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Copy pathPASCAL_v1.00_simulator.R
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PASCAL_v1.00_simulator.R
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Simulator <- function(){
#Object retrival - individual-specific parameters & other things
IND <- IterationID
StartPing <- STime[IND]
StartDepth <- SDepth[IND]
DV <- DVP[IND]
DVM <- DVPM[IND]
SD <- SDP[IND]
SA <- SAP[IND]
GA <- GAP[IND]
OD <- ODP[IND]
RAMSlo <- RAModel$coefficients[2]
RAMInt <- RAModel$coefficients[1]
LifetimeMaxCW <- WCrc[1, 3]
LifeState <- as.factor("ALIVE")
DiapauseStage <- NA
CessasionStage <- NA
DiapauseStartTime <- NA
DiapauseEndTime <- NA
DiapauseStartSW <- NA
FEPState <- 0
FEPTime <- NA
#ParOutput <- NULL
###############
#Egg-Nauplius I
###############
S <- 0
DTTrack <- NULL
CurrentCW <- .subset2(WCrc, 3)[(S + 1)]
CurrentSW <- 0
CurrentRW <- 0
Suvivorship <- 1
CurrentEggProduction <- 0
CurrentFitness <- 0
CurrentPing <- StartPing - 1
CurrentDepth <- StartDepth
repeat{
CurrentPing <- CurrentPing + 1
CurrentTemp <- .subset2(Temperature, CurrentPing)[CurrentDepth]
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentDT <- round(((EDF * (CurrentTemp + 9.11)^-2.05) * 24), 0)
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - CurrentPRisk)
DTTrack <- append(DTTrack, CurrentDT)
ElapsedPing <- CurrentPing - StartPing
if(Suvivorship < 0.0001){
LifeState <- as.factor("DEAD")
CessasionStage <- S
break
}else if(ElapsedPing >= mean(DTTrack)){
S <- 1
break
}else{
#Proceed iteration
}
}
#############################
#DVM Pre-processing directive
#############################
#DVPM Adjust - one time only
DVModel_PreC4 <- lm(c(DV, DV / DVM) ~ c(WCrc[1, 3], MFW))
DVModel_PostC4 <- lm(c(DV, DV / DVM) ~ c(WCrc[1, 3], MFW))
#############################
#Non-feeding nauplii (NI-NII)
#############################
if(LifeState == "DEAD"){
#Do nothing and proceed
}else{
repeat{
CurrentPing <- CurrentPing + 1
CurrentTWMG <- (CurrentCW * WCF) / 1000
MaxDistance <- round((3.7036 * CurrentCW^0.5853), 0)
MigrationCeiling <- CurrentDepth - MaxDistance
MigrationFloor <- CurrentDepth + MaxDistance
MigrationCeiling <- ifelse(MigrationCeiling < MinDepth, yes = MinDepth, no = MigrationCeiling)
MigrationFloor <- ifelse(MigrationFloor > MaxDepth, yes = MaxDepth, no = MigrationFloor)
SearchRange <- MigrationCeiling:MigrationFloor
DVAdj <- (CurrentCW * DVModel_PreC4$coefficients[2]) + DVModel_PreC4$coefficients[1]
CurrentVI <- .subset2(VIrad, CurrentPing)[CurrentDepth]
if(CurrentVI <= DVAdj){
#1.Growth potential estimation
TempRange <- .subset2(Temperature, CurrentPing)[SearchRange]
GmaxRange <- GEF * exp(0.110 * TempRange)
GPotentialRange <- GmaxRange * CurrentTWMG
#2.Decision making
GloTempRange <- .subset2(Temperature, CurrentPing)[1:100] #Values of upper 100m only used
GloGmaxRange <- GEF * exp(0.110 * GloTempRange)
GloGPotentialRange <- GloGmaxRange * CurrentTWMG
GPotentialMaxRange <- which(GPotentialRange == max(GPotentialRange)) #Set of index locations towards MinDepth -> MaxDepth
if(max(GPotentialRange) < max(GloGPotentialRange)){
