R/MP_3a_fwdBD.R
In ElsevierSoftwareX/SOFTX-D-15-00067: Bio-Economic Impact Assessment of Management strategies using FLR
#-------------------------------------------------------------------------------
# OBSERVATION MODEL FUNCTIONS
# - gmeanHistGrowth(stock, y0,y1)
# - fwdBD(stock,fwdControl)
# - biomass.tg, catch.tg, discards.tg, f.tg, fdisc.tg, fland.tg, landings.tg
#
# Dorleta GarcYYYa
# Created: 15/12/2010 19:58:56
# Changed: 16/12/2010 12:35:50
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# fwdBD(stock, ctrl, growth.years)
# - growth.years: Year range used to calculate population growth to be used in the forecast.
#-------------------------------------------------------------------------------
fwdBD <- function(stock, ctrl, growth.years)
{
options(warn = -1)
if (!validObject(stock))
stop("stock object not valid")
if (!validObject(ctrl))
stop("ctrl not valid")
yrs <- sort(as.numeric(as.character(unique(ctrl@target[, "year"]))))
## check years
## years in ctrl have to be in order
if (!all(yrs==sort(yrs)))
stop("years in ctrl not in order")
## no gaps in years
if (length(min(yrs):max(yrs))!=length(unique(yrs)))
stop("years in ctrl not contiguous")
## years in ctrl have to be in FLStock stock
if (!all(ac(yrs) %in% ac(dims(stock)$minyear:(dims(stock)$maxyear))))
stop("years in ctrl outside of those in stock object")
## Need year+1 in FLStock object
if (max(yrs) == dims(stock)$maxyear){
endYr<-dims(stock)$maxyear+1
stock <- window(stock, end=dims(stock)$maxyear+1)}
else
endYr<-NULL
## check iters in ctrl are '1 or n' and correct if necessary
# ctrl@trgtArray <- chkBDTrgtArrayIters(stock,ctrl@trgtArray,sr)
ctrl@target <- chkBDTargetQuantity(ctrl@target,object)
stock.n(stock)[1,ac(min(ctrl@target[,"year"]))]<-NA
for(yr in yrs){
y <- yr - dims(stock)$minyear + 1 # yr position.
control <- ctrl@target[ctrl@target$year == yr, ]
# There must ONE and ONLY ONE target.
if(all(is.na(control$val))) stop('Target is missing in year: ', yr)
if(sum(!is.na(control$val)) > 1) stop('Only one target per year is allowed. Several targets in year: ', yr)
# In each row a CONSTRAINT OR A TARGET but NOT BOTH.
mi <- !is.na(control$min)
ma <- !is.na(control$max)
va <- which(!is.na(control$val)) # WE KNOW there is only 1 with TRUE.
if(any(c(mi[va], ma[va]))) stop('Constraints and targets can not be mixed. Mixed in year : ', yr)
gr <- gmeanHistGrowth(stock, growth.years)
# Fist apply the TARGET, and then the CONSTRAINTS in order of appearance.
# TARGET's ROW.
tg <- control[va,]
tg.fun <- paste(as.character(tg[1,"quantity"]), "tg", sep = ".")
tg.val <- as.numeric(tg[1,'val'])
# If the target is relative calculate the absolute value.
if(!is.na(tg['rel.year'])){ # => IT IS RELATIVE. EXTRACT the QUANTITY in THAT YEAR and multitply by the RELATIVE target.
yrel <- as.numeric((tg['rel.year'] - dims(stock)$minyear + 1))
quan <- as.character(tg[1,'quantity'])
tg.val <- getQuantity(stock, quan, yrel)*tg.val
}
# Apply target function
res.tg <- eval(call(tg.fun, stock = stock , gr = gr, target = tg.val, year = y))
# Update Stock.
stock@stock.n[,y,] <- res.tg$biomass/stock@stock.wt[,y,]
stock@stock[,y,] <- res.tg$biomass
stock@stock.n[,y+1,] <- res.tg$biomass_next/stock@stock.wt[,y,]
stock@stock[,y+1,] <- res.tg$biomass_next
stock@catch.n[,y,] <- res.tg$catch/stock@catch.wt[,y,]
stock@catch[,y,] <- res.tg$catch
stock@landings.n[,y,] <- res.tg$landings/stock@landings.wt[,y,]
stock@landings[,y,] <- res.tg$landings
stock@discards.n[,y,] <- res.tg$discards/stock@discards.wt[,y,]
stock@discards[,y,] <- res.tg$discards
stock@harvest[,y,] <- res.tg$f
# CONSTRAINTS.
cnst <- control[-va,] # data frame with the constraints.
