]]
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear >= M$traceThisYear ){
sink("../logs/debug_Cohort_IncompleteBroodID.log", append=TRUE)
cat(paste("1991 calcestmcohrt2",M$ShakerMethod,BroodYear, Age,
Chort, "avgMatRte", D$AverageMatRate[D$LastAge[BroodYear]], "termRun", TerminalRun, "\n"))
sink()
}
#'RECONSTRUCT COHORT SIZES BroodYear ADDING CATCH, ESCAPEMENT, AND NATURAL MORTALITY
for( A in D$LastAge[BroodYear]:Age ){
Chort <- Chort + D$Escape[BroodYear, A] + TotalCatch_Age( D, M, BroodYear, A )
if( M$isTraceCalc & M$ShakerMethod == M$traceThisShakerMethod & BroodYear >= M$traceThisYear ){
sink("../logs/debug_Cohort_IncompleteBroodID.log", append=TRUE)
cat(paste("1996 calcestmcohrt2",M$ShakerMethod,BroodYear, A, "accum", Chort, "escape",
D$Escape[BroodYear, A], "totCat", TotalCatch_Age(D, M, BroodYear, A), "surv",
D$survivaldf$SurvivalRate[D$survivaldf$Age==A], "\n"))
sink()
}
if( A != Age ){ Chort = Chort/ D$survivaldf$SurvivalRate[D$survivaldf$Age==A] }
}
#'COHORT SIZE AFTER NATURAL MORTALITY
if( is.na(Chort) ){
return(0.0)
}else{
return(Chort)
}
}
#Function CalcEstmCohrt2(ByRef BroodYear As Integer, ByRef Age As Integer) As Single
#'This subroutine increases current age cohort sizes to correct for the lack of
#'recoveries in older age classes in incomplete brood years (used by Calendar Year shaker
#'option and Brood Year shaker option with oldest age and in final calculation of harvest rates).
#'local variables
#Dim Chort, TerminalRun As Single
#If MissingBroodYearFlag(BroodYear) = True Then Exit Function
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2522 CalcEstmCohrt2 call TotalTerminalCatch_age", ShakerMethod, BroodYear, Age)
#
#TerminalRun = TotalTerminalCatch_Age(BroodYear, LastAge(BroodYear), pass) + Escape(BroodYear, LastAge(BroodYear))
#'USE AVERAGE MATURATION RATE TO ESTIMATE COHORT SIZE AFTER MATURATION FOR INCOMPLETE BROOD
#Chort = (1 - AverageMatRate(LastAge(BroodYear))) * TerminalRun / AverageMatRate(LastAge(BroodYear))
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1991 calcestmcohrt2", ShakerMethod, BroodYear, Age, Chort, "avgMatRte", AverageMatRate(LastAge(BroodYear)), "termRun", TerminalRun)
#'RECONSTRUCT COHORT SIZES BroodYear ADDING CATCH, ESCAPEMENT, AND NATURAL MORTALITY
#For A As Integer = LastAge(BroodYear) To Age Step -1
# Chort = Chort + Escape(BroodYear, A) + TotalCatch_Age(BroodYear, A, pass)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1996 calcestmcohrt2", ShakerMethod, BroodYear, A, "accum", Chort, "escape", Escape(BroodYear, A), "totCat", TotalCatch_Age(BroodYear, A, pass), "surv", SurvivalRate(A))
# If A <> Age Then Chort = Chort / SurvivalRate(A)
#Next A
#'COHORT SIZE AFTER NATURAL MORTALITY
#If Single.IsNaN(Chort) Then
# CalcEstmCohrt2 = 0.0
#
#Else
# CalcEstmCohrt2 = Chort
#
#End If
#End Function
}
#' @title CalcEstmCohrt
#'
#' @description .
#'
#' @param BroodYear integer indicating brood year
#'
#' @param Age integer indicating age
#'
#' @details This subroutine estimates future age cohort sizes so that shakers can be
#' calculated for incomplete brood years (Brood Year shaker option only).