GPotentialMaxPos <- min(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}else{
GPotentialMaxPos <- max(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}
#3.Final estimations
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * TempRange[GPotentialMaxPos])
m <- 0.858 * exp(-0.008 * TempRange[GPotentialMaxPos])
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
NetGPotential <- max(GPotentialRange) - CurrentSWCost
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}else{
#1.Decision making
VIRadRange <- .subset2(VIrad, CurrentPing)[SearchRange]
PRiskMinRange <- which(VIRadRange <= DVAdj)
if(length(PRiskMinRange) == 0){
PRiskMinPos <- which.max(SearchRange)
FutureDepth <- SearchRange[PRiskMinPos]
}else if(length(PRiskMinRange) == 1){
PRiskMinPos <- PRiskMinRange
FutureDepth <- SearchRange[PRiskMinPos]
}else{
PRiskMinPos <- PRiskMinRange[1]
FutureDepth <- SearchRange[PRiskMinPos]
}
#2.Estimations
CurrentTemp <- .subset2(Temperature, CurrentPing)[FutureDepth]
CurrentGmax <- GEF * exp(0.110 * CurrentTemp)
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
NetGPotential <- (CurrentGmax * CurrentTWMG) - CurrentSWCost
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}
if(Suvivorship < 0.0001){
LifeState <- as.factor("DEAD")
CessasionStage <- S
break
}else if(CurrentCW >= WCrc[3, 3] & CurrentCW < WCrc[4, 3]){
S <- 2
#Proceed iteration
}else if(CurrentCW >= WCrc[4, 3]){
S <- S + 1
break
}else{
#Proceed iteration
}
}
}
##########################################
#Feeding stages without a store (NII-CIII)
##########################################
if(LifeState == "DEAD"){
#Do nothing and proceed
}else{
repeat{
CurrentPing <- CurrentPing + 1
CurrentTWMG <- (CurrentCW * WCF) / 1000
MaxDistance <- round((3.7036 * CurrentCW^0.5853), 0)
MigrationCeiling <- CurrentDepth - MaxDistance
MigrationFloor <- CurrentDepth + MaxDistance
MigrationCeiling <- ifelse(MigrationCeiling < MinDepth, yes = MinDepth, no = MigrationCeiling)
MigrationFloor <- ifelse(MigrationFloor > MaxDepth, yes = MaxDepth, no = MigrationFloor)
SearchRange <- MigrationCeiling:MigrationFloor
DVAdj <- (CurrentCW * DVModel_PreC4$coefficients[2]) + DVModel_PreC4$coefficients[1]
CurrentVI <- .subset2(VIrad, CurrentPing)[CurrentDepth]
if(CurrentVI <= DVAdj){
#1.Growth potential estimation
TempRange <- .subset2(Temperature, CurrentPing)[SearchRange]
FARange <- .subset2(FA, CurrentPing)[SearchRange]
FACRange <- FARange * (FCF / 1000)
GmaxRange <- GEF * exp(0.110 * TempRange)
a <- 0.7
b <- 1.777 * exp(0.234 * TempRange)
n <- 0.681 * exp(0.0199 * TempRange)
k <- 0.375 * exp(0.0546 * TempRange)
m <- 0.858 * exp(-0.008 * TempRange)
FA_CRange <- (k * CurrentTWMG^(m - n)) / (a * b)
FA_SRange <- FA_CRange + (GmaxRange / (a * b * CurrentTWMG^(n - 1)))
GPotentialRange <- rep(NA, length(FACRange))
for(w in 1:length(FACRange)){
if(FACRange[w] >= FA_SRange[w]){
GPotentialRange[w] <- GmaxRange[w] * CurrentTWMG
}else{
GPotentialRange[w] <- (a * b[w] * CurrentTWMG^n[w] * FACRange[w]) - (k[w] * CurrentTWMG^m[w])
}
}
#2.Decision making
GloTempRange <- .subset2(Temperature, CurrentPing)[1:100]
GloGmaxRange <- GEF * exp(0.110 * GloTempRange)
