R/func_GetIMData.R
In catarinawor/ERAR: This package is a loose translation of the Chinook Technical committee ERA model
Defines functions
GetIMData
#=======================================================
#ERA function GetFirstAndLastBY()
#Translated from VB ERA CIS code
#October 2018
#Author: Catarina Wor
#=======================================================
#=======================================================
#source(utils.R)
#' @title GetIMData
#'
#' @description Get incidental mortality data based on Calendar years and PNV Region (whatever that is).
#'
#'
#'
#' @param M A list passed to MainSub
#' @param D A list containing the outputs of GetWithinBYWeightFlagAndPNVRegionAndAvgMatRates
#'
#' @details This function was directly translated from the VB code, and as is it is extermely unneficient in R.
#' Think about linearizing all the outputs as this program evolves
#'
#' @return D: A list
#'
#'
#'
#' @export
#'
#' @examples
#'
#' @importFrom tidyr spread
#'
#'
GetIMData <- function( D,M ){
# ReDimension Incidental Mortality variables
#Coshak PSL file has 1 more year of data than recoveries
PNV <- list() #array(NA, dim = c(M$LastCalendarYear + 1, M$NumberPSCFisheries, D$MaxAge))
PV <- list() #array(NA, dim = c(M$LastCalendarYear + 1, M$NumberPSCFisheries, D$MaxAge))
#Read in data from ERA_IMInputs table based on the PNVRegion of the stock, Terminal fisheries are specific to a PNVRegion, Preterminal fisheries data is from PNVRegion 1 ("All")
#only get values <= LastCalendarYear unless when emulating Coshak
# Dim CalendarYear, PSCFishery As Integer
# if(!isReplicateCohShak){
# dta <- RODBC::odbcConnectAccess2007(M$datbse)
ERASQL <- paste0( "SELECT ERA_IMInputs.* FROM ERA_IMInputs WHERE CalendarYear <= ", M$LastCalendarYear, " and (PNVRegion = 1 or PNVRegion = ", D$PNVRegion,") Order By PSCFishery, CalendarYear" )
#read from data base
df1 <- RODBC::sqlQuery( M$chnl , query = ERASQL )
#summary(df1)
PSCFishery <- df1$PSCFishery
CalendarYear <- df1$CalendarYear
SublegalIMRate <- tidyr::spread(df1[,c("SublegalIMRate","CalendarYear","PSCFishery")],key=PSCFishery,value=SublegalIMRate)
LegalIMRate <- tidyr::spread(df1[,c("LegalIMRate","CalendarYear","PSCFishery")],key=PSCFishery,value=LegalIMRate)
DropoffRate <- tidyr::spread(df1[,c("DropoffRate","CalendarYear","PSCFishery")],key=PSCFishery,value= DropoffRate)
df1$ExtraLegalIMRate[is.na(df1$ExtraLegalIMRate)] <- 0
ExtraLegalIMRate <- tidyr::spread(df1[,c("ExtraLegalIMRate","CalendarYear","PSCFishery")],key=PSCFishery,value=ExtraLegalIMRate)
CNRMethod <- tidyr::spread(df1[,c("CNRMethod","CalendarYear","PSCFishery")],key=PSCFishery,value=CNRMethod )
df1$RetentionMethod[is.na(df1$RetentionMethod)] <- 0
RetentionMethod <- tidyr::spread(df1[,c("RetentionMethod","CalendarYear","PSCFishery")],key=PSCFishery,value= RetentionMethod )
df1$CNRLegalEncounterEst[is.na(df1$CNRLegalEncounterEst)] <- 0
CNRLegalEncounterEst <- tidyr::spread(df1[,c("CNRLegalEncounterEst","CalendarYear","PSCFishery")],key=PSCFishery,value= CNRLegalEncounterEst )
df1$CNRSubLegalEncounterEst[is.na(df1$CNRSubLegalEncounterEst)] <- 0
CNRSubLegalEncounterEst <- df1$CNRSubLegalEncounterEst
df1$CNRExtraLegalEncounterEst[is.na(df1$CNRExtraLegalEncounterEst)]<- 0
CNRExtraLegalEncounterEst <- tidyr::spread(df1[,c("CNRExtraLegalEncounterEst","CalendarYear","PSCFishery")],key=PSCFishery,value= CNRExtraLegalEncounterEst )
df1$LandedCatchEst[is.na(df1$LandedCatchEst)] <- 0
LandedCatchEst <- tidyr::spread(df1[,c("LandedCatchEst","CalendarYear","PSCFishery")],key=PSCFishery,value=LandedCatchEst )
df1$LegalShakerEst[is.na(df1$LegalShakerEst)] <- 0
LegalShakerEst <- tidyr::spread(df1[,c("LegalShakerEst","CalendarYear","PSCFishery")],key=PSCFishery,value= LegalShakerEst )
df1$SubLegalShakerEst[is.na(df1$SubLegalShakerEst)] <- 0
SubLegalShakerEst <- tidyr::spread(df1[,c("SubLegalShakerEst","CalendarYear","PSCFishery")],key=PSCFishery,value=SubLegalShakerEst )
df1$ExtraLegalShakerEst[is.na(df1$ExtraLegalShakerEst)] <-0
ExtraLegalShakerEst <- tidyr::spread(df1[,c("ExtraLegalShakerEst","CalendarYear","PSCFishery")],key=PSCFishery,value= ExtraLegalShakerEst )
df1$LegalSelectivityFactor[is.na(df1$LegalSelectivityFactor)] <-0
LegalSelectivityFactor <- tidyr::spread(df1[,c("LegalSelectivityFactor","CalendarYear","PSCFishery")],key=PSCFishery,value=LegalSelectivityFactor )