if(dim(cnst)[1] == 0) next
for(cn in 1:dim(cnst)[1]){
cnst.qnt <- as.character(cnst[cn,'quantity']) # c("biomass","catch","landings","discards","f", "f.landings","f.discards")
cnst.min <- ifelse(is.na(cnst[cn,'min']), 0, as.numeric(cnst[cn,'min']))
cnst.max <- ifelse(is.na(cnst[cn,'max']), Inf, as.numeric(cnst[cn,'max']))
# current value of 'quantity' (absolute value)
quan <- getQuantity(stock, cnst.qnt, y)
# If the constraints are relative we have to extract the 'absolute values'.
if(!is.na(cnst[cn,'rel.year'])){ # => IT IS RELATIVE. EXTRACT the QUANTITY in THAT YEAR and multitply by the RELATIVE target.
yrel <- cnst[cn,'rel.year'] - dims(stock)$minyear + 1
yy <- getQuantity(stock, cnst.qnt, yrel)
cnst.min <- yy*cnst.min
cnst.max <- yy*cnst.max
}
if(quan > cnst.min & quan < cnst.max) next
new.tg <- ifelse(quan < cnst.min, cnst.min, cnst.max)
new.tg.fun <- paste(cnst.qnt, "tg", sep = ".")
# Apply target function
res.new.tg <- eval(call(new.tg.fun, stock = stock , gr = gr, target = new.tg, year = y))
# Update Stock.
stock@stock.n[,y,] <- res.new.tg$biomass/stock@stock.wt[,y,]
stock@stock[,y,] <- res.new.tg$biomass
stock@stock.n[,y+1,] <- res.new.tg$biomass_next/stock@stock.wt[,y,]
stock@stock[,y+1,] <- res.new.tg$biomass_next
stock@catch.n[,y,] <- res.new.tg$catch/stock@catch.wt[,y,]
stock@catch[,y,] <- res.new.tg$catch
stock@landings.n[,y,] <- res.new.tg$landings/stock@landings.wt[,y,]
stock@landings[,y,] <- res.new.tg$landings
stock@discards.n[,y,] <- res.new.tg$discards/stock@discards.wt[,y,]
stock@discards[,y,] <- res.new.tg$discards
stock@harvest[,y,] <- res.new.tg$f
}
}
options(warn = 0)
return(stock)
}
#-------------------------------------------------------------------------------
# gmeanHistGrowth: Calculate the geometric mean growth to be used for the
# projection in fwd.
#-------------------------------------------------------------------------------
gmeanHistGrowth <- function(stock, years){ # y0:y1, pueden ser numericos o caracteres.
it <- dim(stock@m)[6]
ny <- length(years)
bio <- matrix(quantSums(stock@stock.n*stock@stock.wt)[,years,drop=T],ny,it) # matrix[ny,it]
cw <- matrix(computeCatch(stock)[,years,drop=T],ny,it) # matrix[ny,it]
# The growth is calculated in percemtage to avoid the problem with negative values
# in the calculation of geometric mean.
growth <- matrix((bio[-1,]+ cw[-ny,])/ bio[-ny,] , ny-1,it)
res <- apply(growth,2, function(x) prod(x)^(1/(ny-1)))
# The percentage is applied to last year biomass.
res <- bio[ny]*(res - 1) # res > 1 => positive growth ** res < 1 => negative growth.
return(res)
}
#-------------------------------------------------------------------------------
# getQuantity: Extract 'quantity' from a FLStockobject
# quantity = "biomass","catch","landings","discards","f", "f.landings","f.discards"
# year = single year ', 'POSITION!!)
#-------------------------------------------------------------------------------
getQuantity <- function(stock, quantity, year){
if(quantity %in% c("catch","landings","discards")) return(c(slot(stock, quantity)[,year,]))
if(quantity == 'biomass') return(c((stock@stock.wt*stock@stock.n)[,year,]))
if(quantity == 'f') return(stock@harvest[,year,])
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T]
if(quantity == 'f.landings') return(c(stock@harvest*(1-dr)))
return(c(stock@harvest*dr)) # tg['quantity'] == 'f.discards'