GloFARange <- .subset2(FA, CurrentPing)[1:100]
GloFACRange <- GloFARange * (FCF / 1000)
a <- 0.7
Glo_b <- 1.777 * exp(0.234 * GloTempRange)
Glo_n <- 0.681 * exp(0.0199 * GloTempRange)
Glo_k <- 0.375 * exp(0.0546 * GloTempRange)
Glo_m <- 0.858 * exp(-0.008 * GloTempRange)
GloFA_CRange <- (Glo_k * CurrentTWMG^(Glo_m - Glo_n)) / (a * Glo_b)
GloFA_SRange <- GloFA_CRange + (GloGmaxRange / (a * Glo_b * CurrentTWMG^(Glo_n - 1)))
for(x in 1:length(GloFACRange)){
if(GloFACRange[x] >= GloFA_SRange[x]){
GloGPotentialRange[x] <- GloGmaxRange[x] * CurrentTWMG
}else{
GloGPotentialRange[x] <- (a * Glo_b[x] * CurrentTWMG^Glo_n[x] * GloFACRange[x]) - (Glo_k[x] * CurrentTWMG^Glo_m[x])
}
}
GPotentialMaxRange <- which(GPotentialRange == max(GPotentialRange))
if(max(GPotentialRange) < max(GloGPotentialRange)){
GPotentialMaxPos <- min(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}else{
GPotentialMaxPos <- max(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}
#3.Estimation
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * TempRange[GPotentialMaxPos])
m <- 0.858 * exp(-0.008 * TempRange[GPotentialMaxPos])
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
GrossGPotential <- max(GPotentialRange)
NetGPotential <- GrossGPotential - CurrentSWCost
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}else{
#1.Decision making
VIRadRange <- .subset2(VIrad, CurrentPing)[SearchRange]
PRiskMinRange <- which(VIRadRange <= DVAdj)
if(length(PRiskMinRange) == 0){
PRiskMinPos <- which.max(SearchRange)
FutureDepth <- SearchRange[PRiskMinPos]
}else if(length(PRiskMinRange) == 1){
PRiskMinPos <- PRiskMinRange
FutureDepth <- SearchRange[PRiskMinPos]
}else{
PRiskMinPos <- PRiskMinRange[1]
FutureDepth <- SearchRange[PRiskMinPos]
}
#2.Estimations
CurrentTemp <- .subset2(Temperature, CurrentPing)[FutureDepth]
CurrentGmax <- GEF * exp(0.110 * CurrentTemp)
CurrentFA <- .subset2(FA, CurrentPing)[FutureDepth]
CurrentFAC <- CurrentFA * (FCF / 1000)
a <- 0.7
b <- 1.777 * exp(0.234 * CurrentTemp)
n <- 0.681 * exp(0.0199 * CurrentTemp)
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentFA_C <- (k * CurrentTWMG^(m - n)) / (a * b)
CurrentFA_S <- CurrentFA_C + (CurrentGmax / (a * b * CurrentTWMG^(n - 1)))
if(CurrentFAC >= CurrentFA_S){
GrossGPotential <- CurrentGmax * CurrentTWMG
}else{
GrossGPotential <- (a * b * CurrentTWMG^n * CurrentFAC) - (k * CurrentTWMG^m)
}
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
NetGPotential <- GrossGPotential - CurrentSWCost
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}
if(Suvivorship < 0.0001){
LifeState <- as.factor("DEAD")
CessasionStage <- S
break
}else if(CurrentCW >= WCrc[5, 3] & CurrentCW < WCrc[6, 3]){
S <- 4
}else if(CurrentCW >= WCrc[6, 3] & CurrentCW < WCrc[7, 3]){
S <- 5
}else if(CurrentCW >= WCrc[7, 3] & CurrentCW < WCrc[8, 3]){
S <- 6
}else if(CurrentCW >= WCrc[8, 3] & CurrentCW < WCrc[9, 3]){
S <- 7
}else if(CurrentCW >= WCrc[9, 3] & CurrentCW < WCrc[10, 3]){
S <- 8
}else if(CurrentCW >= WCrc[10, 3] & CurrentCW < WCrc[11, 3]){
S <- 9
}else if(CurrentCW >= WCrc[11, 3]){
S <- 10
break
}else{
#Proceed iteration
}
}
}