df1$SublegalSelectivityFactor[is.na(df1$SublegalSelectivityFactor)] <- 0
SublegalSelectivityFactor <- tidyr::spread(df1[,c("SublegalSelectivityFactor","CalendarYear","PSCFishery")],key=PSCFishery,value=SublegalSelectivityFactor )
df1$ExtraLegalSelectivityFactor[is.na(df1$ExtraLegalSelectivityFactor)] <- 0
ExtraLegalSelectivityFactor <- tidyr::spread(df1[,c("ExtraLegalSelectivityFactor","CalendarYear","PSCFishery")],key=PSCFishery,value=ExtraLegalSelectivityFactor )
df1$MonitoredLegalCatch[is.na(df1$MonitoredLegalCatch)] <- 0
MonitoredLegalCatch <- tidyr::spread(df1[,c("MonitoredLegalCatch","CalendarYear","PSCFishery")],key=PSCFishery,value= MonitoredLegalCatch )
df1$MonitoredLegalReleases[is.na(df1$MonitoredLegalReleases)] <- 0
MonitoredLegalReleases <- tidyr::spread(df1[,c("MonitoredLegalReleases","CalendarYear","PSCFishery")],key=PSCFishery,value= MonitoredLegalReleases )
df1$SeasonUnits[is.na(df1$SeasonUnits)] <- 0
SeasonUnits <- tidyr::spread(df1[,c("SeasonUnits","CalendarYear","PSCFishery")],key=PSCFishery,value= SeasonUnits )
df1$SeasonLength[is.na(df1$SeasonLength)] <- 0
SeasonLength <- tidyr::spread(df1[,c("SeasonLength","CalendarYear","PSCFishery")],key=PSCFishery,value= SeasonLength )
df1$CNRSeasonLength[is.na(df1$CNRSeasonLength)] <- 0
CNRSeasonLength <- tidyr::spread(df1[,c("CNRSeasonLength","CalendarYear","PSCFishery")],key=PSCFishery,value= CNRSeasonLength )
df1$RetentionEffort[is.na(df1$RetentionEffort)] <- 0
RetentionEffort <- tidyr::spread(df1[,c("RetentionEffort","CalendarYear","PSCFishery")],key=PSCFishery,value=RetentionEffort )
df1$CNREffort[is.na(df1$CNREffort)] <- 0
CNREffort <- tidyr::spread(df1[,c("CNREffort","CalendarYear","PSCFishery")],key=PSCFishery,value= CNREffort )
df1$Reavailability[is.na(df1$Reavailability)] <- 0
Reavailability <- tidyr::spread(df1[,c("Reavailability","CalendarYear","PSCFishery")],key=PSCFishery,value=Reavailability )
PNV[[1]] <- tidyr::spread(df1[,c("Age2PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age2PNV )
PNV[[2]] <- tidyr::spread(df1[,c("Age3PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age3PNV )
PNV[[3]] <- tidyr::spread(df1[,c("Age4PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age4PNV )
PNV[[4]] <- tidyr::spread(df1[,c("Age5PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age5PNV )
PV[[1]]<- 1 - PNV[[1]]
PV[[2]]<- 1 - PNV[[2]]
PV[[3]]<- 1 - PNV[[3]]
PV[[4]]<- 1 - PNV[[4]]
LastIMDataYear <- max(CalendarYear)
# 'Assign Age 5 PNV to Age 6 for stocks that go from age 2 to age 6, necessary because we only have PNVs for four ages
if(D$OceanStartAge ==2 & D$MaxAge==6){
PNV[[5]]<-PNV[[4]]
PV[[5]]<-PV[[4]]
}
ERASQL2 <- paste0("SELECT PSCFishery,Age,SizeClass,AvgQ FROM ERA_CatchabilityCoefficients WHERE ERAStock = '", D$CurrentStock ,"' AND ShakerMethod = '" ,M$ShakerMethod ,"'")
df2 <- RODBC::sqlQuery( M$chnl , query = ERASQL2 )
GetIMDataErr <- 0
if(nrow(df2)==0){
sink("../logs/GetIMData.log", append=TRUE)
cat("Catchability coefficients for ",D$CurrentStock, " is missing in the ERA_CatchabilityCoefficients table. Program is going to stop.\n")
sink()
GetIMDataErr <- 1
}
#
df2select_L<- df2[df2$Age<D$MaxAge&df2$SizeClass=="L",c("PSCFishery", "Age", "AvgQ")]
LegalCatchabilityCoefficient <- tidyr::spread(df2select_L,key=PSCFishery,value=AvgQ)
df2select_S<- df2[df2$Age<D$MaxAge&df2$SizeClass!="L",c("PSCFishery", "Age", "AvgQ")]
SubLegalCatchabilityCoefficient <- tidyr::spread(df2select_L,key=PSCFishery,value=AvgQ)
return(list(IMdf=df1,catchabilitydf=df2, PNV=PNV,PV=PV,
GetIMDataErr=GetIMDataErr))
#return( list(IM_PSCFishery=PSCFishery,
# IM_CalendarYear=CalendarYear,
# SublegalIMRate=SublegalIMRate,
# LegalIMRate=LegalIMRate,
# DropoffRate=DropoffRate,
# ExtraLegalIMRate=ExtraLegalIMRate,
# CNRMethod=CNRMethod,
# RetentionMethod=RetentionMethod,
# CNRLegalEncounterEst=CNRLegalEncounterEst,
# CNRSubLegalEncounterEst=CNRSubLegalEncounterEst,
# CNRExtraLegalEncounterEst=CNRExtraLegalEncounterEst,
# LandedCatchEst=LandedCatchEst,
# LegalShakerEst=LegalShakerEst,
# SubLegalShakerEst=SubLegalShakerEst,
# ExtraLegalShakerEst=ExtraLegalShakerEst,
# LegalSelectivityFactor=LegalSelectivityFactor,
# SublegalSelectivityFactor=SublegalSelectivityFactor,
# ExtraLegalSelectivityFactor=ExtraLegalSelectivityFactor,
# MonitoredLegalCatch=MonitoredLegalCatch,
# MonitoredLegalReleases=MonitoredLegalReleases,
# SeasonUnits=SeasonUnits,
# SeasonLength=SeasonLength,
# CNRSeasonLength=CNRSeasonLength,
# RetentionEffort=RetentionEffort,
# CNREffort=CNREffort,
# Reavailability=Reavailability,
# PNV= PNV,
# PV=PV,
# LegalCatchabilityCoefficient=LegalCatchabilityCoefficient,
# SubLegalCatchabilityCoeificient=SubLegalCatchabilityCoeificient,
# GetIMDataErr=GetIMDataErr
# ))
#Original VB code