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
CalcEstmCohrt <- function( D, M, BY,Age ){
#print("Enter CalcEstmCohrt")
stopifnot(!D$MissingBroodYearFlag$Flag[BY])
for(CurrAge in (D$LastAge[BY]+1):Age){
PrevAge <- CurrAge - 1
if(PrevAge == D$LastAge[BY]){
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2501 CalcEstmCohrt call TotalTerminalCatch_Age", ShakerMethod, BroodYear, Age)
MatRun <- TotalTerminalCatch_Age(D, M, BY, PrevAge, D$pass) + D$Escape[BY, PrevAge]
}else{
#'Use Average Ocean Harvest Rate at current age and Avg Maturity Rate to
#'estimate mature run
MatRun <- cohrt * (1 - D$AveragePreTermER[CurrAge]) * D$AverageMatRate[PrevAge]
}
#'Use Avg Mat Rate to estimate incomplete cohort
cohrt <- (1 - D$AverageMatRate[PrevAge]) * MatRun / D$AverageMatRate[PrevAge]
#If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1974 calcestmcohrt", ShakerMethod, BroodYear, CurrAge, cohrt, (1 - AverageMatRate(PrevAge)), MatRun, AverageMatRate(PrevAge))
cohrt <- cohrt * D$survivaldf$SurvivalRate[D$survivaldf$Age==CurrAge]
}
if(is.na(cohrt)){
CalcEstmCohrt <- 0
}else{
CalcEstmCohrt <- cohrt
}
return(CalcEstmCohrt)
#========================================================================
#Original vb code
#========================================================================
#'This subroutine estimates future age cohort sizes so that shakers can be
# 'calculated for incomplete brood years (Brood Year shaker option only).
# Dim cohrt, MatRun As Single
# Dim CurrAge, PrevAge As Integer
# If MissingBroodYearFlag(BroodYear) = True Then Exit Function
# For CurrAge = LastAge(BroodYear) + 1 To Age
# PrevAge = CurrAge - 1
# If PrevAge = LastAge(BroodYear) Then
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod Then WriteLine(debug_terminalCatchID, "2501 CalcEstmCohrt call TotalTerminalCatch_Age", ShakerMethod, BroodYear, Age)
#
# MatRun = TotalTerminalCatch_Age(BroodYear, PrevAge, pass) + Escape(BroodYear, PrevAge)
# Else
# 'Use Average Ocean Harvest Rate at current age and Avg Maturity Rate to
# 'estimate mature run
# MatRun = cohrt * (1 - AveragePreTermER(CurrAge)) * AverageMatRate(PrevAge)
# End If
# 'Use Avg Mat Rate to estimate incomplete cohort
# cohrt = (1 - AverageMatRate(PrevAge)) * MatRun / AverageMatRate(PrevAge)
# If isTraceCalc = True And ShakerMethod = traceThisShakerMethod And BroodYear >= traceThisYear Then WriteLine(debug_Cohort_IncompleteBroodID, "1974 calcestmcohrt", ShakerMethod, BroodYear, CurrAge, cohrt, (1 - AverageMatRate(PrevAge)), MatRun, AverageMatRate(PrevAge))
# cohrt = cohrt * SurvivalRate(CurrAge)
# Next CurrAge
# If Single.IsNaN(cohrt) Then
# CalcEstmCohrt = 0.0
# Else
#
# CalcEstmCohrt = cohrt
# End If
}
#' @title FindBY
#'
#' @description .
#'
#' @param BY integer indicating brood year
#'
#' @details 'give a brood year where Brood(BY%).MissingByFlg = true
#' 'return the next brood year where Brood(BY%).MissingByFlg = false
#'
#'
#' @return
#'
#' @export
#'
#' @examples
#'
#'
FindBY <- function(BY, D){
#'give a brood year where Brood(BY%).MissingByFlg = true
#'return the next brood year where Brood(BY%).MissingByFlg = false
BY <- BY + 1
while(D$MissingBroodYearFlag$Flag[BY]){
if(BY > D$LastBY){
BY <- D$LastBY
break
}else{
BY <- BY + 1
}
}
return(BY)
#-------------------------------------
#Original VB code
#'give a brood year where Brood(BY%).MissingByFlg = true
# 'return the next brood year where Brood(BY%).MissingByFlg = false
# Do
# by = by + 1
# If by > LastBY Then
# by = LastBY
# Exit Do
# End If
# Loop Until MissingBroodYearFlag(by) = False
# FindBY = by
}
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