}
#-------------------------------------------------------------------------------
# KKK.tg(stock, gr, KKK, year): Project the population based on targets.
# - stock: FLStock object with na = 1.
# - gr: Growth of the population in 'year'
# - KKK: The constraint 'numeric(it)'.
# - year: Projected year - NUMERIC.
#-------------------------------------------------------------------------------
# When the target is biomass, it is the desired biomass in [year+1] because
# the biomass in [year] is the product of what happens in [year-1].
biomass.tg <- function(stock, gr, target, year){ # bio[year+1] -> catch (land, disc)?, f?
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
Cy <- By + gr - target # [it]
Cy <- ifelse(Cy < 0, 0, Cy)
Fy <- Cy/target
By1 <- By + gr - Cy
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
return(list(catch = Cy, discards = Cy*dr, landings = Cy*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
catch.tg <- function(stock, gr, target, year){ #
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
By1 <- By + gr - target
catch <- ifelse(target > By, 0.9*By, target)
Fy <- catch/By # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
landings.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
catch <- target/(1-dr)
By1 <- By + gr - catch
catch <- ifelse(catch > By, 0.9*By, catch)
Fy <- catch/By # [it]
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
discards.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
catch <- target/dr
catch <- ifelse(catch > By, 0.9*By, catch)
Fy <- catch/By # [it]
By1 <- By + gr - catch
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
f.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
Fy <- target
if(Fy >= 1) stop('Harvest rate must be < 1')
catch <- Fy*By
By1 <- By + gr - catch
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
f.landings.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
Fy <- target/(1-dr)
if(Fy >= 1) stop('Harvest rate must be < 1')
catch <- Fy*By
By1 <- By + gr - catch
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
f.discards.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
Fy <- target/dr
if(Fy >= 1) stop('Harvest rate must be < 1')
catch <- Fy*By
By1 <- By + gr - catch
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
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#-------------------------------------------------------------------------------
# OBSERVATION MODEL FUNCTIONS
# - gmeanHistGrowth(stock, y0,y1)
# - fwdBD(stock,fwdControl)
# - biomass.tg, catch.tg, discards.tg, f.tg, fdisc.tg, fland.tg, landings.tg
#
# Dorleta GarcYYYa
# Created: 15/12/2010 19:58:56
# Changed: 16/12/2010 12:35:50
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# fwdBD(stock, ctrl, growth.years)
# - growth.years: Year range used to calculate population growth to be used in the forecast.
#-------------------------------------------------------------------------------
fwdBD <- function(stock, ctrl, growth.years)
{
options(warn = -1)
if (!validObject(stock))
stop("stock object not valid")
if (!validObject(ctrl))
stop("ctrl not valid")
yrs <- sort(as.numeric(as.character(unique(ctrl@target[, "year"]))))
## check years
## years in ctrl have to be in order
if (!all(yrs==sort(yrs)))
stop("years in ctrl not in order")
## no gaps in years
if (length(min(yrs):max(yrs))!=length(unique(yrs)))
stop("years in ctrl not contiguous")
## years in ctrl have to be in FLStock stock
if (!all(ac(yrs) %in% ac(dims(stock)$minyear:(dims(stock)$maxyear))))
stop("years in ctrl outside of those in stock object")
## Need year+1 in FLStock object
if (max(yrs) == dims(stock)$maxyear){
endYr<-dims(stock)$maxyear+1
stock <- window(stock, end=dims(stock)$maxyear+1)}
else
endYr<-NULL
## check iters in ctrl are '1 or n' and correct if necessary
# ctrl@trgtArray <- chkBDTrgtArrayIters(stock,ctrl@trgtArray,sr)
ctrl@target <- chkBDTargetQuantity(ctrl@target,object)
stock.n(stock)[1,ac(min(ctrl@target[,"year"]))]<-NA
for(yr in yrs){
y <- yr - dims(stock)$minyear + 1 # yr position.
control <- ctrl@target[ctrl@target$year == yr, ]
# There must ONE and ONLY ONE target.
if(all(is.na(control$val))) stop('Target is missing in year: ', yr)
if(sum(!is.na(control$val)) > 1) stop('Only one target per year is allowed. Several targets in year: ', yr)
# In each row a CONSTRAINT OR A TARGET but NOT BOTH.
mi <- !is.na(control$min)
ma <- !is.na(control$max)
va <- which(!is.na(control$val)) # WE KNOW there is only 1 with TRUE.