#===================================================================================
#'ReDimension Incidental Mortality variables
# 'Coshak PSL file has 1 more year of data than recoveries
# ReDim PNV(LastCalendarYear + 1, NumberPSCFisheries, MaxAge)
# ReDim PV(LastCalendarYear + 1, NumberPSCFisheries, MaxAge)
# ReDim LegalCatchabilityCoeifficient(MaxAge, NumberPSCFisheries)
# ReDim SubLegalCatchabilityCoeifficient(MaxAge, NumberPSCFisheries)
# ReDim CNRMethod(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim RetentionMethod(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRLegalEncounterEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRSubLegalEncounterEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRExtraLegalEncounterEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LandedCatchEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LegalShakerEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SubLegalShakerEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim ExtraLegalShakerEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim MonitoredLegalCatch(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim MonitoredLegalReleases(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SeasonUnits(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SeasonLength(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRSeasonLength(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim RetentionEffort(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNREffort(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim Reavailability(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SublegalIMRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LegalIMRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim ExtraLegalIMRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim DropoffRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LegalSelectivityFactor(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SublegalSelectivityFactor(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim ExtraLegalSelectivityFactor(LastCalendarYear + 1, NumberPSCFisheries)
#
# LastIMDataYear = 0
#
# 'Read in data from ERA_IMInputs table based on the PNVRegion of the stock, Terminal fisheries are specific to a PNVRegion, Preterminal fisheries data is from PNVRegion 1 ("All")
# 'only get values <= LastCalendarYear unless when emulating Coshak
# Dim CalendarYear, PSCFishery As Integer
# 'If isReplicateCohShak = False Then
# ERASQL = "SELECT ERA_IMInputs.* FROM ERA_IMInputs WHERE CalendarYear <= " & LastCalendarYear & " and (PNVRegion = 1 or PNVRegion = " & PNVRegion & ") Order By PSCFishery, CalendarYear"
# 'Else
# 'ERASQL = "SELECT ERA_IMInputs.* FROM ERA_IMInputs WHERE (PNVRegion = 1 or PNVRegion = " & PNVRegion & ") Order By PSCFishery, CalendarYear"
# 'End If
# ERACommand = New OleDbCommand(ERASQL, CISDBConnection)
# CISDataReader = ERACommand.ExecuteReader()
# Do While CISDataReader.Read()
# PSCFishery = CISDataReader(0)
# CalendarYear = CISDataReader(3)
# SublegalIMRate(CalendarYear, PSCFishery) = CISDataReader(4)
# LegalIMRate(CalendarYear, PSCFishery) = CISDataReader(5)
# DropoffRate(CalendarYear, PSCFishery) = CISDataReader(6)
# ExtraLegalIMRate(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(7)), CISDataReader(7), 0)
# CNRMethod(CalendarYear, PSCFishery) = CISDataReader(8)
# RetentionMethod(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(9)), CISDataReader(9), 0)
# CNRLegalEncounterEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(13)), CISDataReader(13), 0)
# CNRSubLegalEncounterEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(14)), CISDataReader(14), 0)
# CNRExtraLegalEncounterEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(15)), CISDataReader(15), 0)
# LandedCatchEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(16)), CISDataReader(16), 