#####################################
#Feeding stages with a store (CIV-CV)
#####################################
if(LifeState == "DEAD"){
#Do nothing and proceed
}else{
repeat{
CurrentPing <- CurrentPing + 1
CurrentTWMG <- ((CurrentCW + CurrentSW) * WCF) / 1000
MaxDistance <- round((3.7036 * CurrentCW^0.5853), 0)
MigrationCeiling <- CurrentDepth - MaxDistance
MigrationFloor <- CurrentDepth + MaxDistance
MigrationCeiling <- ifelse(MigrationCeiling < MinDepth, yes = MinDepth, no = MigrationCeiling)
MigrationFloor <- ifelse(MigrationFloor > MaxDepth, yes = MaxDepth, no = MigrationFloor)
SearchRange <- MigrationCeiling:MigrationFloor
DVAdj <- (CurrentCW * DVModel_PostC4$coefficients[2]) + DVModel_PostC4$coefficients[1]
CurrentVI <- .subset2(VIrad, CurrentPing)[CurrentDepth]
if(CurrentVI <= DVAdj){
#1.Growth potential estimation
TempRange <- .subset2(Temperature, CurrentPing)[SearchRange]
FARange <- .subset2(FA, CurrentPing)[SearchRange]
FACRange <- FARange * (FCF / 1000)
GmaxRange <- GEF * exp(0.110 * TempRange)
a <- 0.7
b <- 1.777 * exp(0.234 * TempRange)
n <- 0.681 * exp(0.0199 * TempRange)
k <- 0.375 * exp(0.0546 * TempRange)
m <- 0.858 * exp(-0.008 * TempRange)
FA_CRange <- (k * CurrentTWMG^(m - n)) / (a * b)
FA_SRange <- FA_CRange + (GmaxRange / (a * b * CurrentTWMG^(n - 1)))
GPotentialRange <- rep(NA, length(FACRange))
for(w in 1:length(FACRange)){
if(FACRange[w] >= FA_SRange[w]){
GPotentialRange[w] <- GmaxRange[w] * CurrentTWMG
}else{
GPotentialRange[w] <- (a * b[w] * CurrentTWMG^n[w] * FACRange[w]) - (k[w] * CurrentTWMG^m[w])
}
}
#2.Decision making
GloTempRange <- .subset2(Temperature, CurrentPing)[1:100]
GloGmaxRange <- GEF * exp(0.110 * GloTempRange)
GloFARange <- .subset2(FA, CurrentPing)[1:100]
GloFACRange <- GloFARange * (FCF / 1000)
a <- 0.7
Glo_b <- 1.777 * exp(0.234 * GloTempRange)
Glo_n <- 0.681 * exp(0.0199 * GloTempRange)
Glo_k <- 0.375 * exp(0.0546 * GloTempRange)
Glo_m <- 0.858 * exp(-0.008 * GloTempRange)
GloFA_CRange <- (Glo_k * CurrentTWMG^(Glo_m - Glo_n)) / (a * Glo_b)
GloFA_SRange <- GloFA_CRange + (GloGmaxRange / (a * Glo_b * CurrentTWMG^(Glo_n - 1)))
for(x in 1:length(GloFACRange)){
if(GloFACRange[x] >= GloFA_SRange[x]){
GloGPotentialRange[x] <- GloGmaxRange[x] * CurrentTWMG
}else{
GloGPotentialRange[x] <- (a * Glo_b[x] * CurrentTWMG^Glo_n[x] * GloFACRange[x]) - (Glo_k[x] * CurrentTWMG^Glo_m[x])
}
}
GPotentialMaxRange <- which(GPotentialRange == max(GPotentialRange))
if(max(GPotentialRange) < max(GloGPotentialRange)){
GPotentialMaxPos <- min(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}else{
GPotentialMaxPos <- max(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}
#2.Estimation
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * TempRange[GPotentialMaxPos])
m <- 0.858 * exp(-0.008 * TempRange[GPotentialMaxPos])
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
GrossGPotential <- max(GPotentialRange)
NetGPotential <- GrossGPotential - CurrentSWCost
if(NetGPotential >= 0){
CurrentSPotential <- CurrentSW + (NetGPotential * GA) #Allocation to store
NetGPotential <- NetGPotential * (1 - GA)
}else{
if(CurrentSW >= abs(NetGPotential)){