if(any(c(mi[va], ma[va]))) stop('Constraints and targets can not be mixed. Mixed in year : ', yr)
gr <- gmeanHistGrowth(stock, growth.years)
# Fist apply the TARGET, and then the CONSTRAINTS in order of appearance.
# TARGET's ROW.
tg <- control[va,]
tg.fun <- paste(as.character(tg[1,"quantity"]), "tg", sep = ".")
tg.val <- as.numeric(tg[1,'val'])
# If the target is relative calculate the absolute value.
if(!is.na(tg['rel.year'])){ # => IT IS RELATIVE. EXTRACT the QUANTITY in THAT YEAR and multitply by the RELATIVE target.
yrel <- as.numeric((tg['rel.year'] - dims(stock)$minyear + 1))
quan <- as.character(tg[1,'quantity'])
tg.val <- getQuantity(stock, quan, yrel)*tg.val
}
# Apply target function
res.tg <- eval(call(tg.fun, stock = stock , gr = gr, target = tg.val, year = y))
# Update Stock.
stock@stock.n[,y,] <- res.tg$biomass/stock@stock.wt[,y,]
stock@stock[,y,] <- res.tg$biomass
stock@stock.n[,y+1,] <- res.tg$biomass_next/stock@stock.wt[,y,]
stock@stock[,y+1,] <- res.tg$biomass_next
stock@catch.n[,y,] <- res.tg$catch/stock@catch.wt[,y,]
stock@catch[,y,] <- res.tg$catch
stock@landings.n[,y,] <- res.tg$landings/stock@landings.wt[,y,]
stock@landings[,y,] <- res.tg$landings
stock@discards.n[,y,] <- res.tg$discards/stock@discards.wt[,y,]
stock@discards[,y,] <- res.tg$discards
stock@harvest[,y,] <- res.tg$f
# CONSTRAINTS.
cnst <- control[-va,] # data frame with the constraints.
if(dim(cnst)[1] == 0) next
for(cn in 1:dim(cnst)[1]){
cnst.qnt <- as.character(cnst[cn,'quantity']) # c("biomass","catch","landings","discards","f", "f.landings","f.discards")
cnst.min <- ifelse(is.na(cnst[cn,'min']), 0, as.numeric(cnst[cn,'min']))
cnst.max <- ifelse(is.na(cnst[cn,'max']), Inf, as.numeric(cnst[cn,'max']))
# current value of 'quantity' (absolute value)
quan <- getQuantity(stock, cnst.qnt, y)
# If the constraints are relative we have to extract the 'absolute values'.
if(!is.na(cnst[cn,'rel.year'])){ # => IT IS RELATIVE. EXTRACT the QUANTITY in THAT YEAR and multitply by the RELATIVE target.
yrel <- cnst[cn,'rel.year'] - dims(stock)$minyear + 1
yy <- getQuantity(stock, cnst.qnt, yrel)
cnst.min <- yy*cnst.min
cnst.max <- yy*cnst.max
}
if(quan > cnst.min & quan < cnst.max) next
new.tg <- ifelse(quan < cnst.min, cnst.min, cnst.max)
new.tg.fun <- paste(cnst.qnt, "tg", sep = ".")
# Apply target function
res.new.tg <- eval(call(new.tg.fun, stock = stock , gr = gr, target = new.tg, year = y))
# Update Stock.
stock@stock.n[,y,] <- res.new.tg$biomass/stock@stock.wt[,y,]
stock@stock[,y,] <- res.new.tg$biomass
stock@stock.n[,y+1,] <- res.new.tg$biomass_next/stock@stock.wt[,y,]
stock@stock[,y+1,] <- res.new.tg$biomass_next
stock@catch.n[,y,] <- res.new.tg$catch/stock@catch.wt[,y,]
stock@catch[,y,] <- res.new.tg$catch
stock@landings.n[,y,] <- res.new.tg$landings/stock@landings.wt[,y,]
stock@landings[,y,] <- res.new.tg$landings
stock@discards.n[,y,] <- res.new.tg$discards/stock@discards.wt[,y,]
stock@discards[,y,] <- res.new.tg$discards
stock@harvest[,y,] <- res.new.tg$f
}
}
options(warn = 0)
return(stock)
}
#-------------------------------------------------------------------------------
# gmeanHistGrowth: Calculate the geometric mean growth to be used for the
# projection in fwd.
#-------------------------------------------------------------------------------
gmeanHistGrowth <- function(stock, years){ # y0:y1, pueden ser numericos o caracteres.