0)
# LegalShakerEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(17)), CISDataReader(17), 0)
# SubLegalShakerEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(18)), CISDataReader(18), 0)
# ExtraLegalShakerEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(19)), CISDataReader(19), 0)
# LegalSelectivityFactor(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(20)), CISDataReader(20), 0)
# SublegalSelectivityFactor(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(21)), CISDataReader(21), 0)
# ExtraLegalSelectivityFactor(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(22)), CISDataReader(22), 0)
# MonitoredLegalCatch(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(23)), CISDataReader(23), 0)
# MonitoredLegalReleases(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(24)), CISDataReader(24), 0)
# SeasonUnits(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(9)), CISDataReader(9), 0)
# SeasonLength(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(26)), CISDataReader(26), 0)
# CNRSeasonLength(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(27)), CISDataReader(27), 0)
# RetentionEffort(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(28)), CISDataReader(28), 0)
# CNREffort(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(29)), CISDataReader(29), 0)
# Reavailability(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(30)), CISDataReader(30), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge) = If(IsNumeric(CISDataReader(31)), CISDataReader(31), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge + 1) = If(IsNumeric(CISDataReader(32)), CISDataReader(32), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge + 2) = If(IsNumeric(CISDataReader(33)), CISDataReader(33), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge + 3) = If(IsNumeric(CISDataReader(34)), CISDataReader(34), 0)
# PV(CalendarYear, PSCFishery, OceanStartAge) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge)
# PV(CalendarYear, PSCFishery, OceanStartAge + 1) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge + 1)
# PV(CalendarYear, PSCFishery, OceanStartAge + 2) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge + 2)
# PV(CalendarYear, PSCFishery, OceanStartAge + 3) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge + 3)
# If CalendarYear > LastIMDataYear Then LastIMDataYear = CalendarYear
# Loop
# CISDataReader.Close()
# 'Assign Age 5 PNV to Age 6 for stocks that go from age 2 to age 6, necessary because we only have PNVs for four ages
# If OceanStartAge = 2 And MaxAge = 6 Then
# For CY As Integer = 1960 To LastCalendarYear 'set to 1960 to speed up the loop
# For Fish As Integer = 1 To NumberPSCFisheries
# PNV(CY, Fish, MaxAge) = PNV(CY, Fish, OceanStartAge + 3)
# PV(CY, Fish, MaxAge) = 1 - PNV(CY, Fish, MaxAge)
# Next Fish
# Next CY
# End If
# 'Read in data from catchability coefficients
# 'ERASQL = "SELECT PSCFishery,Age,SizeClass,AvgQ FROM ERA_CatchabilityCoefficients INNER JOIN PSCtoModelFisheryMapping ON ERA_CatchabilityCoefficients.ModelFishery = PSCtoModelFisheryMapping.ModelFishery WHERE ERAStock = '" & CurrentStock & "' AND ShakerMethod = '" & ShakerMethod & "'"
# ERASQL = "SELECT PSCFishery,Age,SizeClass,AvgQ FROM ERA_CatchabilityCoefficients WHERE ERAStock = '" & CurrentStock & "' AND ShakerMethod = '" & ShakerMethod & "'"
# ERACommand = New OleDbCommand(ERASQL, CISDBConnection)
# CISDataReader = ERACommand.ExecuteReader()
# If CISDataReader.HasRows Then
# Do While CISDataReader.Read()
# If Not CISDataReader(1) > MaxAge Then
# PSCFishery = CISDataReader(0)
# If CISDataReader(2) = "L" Then
# LegalCatchabilityCoeifficient(CISDataReader(1), PSCFishery) = CISDataReader(3)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod and ShakerMethod = "B" Then WriteLine(debug_CNRNoDirID, "1771 get IMdata", LegalCatchabilityCoeifficient(CISDataReader(1), PSCFishery), CISDataReader(1), PSCFishery)
# Else
# SubLegalCatchabilityCoeifficient(CISDataReader(1), PSCFishery) = CISDataReader(3)
# End If
# End If
# Loop
# CISDataReader.Close()
# Else
# 'exit sub
# MsgBox("Catchability coefficients for " & CurrentStock & " is missing in the ERA_CatchabilityCoefficients table. Program is going to stop.")
# End
# End If
}
catarinawor/ERAR documentation built on Sept. 21, 2019, 8:25 a.m.