CurrentSPotential <- CurrentSW - abs(NetGPotential) #Loss compensated 100% from store
NetGPotential <- 0
}else{
CurrentSPotential <- 0
NetGPotential <- NetGPotential + CurrentSW #Loss compensated to max.extent if possible
}
}
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentSW <- CurrentSPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}else{
#1.Decision making
VIRadRange <- .subset2(VIrad, CurrentPing)[SearchRange]
PRiskMinRange <- which(VIRadRange <= DVAdj)
if(length(PRiskMinRange) == 0){
PRiskMinPos <- which.max(SearchRange)
FutureDepth <- SearchRange[PRiskMinPos]
}else if(length(PRiskMinRange) == 1){
PRiskMinPos <- PRiskMinRange
FutureDepth <- SearchRange[PRiskMinPos]
}else{
PRiskMinPos <- PRiskMinRange[1]
FutureDepth <- SearchRange[PRiskMinPos]
}
#2.Estimations
CurrentTemp <- .subset2(Temperature, CurrentPing)[FutureDepth]
CurrentGmax <- GEF * exp(0.110 * CurrentTemp)
CurrentFA <- .subset2(FA, CurrentPing)[FutureDepth]
CurrentFAC <- CurrentFA * (FCF / 1000)
a <- 0.7
b <- 1.777 * exp(0.234 * CurrentTemp)
n <- 0.681 * exp(0.0199 * CurrentTemp)
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentFA_C <- (k * CurrentTWMG^(m - n)) / (a * b)
CurrentFA_S <- CurrentFA_C + (CurrentGmax / (a * b * CurrentTWMG^(n - 1)))
if(CurrentFAC >= CurrentFA_S){
GrossGPotential <- CurrentGmax * CurrentTWMG
}else{
GrossGPotential <- (a * b * CurrentTWMG^n * CurrentFAC) - (k * CurrentTWMG^m)
}
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
NetGPotential <- GrossGPotential - CurrentSWCost
if(NetGPotential >= 0){
CurrentSPotential <- CurrentSW + (NetGPotential * GA) #Allocation to store
NetGPotential <- NetGPotential * (1 - GA)
}else{
if(CurrentSW >= abs(NetGPotential)){
CurrentSPotential <- CurrentSW - abs(NetGPotential) #Loss compensated 100% from store
NetGPotential <- 0
}else{
CurrentSPotential <- 0
NetGPotential <- NetGPotential + CurrentSW #Loss compensated to max.extent if possible
}
}
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentSW <- CurrentSPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}
if(Suvivorship < 0.0001){
LifeState <- as.factor("DEAD")
CessasionStage <- S
break
}else if((CurrentSW / (CurrentCW * WCF)) >= SD){
DiapauseStage <- S
break
}else if(CurrentCW >= WCrc[12, 3] & CurrentCW < WCrc[13, 3]){
S <- 11
}else if(CurrentCW >= WCrc[13, 3]){
S <- 12
break
}else{
#Proceed iteration
}
}
}
####################
#Diapause simulation
####################
if(LifeState == "DEAD"){
#Do nothing and proceed
}else{
if(is.na(DiapauseStage) == TRUE){
#No diapause - direct development to CVI-F
}else{
###############
#Diapause entry
###############
repeat{
CurrentPing <- CurrentPing + 1
CurrentTWMG <- ((CurrentCW + CurrentSW) * WCF) / 1000
MaxDistance <- round((3.7036 * CurrentCW^0.5853), 0)
MigrationCeiling <- CurrentDepth - MaxDistance
MigrationFloor <- CurrentDepth + MaxDistance
MigrationCeiling <- ifelse(MigrationCeiling < MinDepth, yes = MinDepth, no = MigrationCeiling)
MigrationFloor <- ifelse(MigrationFloor > MaxDepth, yes = MaxDepth, no = MigrationFloor)
SearchRange <- MigrationCeiling:MigrationFloor
#1.Decision making