it <- dim(stock@m)[6]
ny <- length(years)
bio <- matrix(quantSums(stock@stock.n*stock@stock.wt)[,years,drop=T],ny,it) # matrix[ny,it]
cw <- matrix(computeCatch(stock)[,years,drop=T],ny,it) # matrix[ny,it]
# The growth is calculated in percemtage to avoid the problem with negative values
# in the calculation of geometric mean.
growth <- matrix((bio[-1,]+ cw[-ny,])/ bio[-ny,] , ny-1,it)
res <- apply(growth,2, function(x) prod(x)^(1/(ny-1)))
# The percentage is applied to last year biomass.
res <- bio[ny]*(res - 1) # res > 1 => positive growth ** res < 1 => negative growth.
return(res)
}
#-------------------------------------------------------------------------------
# getQuantity: Extract 'quantity' from a FLStockobject
# quantity = "biomass","catch","landings","discards","f", "f.landings","f.discards"
# year = single year ', 'POSITION!!)
#-------------------------------------------------------------------------------
getQuantity <- function(stock, quantity, year){
if(quantity %in% c("catch","landings","discards")) return(c(slot(stock, quantity)[,year,]))
if(quantity == 'biomass') return(c((stock@stock.wt*stock@stock.n)[,year,]))
if(quantity == 'f') return(stock@harvest[,year,])
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T]
if(quantity == 'f.landings') return(c(stock@harvest*(1-dr)))
return(c(stock@harvest*dr)) # tg['quantity'] == 'f.discards'
}
#-------------------------------------------------------------------------------
# KKK.tg(stock, gr, KKK, year): Project the population based on targets.
# - stock: FLStock object with na = 1.
# - gr: Growth of the population in 'year'
# - KKK: The constraint 'numeric(it)'.
# - year: Projected year - NUMERIC.
#-------------------------------------------------------------------------------
# When the target is biomass, it is the desired biomass in [year+1] because
# the biomass in [year] is the product of what happens in [year-1].
biomass.tg <- function(stock, gr, target, year){ # bio[year+1] -> catch (land, disc)?, f?
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
Cy <- By + gr - target # [it]
Cy <- ifelse(Cy < 0, 0, Cy)
Fy <- Cy/target
By1 <- By + gr - Cy
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
return(list(catch = Cy, discards = Cy*dr, landings = Cy*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
catch.tg <- function(stock, gr, target, year){ #
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
By1 <- By + gr - target
catch <- ifelse(target > By, 0.9*By, target)
Fy <- catch/By # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
landings.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
catch <- target/(1-dr)
By1 <- By + gr - catch
catch <- ifelse(catch > By, 0.9*By, catch)
Fy <- catch/By # [it]
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
discards.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
catch <- target/dr
catch <- ifelse(catch > By, 0.9*By, catch)
Fy <- catch/By # [it]
By1 <- By + gr - catch
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
f.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
Fy <- target
if(Fy >= 1) stop('Harvest rate must be < 1')
catch <- Fy*By
By1 <- By + gr - catch
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
f.landings.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
Fy <- target/(1-dr)
if(Fy >= 1) stop('Harvest rate must be < 1')
catch <- Fy*By
By1 <- By + gr - catch
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
f.discards.tg <- function(stock, gr, target, year){
By_1 <- (stock@stock.n*stock@stock.wt)[,year-1,drop=T] # [it]
Cy_1 <- (stock@catch)[,year-1,drop = T] # [it]
By <- By_1 + gr - Cy_1 # [it]
# Discards and landings (3 years average for the ratio)
dr <- yearMeans((stock@discards/stock@catch)[,(year-3):(year-1),])[drop=T] # [it]
Fy <- target/dr
if(Fy >= 1) stop('Harvest rate must be < 1')
catch <- Fy*By
By1 <- By + gr - catch
return(list(catch = catch, discards = catch*dr, landings = catch*(1-dr), f = Fy, biomass = By, biomass_next = By1))
}
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