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Defines functions GetIMData
#=======================================================
#ERA function GetFirstAndLastBY()
#Translated from VB ERA CIS code
#October 2018
#Author: Catarina Wor
#=======================================================
#=======================================================
#source(utils.R)
#' @title GetIMData
#'
#' @description Get incidental mortality data based on Calendar years and PNV Region (whatever that is).
#'
#'
#'
#' @param M A list passed to MainSub
#' @param D A list containing the outputs of GetWithinBYWeightFlagAndPNVRegionAndAvgMatRates
#'
#' @details This function was directly translated from the VB code, and as is it is extermely unneficient in R.
#' Think about linearizing all the outputs as this program evolves
#'
#' @return D: A list
#'
#'
#'
#' @export
#'
#' @examples
#'
#' @importFrom tidyr spread
#'
#'
GetIMData <- function( D,M ){
# ReDimension Incidental Mortality variables
#Coshak PSL file has 1 more year of data than recoveries
PNV <- list() #array(NA, dim = c(M$LastCalendarYear + 1, M$NumberPSCFisheries, D$MaxAge))
PV <- list() #array(NA, dim = c(M$LastCalendarYear + 1, M$NumberPSCFisheries, D$MaxAge))
#Read in data from ERA_IMInputs table based on the PNVRegion of the stock, Terminal fisheries are specific to a PNVRegion, Preterminal fisheries data is from PNVRegion 1 ("All")
#only get values <= LastCalendarYear unless when emulating Coshak
# Dim CalendarYear, PSCFishery As Integer
# if(!isReplicateCohShak){
# dta <- RODBC::odbcConnectAccess2007(M$datbse)
ERASQL <- paste0( "SELECT ERA_IMInputs.* FROM ERA_IMInputs WHERE CalendarYear <= ", M$LastCalendarYear, " and (PNVRegion = 1 or PNVRegion = ", D$PNVRegion,") Order By PSCFishery, CalendarYear" )
#read from data base
df1 <- RODBC::sqlQuery( M$chnl , query = ERASQL )
#summary(df1)
PSCFishery <- df1$PSCFishery
CalendarYear <- df1$CalendarYear
SublegalIMRate <- tidyr::spread(df1[,c("SublegalIMRate","CalendarYear","PSCFishery")],key=PSCFishery,value=SublegalIMRate)
LegalIMRate <- tidyr::spread(df1[,c("LegalIMRate","CalendarYear","PSCFishery")],key=PSCFishery,value=LegalIMRate)
DropoffRate <- tidyr::spread(df1[,c("DropoffRate","CalendarYear","PSCFishery")],key=PSCFishery,value= DropoffRate)
df1$ExtraLegalIMRate[is.na(df1$ExtraLegalIMRate)] <- 0
ExtraLegalIMRate <- tidyr::spread(df1[,c("ExtraLegalIMRate","CalendarYear","PSCFishery")],key=PSCFishery,value=ExtraLegalIMRate)
CNRMethod <- tidyr::spread(df1[,c("CNRMethod","CalendarYear","PSCFishery")],key=PSCFishery,value=CNRMethod )
df1$RetentionMethod[is.na(df1$RetentionMethod)] <- 0
RetentionMethod <- tidyr::spread(df1[,c("RetentionMethod","CalendarYear","PSCFishery")],key=PSCFishery,value= RetentionMethod )
df1$CNRLegalEncounterEst[is.na(df1$CNRLegalEncounterEst)] <- 0
CNRLegalEncounterEst <- tidyr::spread(df1[,c("CNRLegalEncounterEst","CalendarYear","PSCFishery")],key=PSCFishery,value= CNRLegalEncounterEst )
df1$CNRSubLegalEncounterEst[is.na(df1$CNRSubLegalEncounterEst)] <- 0
CNRSubLegalEncounterEst <- df1$CNRSubLegalEncounterEst
df1$CNRExtraLegalEncounterEst[is.na(df1$CNRExtraLegalEncounterEst)]<- 0
CNRExtraLegalEncounterEst <- tidyr::spread(df1[,c("CNRExtraLegalEncounterEst","CalendarYear","PSCFishery")],key=PSCFishery,value= CNRExtraLegalEncounterEst )
df1$LandedCatchEst[is.na(df1$LandedCatchEst)] <- 0
LandedCatchEst <- tidyr::spread(df1[,c("LandedCatchEst","CalendarYear","PSCFishery")],key=PSCFishery,value=LandedCatchEst )
df1$LegalShakerEst[is.na(df1$LegalShakerEst)] <- 0
LegalShakerEst <- tidyr::spread(df1[,c("LegalShakerEst","CalendarYear","PSCFishery")],key=PSCFishery,value= LegalShakerEst )
df1$SubLegalShakerEst[is.na(df1$SubLegalShakerEst)] <- 0
SubLegalShakerEst <- tidyr::spread(df1[,c("SubLegalShakerEst","CalendarYear","PSCFishery")],key=PSCFishery,value=SubLegalShakerEst )
df1$ExtraLegalShakerEst[is.na(df1$ExtraLegalShakerEst)] <-0
ExtraLegalShakerEst <- tidyr::spread(df1[,c("ExtraLegalShakerEst","CalendarYear","PSCFishery")],key=PSCFishery,value= ExtraLegalShakerEst )
df1$LegalSelectivityFactor[is.na(df1$LegalSelectivityFactor)] <-0
LegalSelectivityFactor <- tidyr::spread(df1[,c("LegalSelectivityFactor","CalendarYear","PSCFishery")],key=PSCFishery,value=LegalSelectivityFactor )