CurrentOD <- which(SearchRange == OD)
if(length(CurrentOD) == 1){
FutureDepth <- OD
}else{
if(max(SearchRange) > OD){
FutureDepth <- SearchRange[1]
}else{
FutureDepth <- SearchRange[length(SearchRange)]
}
}
#2.Estimation
CurrentTemp <- .subset2(Temperature, CurrentPing)[FutureDepth]
CurrentGmax <- GEF * exp(0.110 * CurrentTemp)
CurrentFA <- .subset2(FA, CurrentPing)[FutureDepth]
CurrentFAC <- CurrentFA * (FCF / 1000)
a <- 0.7
b <- 1.777 * exp(0.234 * CurrentTemp)
n <- 0.681 * exp(0.0199 * CurrentTemp)
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentFA_C <- (k * CurrentTWMG^(m - n)) / (a * b)
CurrentFA_S <- CurrentFA_C + (CurrentGmax / (a * b * CurrentTWMG^(n - 1)))
if(CurrentFAC >= CurrentFA_S){
GrossGPotential <- CurrentGmax * CurrentTWMG
}else{
GrossGPotential <- (a * b * CurrentTWMG^n * CurrentFAC) - (k * CurrentTWMG^m)
}
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
NetGPotential <- GrossGPotential - CurrentSWCost
if(NetGPotential >= 0){
CurrentSPotential <- CurrentSW + (NetGPotential * GA) #Allocation to store
NetGPotential <- NetGPotential * (1 - GA)
}else{
if(CurrentSW >= abs(NetGPotential)){
CurrentSPotential <- CurrentSW - abs(NetGPotential) #Loss compensated 100% from store
NetGPotential <- 0
}else{
CurrentSPotential <- 0
NetGPotential <- NetGPotential + CurrentSW #Loss compensated to max.extent if possible
}
}
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentSW <- CurrentSPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
if(Suvivorship < 0.0001){
LifeState <- as.factor("DEAD")
CessasionStage <- S
break
}else if(CurrentDepth == OD){
DiapauseStartTime <- CurrentPing
DiapauseStartSW <- CurrentSW
break
}else{
#Proceed iteration
}
}
#####################
#Diapause progression
#####################
if(LifeState == "DEAD"){
#Do nothing and proceed
}else{
CurrentTemp <- .subset2(ODParameters, 2)[ODParameters$Depths == OD]
CurrentPProb <- .subset2(ODParameters, 3)[ODParameters$Depths == OD]
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentTWMG <- ((CurrentCW + CurrentSW) * WCF) / 1000
MCost_ceiling <- k * CurrentTWMG^m * MRF
ExpendedSW <- CurrentSW - (CurrentSW * (1 - SA))
EndSW <- CurrentSW - ExpendedSW
EndTWMG <- ((CurrentCW + EndSW) * WCF) / 1000
MCost_floor <- k * EndTWMG^m * MRF
MeanMCost <- (MCost_ceiling + MCost_floor) / 2
DiapauseHrs <- round(ExpendedSW / MeanMCost, 0)
round(ExpendedSW / MCost_floor, 0)
CurrentSW <- EndSW
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
DiapauseSuvivorship <- (1 - CurrentPRisk)^DiapauseHrs
Suvivorship <- Suvivorship * DiapauseSuvivorship
if(Suvivorship < 0.0001){
LifeState <- as.factor("DEAD")
CessasionStage <- S
}else{
#Do nothing
}
DiapauseEndTime <- CurrentPing + DiapauseHrs
CurrentPing <- DiapauseEndTime
}
##############
#Diapause exit
##############
if(LifeState == "DEAD"){
#Do nothing and proceed
}else{
repeat{
CurrentPing <- CurrentPing + 1
CurrentTWMG <- ((CurrentCW + CurrentSW) * WCF) / 1000
MaxDistance <- round((3.7036 * CurrentCW^0.5853), 0)
MigrationCeiling <- CurrentDepth - MaxDistance
MigrationFloor <- CurrentDepth + MaxDistance