df1$SublegalSelectivityFactor[is.na(df1$SublegalSelectivityFactor)] <- 0
SublegalSelectivityFactor <- tidyr::spread(df1[,c("SublegalSelectivityFactor","CalendarYear","PSCFishery")],key=PSCFishery,value=SublegalSelectivityFactor )
df1$ExtraLegalSelectivityFactor[is.na(df1$ExtraLegalSelectivityFactor)] <- 0
ExtraLegalSelectivityFactor <- tidyr::spread(df1[,c("ExtraLegalSelectivityFactor","CalendarYear","PSCFishery")],key=PSCFishery,value=ExtraLegalSelectivityFactor )
df1$MonitoredLegalCatch[is.na(df1$MonitoredLegalCatch)] <- 0
MonitoredLegalCatch <- tidyr::spread(df1[,c("MonitoredLegalCatch","CalendarYear","PSCFishery")],key=PSCFishery,value= MonitoredLegalCatch )
df1$MonitoredLegalReleases[is.na(df1$MonitoredLegalReleases)] <- 0
MonitoredLegalReleases <- tidyr::spread(df1[,c("MonitoredLegalReleases","CalendarYear","PSCFishery")],key=PSCFishery,value= MonitoredLegalReleases )
df1$SeasonUnits[is.na(df1$SeasonUnits)] <- 0
SeasonUnits <- tidyr::spread(df1[,c("SeasonUnits","CalendarYear","PSCFishery")],key=PSCFishery,value= SeasonUnits )
df1$SeasonLength[is.na(df1$SeasonLength)] <- 0
SeasonLength <- tidyr::spread(df1[,c("SeasonLength","CalendarYear","PSCFishery")],key=PSCFishery,value= SeasonLength )
df1$CNRSeasonLength[is.na(df1$CNRSeasonLength)] <- 0
CNRSeasonLength <- tidyr::spread(df1[,c("CNRSeasonLength","CalendarYear","PSCFishery")],key=PSCFishery,value= CNRSeasonLength )
df1$RetentionEffort[is.na(df1$RetentionEffort)] <- 0
RetentionEffort <- tidyr::spread(df1[,c("RetentionEffort","CalendarYear","PSCFishery")],key=PSCFishery,value=RetentionEffort )
df1$CNREffort[is.na(df1$CNREffort)] <- 0
CNREffort <- tidyr::spread(df1[,c("CNREffort","CalendarYear","PSCFishery")],key=PSCFishery,value= CNREffort )
df1$Reavailability[is.na(df1$Reavailability)] <- 0
Reavailability <- tidyr::spread(df1[,c("Reavailability","CalendarYear","PSCFishery")],key=PSCFishery,value=Reavailability )
PNV[[1]] <- tidyr::spread(df1[,c("Age2PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age2PNV )
PNV[[2]] <- tidyr::spread(df1[,c("Age3PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age3PNV )
PNV[[3]] <- tidyr::spread(df1[,c("Age4PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age4PNV )
PNV[[4]] <- tidyr::spread(df1[,c("Age5PNV","CalendarYear","PSCFishery")],key=PSCFishery,value=Age5PNV )
PV[[1]]<- 1 - PNV[[1]]
PV[[2]]<- 1 - PNV[[2]]
PV[[3]]<- 1 - PNV[[3]]
PV[[4]]<- 1 - PNV[[4]]
LastIMDataYear <- max(CalendarYear)
# 'Assign Age 5 PNV to Age 6 for stocks that go from age 2 to age 6, necessary because we only have PNVs for four ages
if(D$OceanStartAge ==2 & D$MaxAge==6){
PNV[[5]]<-PNV[[4]]
PV[[5]]<-PV[[4]]
}
ERASQL2 <- paste0("SELECT PSCFishery,Age,SizeClass,AvgQ FROM ERA_CatchabilityCoefficients WHERE ERAStock = '", D$CurrentStock ,"' AND ShakerMethod = '" ,M$ShakerMethod ,"'")
df2 <- RODBC::sqlQuery( M$chnl , query = ERASQL2 )
GetIMDataErr <- 0
if(nrow(df2)==0){
sink("../logs/GetIMData.log", append=TRUE)
cat("Catchability coefficients for ",D$CurrentStock, " is missing in the ERA_CatchabilityCoefficients table. Program is going to stop.\n")
sink()
GetIMDataErr <- 1
}
#
df2select_L<- df2[df2$Age<D$MaxAge&df2$SizeClass=="L",c("PSCFishery", "Age", "AvgQ")]
LegalCatchabilityCoefficient <- tidyr::spread(df2select_L,key=PSCFishery,value=AvgQ)
df2select_S<- df2[df2$Age<D$MaxAge&df2$SizeClass!="L",c("PSCFishery", "Age", "AvgQ")]
SubLegalCatchabilityCoefficient <- tidyr::spread(df2select_L,key=PSCFishery,value=AvgQ)
return(list(IMdf=df1,catchabilitydf=df2, PNV=PNV,PV=PV,
GetIMDataErr=GetIMDataErr))
#return( list(IM_PSCFishery=PSCFishery,
# IM_CalendarYear=CalendarYear,
# SublegalIMRate=SublegalIMRate,
# LegalIMRate=LegalIMRate,
# DropoffRate=DropoffRate,
# ExtraLegalIMRate=ExtraLegalIMRate,
# CNRMethod=CNRMethod,
# RetentionMethod=RetentionMethod,
# CNRLegalEncounterEst=CNRLegalEncounterEst,
# CNRSubLegalEncounterEst=CNRSubLegalEncounterEst,
# CNRExtraLegalEncounterEst=CNRExtraLegalEncounterEst,
# LandedCatchEst=LandedCatchEst,
# LegalShakerEst=LegalShakerEst,
# SubLegalShakerEst=SubLegalShakerEst,
# ExtraLegalShakerEst=ExtraLegalShakerEst,
# LegalSelectivityFactor=LegalSelectivityFactor,
# SublegalSelectivityFactor=SublegalSelectivityFactor,
# ExtraLegalSelectivityFactor=ExtraLegalSelectivityFactor,
# MonitoredLegalCatch=MonitoredLegalCatch,
# MonitoredLegalReleases=MonitoredLegalReleases,
# SeasonUnits=SeasonUnits,
# SeasonLength=SeasonLength,
# CNRSeasonLength=CNRSeasonLength,
# RetentionEffort=RetentionEffort,
# CNREffort=CNREffort,
# Reavailability=Reavailability,
# PNV= PNV,
# PV=PV,
# LegalCatchabilityCoefficient=LegalCatchabilityCoefficient,
# SubLegalCatchabilityCoeificient=SubLegalCatchabilityCoeificient,
# GetIMDataErr=GetIMDataErr
# ))
#Original VB code
#===================================================================================
#'ReDimension Incidental Mortality variables
# 'Coshak PSL file has 1 more year of data than recoveries
# ReDim PNV(LastCalendarYear + 1, NumberPSCFisheries, MaxAge)
# ReDim PV(LastCalendarYear + 1, NumberPSCFisheries, MaxAge)
# ReDim LegalCatchabilityCoeifficient(MaxAge, NumberPSCFisheries)
# ReDim SubLegalCatchabilityCoeifficient(MaxAge, NumberPSCFisheries)
# ReDim CNRMethod(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim RetentionMethod(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRLegalEncounterEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRSubLegalEncounterEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRExtraLegalEncounterEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LandedCatchEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LegalShakerEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SubLegalShakerEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim ExtraLegalShakerEst(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim MonitoredLegalCatch(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim MonitoredLegalReleases(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SeasonUnits(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SeasonLength(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNRSeasonLength(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim RetentionEffort(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim CNREffort(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim Reavailability(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SublegalIMRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LegalIMRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim ExtraLegalIMRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim DropoffRate(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim LegalSelectivityFactor(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim SublegalSelectivityFactor(LastCalendarYear + 1, NumberPSCFisheries)
# ReDim ExtraLegalSelectivityFactor(LastCalendarYear + 1, NumberPSCFisheries)
#
# LastIMDataYear = 0
#
# 'Read in data from ERA_IMInputs table based on the PNVRegion of the stock, Terminal fisheries are specific to a PNVRegion, Preterminal fisheries data is from PNVRegion 1 ("All")
# 'only get values <= LastCalendarYear unless when emulating Coshak
# Dim CalendarYear, PSCFishery As Integer
# 'If isReplicateCohShak = False Then
# ERASQL = "SELECT ERA_IMInputs.* FROM ERA_IMInputs WHERE CalendarYear <= " & LastCalendarYear & " and (PNVRegion = 1 or PNVRegion = " & PNVRegion & ") Order By PSCFishery, CalendarYear"
# 'Else
# 'ERASQL = "SELECT ERA_IMInputs.* FROM ERA_IMInputs WHERE (PNVRegion = 1 or PNVRegion = " & PNVRegion & ") Order By PSCFishery, CalendarYear"
# 'End If
# ERACommand = New OleDbCommand(ERASQL, CISDBConnection)
# CISDataReader = ERACommand.ExecuteReader()
# Do While CISDataReader.Read()
# PSCFishery = CISDataReader(0)
# CalendarYear = CISDataReader(3)
# SublegalIMRate(CalendarYear, PSCFishery) = CISDataReader(4)
# LegalIMRate(CalendarYear, PSCFishery) = CISDataReader(5)
# DropoffRate(CalendarYear, PSCFishery) = CISDataReader(6)
# ExtraLegalIMRate(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(7)), CISDataReader(7), 0)
# CNRMethod(CalendarYear, PSCFishery) = CISDataReader(8)
# RetentionMethod(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(9)), CISDataReader(9), 0)
# CNRLegalEncounterEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(13)), CISDataReader(13), 0)
# CNRSubLegalEncounterEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(14)), CISDataReader(14), 0)
# CNRExtraLegalEncounterEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(15)), CISDataReader(15), 0)
# LandedCatchEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(16)), CISDataReader(16), 