MigrationCeiling <- ifelse(MigrationCeiling < MinDepth, yes = MinDepth, no = MigrationCeiling)
MigrationFloor <- ifelse(MigrationFloor > MaxDepth, yes = MaxDepth, no = MigrationFloor)
SearchRange <- MigrationCeiling:MigrationFloor
DVAdj <- (CurrentCW * DVModel_PostC4$coefficients[2]) + DVModel_PostC4$coefficients[1]
CurrentVI <- .subset2(VIrad, CurrentPing)[CurrentDepth]
if(CurrentVI <= DVAdj){
#1.Growth potential estimation
TempRange <- .subset2(Temperature, CurrentPing)[SearchRange]
FARange <- .subset2(FA, CurrentPing)[SearchRange]
FACRange <- FARange * (FCF / 1000)
GmaxRange <- GEF * exp(0.110 * TempRange)
a <- 0.7
b <- 1.777 * exp(0.234 * TempRange)
n <- 0.681 * exp(0.0199 * TempRange)
k <- 0.375 * exp(0.0546 * TempRange)
m <- 0.858 * exp(-0.008 * TempRange)
FA_CRange <- (k * CurrentTWMG^(m - n)) / (a * b)
FA_SRange <- FA_CRange + (GmaxRange / (a * b * CurrentTWMG^(n - 1)))
GPotentialRange <- rep(NA, length(FACRange))
for(w in 1:length(FACRange)){
if(FACRange[w] >= FA_SRange[w]){
GPotentialRange[w] <- GmaxRange[w] * CurrentTWMG
}else{
GPotentialRange[w] <- (a * b[w] * CurrentTWMG^n[w] * FACRange[w]) - (k[w] * CurrentTWMG^m[w])
}
}
#2.Decision making
GloTempRange <- .subset2(Temperature, CurrentPing)[1:100]
GloGmaxRange <- GEF * exp(0.110 * GloTempRange)
GloFARange <- .subset2(FA, CurrentPing)[1:100]
GloFACRange <- GloFARange * (FCF / 1000)
a <- 0.7
Glo_b <- 1.777 * exp(0.234 * GloTempRange)
Glo_n <- 0.681 * exp(0.0199 * GloTempRange)
Glo_k <- 0.375 * exp(0.0546 * GloTempRange)
Glo_m <- 0.858 * exp(-0.008 * GloTempRange)
GloFA_CRange <- (Glo_k * CurrentTWMG^(Glo_m - Glo_n)) / (a * Glo_b)
GloFA_SRange <- GloFA_CRange + (GloGmaxRange / (a * Glo_b * CurrentTWMG^(Glo_n - 1)))
for(x in 1:length(GloFACRange)){
if(GloFACRange[x] >= GloFA_SRange[x]){
GloGPotentialRange[x] <- GloGmaxRange[x] * CurrentTWMG
}else{
GloGPotentialRange[x] <- (a * Glo_b[x] * CurrentTWMG^Glo_n[x] * GloFACRange[x]) - (Glo_k[x] * CurrentTWMG^Glo_m[x])
}
}
GPotentialMaxRange <- which(GPotentialRange == max(GPotentialRange))
if(max(GPotentialRange) < max(GloGPotentialRange)){
GPotentialMaxPos <- min(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}else{
GPotentialMaxPos <- max(GPotentialMaxRange) #Single index location
FutureDepth <- SearchRange[GPotentialMaxPos] #Depth corresponding to the single index location above
}
#2.Estimation
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * TempRange[GPotentialMaxPos])
m <- 0.858 * exp(-0.008 * TempRange[GPotentialMaxPos])
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
GrossGPotential <- max(GPotentialRange)
NetGPotential <- GrossGPotential - CurrentSWCost
if(NetGPotential >= 0){
CurrentSPotential <- CurrentSW + 0 #No allocation to store after diapause (1-yr life cycle)
NetGPotential <- NetGPotential #All gains to somatic growth
}else{
MaxStoGAllocation <- GEF * exp(0.110 * .subset2(Temperature, CurrentPing)[FutureDepth]) * CurrentTWMG
if(CurrentSW >= MaxStoGAllocation){
CurrentSPotential <- CurrentSW - MaxStoGAllocation
NetGPotential <- MaxStoGAllocation + NetGPotential
}else if(CurrentSW < MaxStoGAllocation & CurrentSW >= abs(NetGPotential)){
CurrentSPotential <- CurrentSW - abs(NetGPotential)
NetGPotential <- 0
}else{
CurrentSPotential <- 0
NetGPotential <- NetGPotential + CurrentSW
}
}
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentSW <- CurrentSPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}else{
#Minimize risk
#1.Decision making
VIRadRange <- .subset2(VIrad, CurrentPing)[SearchRange]
PRiskMinRange <- which(VIRadRange <= DVAdj)
if(length(PRiskMinRange) == 0){
PRiskMinPos <- which.max(SearchRange)
FutureDepth <- SearchRange[PRiskMinPos]
}else if(length(PRiskMinRange) == 1){
PRiskMinPos <- PRiskMinRange
FutureDepth <- SearchRange[PRiskMinPos]
}else{
PRiskMinPos <- PRiskMinRange[1]
FutureDepth <- SearchRange[PRiskMinPos]
}
#2.Estimations
CurrentTemp <- .subset2(Temperature, CurrentPing)[FutureDepth]
CurrentGmax <- GEF * exp(0.110 * CurrentTemp)
CurrentFA <- .subset2(FA, CurrentPing)[FutureDepth]
CurrentFAC <- CurrentFA * (FCF / 1000)
a <- 0.7
b <- 1.777 * exp(0.234 * CurrentTemp)
n <- 0.681 * exp(0.0199 * CurrentTemp)
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentFA_C <- (k * CurrentTWMG^(m - n)) / (a * b)
CurrentFA_S <- CurrentFA_C + (CurrentGmax / (a * b * CurrentTWMG^(n - 1)))
if(CurrentFAC >= CurrentFA_S){
GrossGPotential <- CurrentGmax * CurrentTWMG
}else{
GrossGPotential <- (a * b * CurrentTWMG^n * CurrentFAC) - (k * CurrentTWMG^m)
}
MovingTime <- abs(FutureDepth - CurrentDepth) / MaxDistance
k <- 0.375 * exp(0.0546 * CurrentTemp)
m <- 0.858 * exp(-0.008 * CurrentTemp)
CurrentSWCost <- k * CurrentTWMG^m * MovingTime * SCF
NetGPotential <- GrossGPotential - CurrentSWCost
if(NetGPotential >= 0){
CurrentSPotential <- CurrentSW + 0 #No allocation to store after diapause (1-yr life cycle)
NetGPotential <- NetGPotential #All gains to somatic growth
}else{
MaxStoGAllocation <- GEF * exp(0.110 * .subset2(Temperature, CurrentPing)[FutureDepth]) * CurrentTWMG
if(CurrentSW >= MaxStoGAllocation){
CurrentSPotential <- CurrentSW - MaxStoGAllocation
NetGPotential <- MaxStoGAllocation + NetGPotential
}else if(CurrentSW < MaxStoGAllocation & CurrentSW >= abs(NetGPotential)){
CurrentSPotential <- CurrentSW - abs(NetGPotential)
NetGPotential <- 0
}else{
CurrentSPotential <- 0
NetGPotential <- NetGPotential + CurrentSW
}
}
CurrentGPotential <- CurrentCW + NetGPotential
if(CurrentGPotential >= LifetimeMaxCW){
LifetimeMaxCW <- CurrentGPotential
CurrentSRisk <- 0
}else{
CWLTreshold <- LifetimeMaxCW / 2
if(CurrentGPotential <= CWLTreshold){
CurrentSRisk <- 1
CurrentGPotential <- CWLTreshold
}else{
CWLoss <- (50 / (LifetimeMaxCW - CWLTreshold)) * (LifetimeMaxCW - CurrentGPotential)
CurrentSRisk <- 0.02 * CWLoss
}
}
CurrentCW <- CurrentGPotential
CurrentSW <- CurrentSPotential
CurrentDepth <- FutureDepth
CurrentPProb <- .subset2(PProb, CurrentPing)[CurrentDepth]
CurrentPRisk <- CurrentPProb * ((CurrentCW * RAMSlo) + RAMInt)
Suvivorship <- Suvivorship * (1 - (CurrentPRisk + CurrentSRisk))
}
if(Suvivorship < 0.0001){
LifeState <- as.factor("DEAD")
CessasionStage <- S
break
}else if(CurrentCW >= WCrc[12, 3] & CurrentCW < WCrc[13, 3]){
S <- 11
}else if(CurrentCW >= WCrc[13, 3]){
S <- 12
break
}else{
#Proceed iteration
}