0)
# LegalShakerEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(17)), CISDataReader(17), 0)
# SubLegalShakerEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(18)), CISDataReader(18), 0)
# ExtraLegalShakerEst(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(19)), CISDataReader(19), 0)
# LegalSelectivityFactor(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(20)), CISDataReader(20), 0)
# SublegalSelectivityFactor(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(21)), CISDataReader(21), 0)
# ExtraLegalSelectivityFactor(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(22)), CISDataReader(22), 0)
# MonitoredLegalCatch(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(23)), CISDataReader(23), 0)
# MonitoredLegalReleases(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(24)), CISDataReader(24), 0)
# SeasonUnits(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(9)), CISDataReader(9), 0)
# SeasonLength(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(26)), CISDataReader(26), 0)
# CNRSeasonLength(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(27)), CISDataReader(27), 0)
# RetentionEffort(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(28)), CISDataReader(28), 0)
# CNREffort(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(29)), CISDataReader(29), 0)
# Reavailability(CalendarYear, PSCFishery) = If(IsNumeric(CISDataReader(30)), CISDataReader(30), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge) = If(IsNumeric(CISDataReader(31)), CISDataReader(31), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge + 1) = If(IsNumeric(CISDataReader(32)), CISDataReader(32), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge + 2) = If(IsNumeric(CISDataReader(33)), CISDataReader(33), 0)
# PNV(CalendarYear, PSCFishery, OceanStartAge + 3) = If(IsNumeric(CISDataReader(34)), CISDataReader(34), 0)
# PV(CalendarYear, PSCFishery, OceanStartAge) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge)
# PV(CalendarYear, PSCFishery, OceanStartAge + 1) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge + 1)
# PV(CalendarYear, PSCFishery, OceanStartAge + 2) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge + 2)
# PV(CalendarYear, PSCFishery, OceanStartAge + 3) = 1 - PNV(CalendarYear, PSCFishery, OceanStartAge + 3)
# If CalendarYear > LastIMDataYear Then LastIMDataYear = CalendarYear
# Loop
# CISDataReader.Close()
# 'Assign Age 5 PNV to Age 6 for stocks that go from age 2 to age 6, necessary because we only have PNVs for four ages
# If OceanStartAge = 2 And MaxAge = 6 Then
# For CY As Integer = 1960 To LastCalendarYear 'set to 1960 to speed up the loop
# For Fish As Integer = 1 To NumberPSCFisheries
# PNV(CY, Fish, MaxAge) = PNV(CY, Fish, OceanStartAge + 3)
# PV(CY, Fish, MaxAge) = 1 - PNV(CY, Fish, MaxAge)
# Next Fish
# Next CY
# End If
# 'Read in data from catchability coefficients
# 'ERASQL = "SELECT PSCFishery,Age,SizeClass,AvgQ FROM ERA_CatchabilityCoefficients INNER JOIN PSCtoModelFisheryMapping ON ERA_CatchabilityCoefficients.ModelFishery = PSCtoModelFisheryMapping.ModelFishery WHERE ERAStock = '" & CurrentStock & "' AND ShakerMethod = '" & ShakerMethod & "'"
# ERASQL = "SELECT PSCFishery,Age,SizeClass,AvgQ FROM ERA_CatchabilityCoefficients WHERE ERAStock = '" & CurrentStock & "' AND ShakerMethod = '" & ShakerMethod & "'"
# ERACommand = New OleDbCommand(ERASQL, CISDBConnection)
# CISDataReader = ERACommand.ExecuteReader()
# If CISDataReader.HasRows Then
# Do While CISDataReader.Read()
# If Not CISDataReader(1) > MaxAge Then
# PSCFishery = CISDataReader(0)
# If CISDataReader(2) = "L" Then
# LegalCatchabilityCoeifficient(CISDataReader(1), PSCFishery) = CISDataReader(3)
# 'If isTraceCalc = True and shakermethod = traceThisShakerMethod and ShakerMethod = "B" Then WriteLine(debug_CNRNoDirID, "1771 get IMdata", LegalCatchabilityCoeifficient(CISDataReader(1), PSCFishery), CISDataReader(1), PSCFishery)
# Else
# SubLegalCatchabilityCoeifficient(CISDataReader(1), PSCFishery) = CISDataReader(3)
# End If
# End If
# Loop
# CISDataReader.Close()
# Else
# 'exit sub
# MsgBox("Catchability coefficients for " & CurrentStock & " is missing in the ERA_CatchabilityCoefficients table. Program is going to stop.")
# End
# End If
}
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