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analysis.R
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analysis.R
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library(MSEtool)
source("analysis_fn.R")
# SWO
OM <- readRDS(file = "OM/OM_ICCAT_SWO.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
SW <- get_ref_pt(Hist, OM,
Year_assess = 1999,
Name = "NAtl~swordfish",
Yr_SRP = 2002, # Year corresponding to ICES Blim (Type 5, no B_SR)
Yr_Fmed = 1979, # First year for calculating median R/S,
Yr_Brecover = NA
)
saveRDS(SW, file = "LRP/LRP_ICCAT_SWO.rds")
SW <- readRDS(file = "LRP/LRP_ICCAT_SWO.rds")
# RS
OM <- readRDS(file = "OM/OM_GoM_RS.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
RS <- get_ref_pt(Hist, OM,
Year_assess = 1990, # 1990 Gulf FMP Amendment 1, 1991 Amendment 3
Name = "GoM~Red~Snapper",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim (Type 4, no B_SR)
Yr_Fmed = 1972, # First year for calculating median R/S
Yr_Brecover = NA
)
saveRDS(RS, file = "LRP/LRP_GoM_RS.rds")
RS <- readRDS(file = "LRP/LRP_GoM_RS.rds")
# NE Acadian redfish
OM <- readRDS(file = "OM/OM_NE_redfish.rds")
OM@cpars$Wt_age_C <- NULL
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
AR <- get_ref_pt(Hist, OM,
Year_assess = 1976,
Name = "NE~Acadian~redfish",
Yr_SRP = 1971, # Year corresponding to ICES Blim
Yr_Fmed = 1960, # First year for calculating median R/S
Yr_SP = 1974,
Yr_Brecover = NA
)
saveRDS(AR, file = "LRP/LRP_NE_redfish.rds")
AR <- readRDS(file = "LRP/LRP_NE_redfish.rds")
# GoM Haddock
#OM <- readRDS("OM/OM_GoM_haddock.rds")
#Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
#
## No formal assessment between 1986-2001 overfished statement
## See Amendment 9 (1999)
#HD <- get_ref_pt(Hist, OM,
# Year_assess = 1999,
# Name = "G.M.~haddock",
# Yr_SRP = 2010, # Year corresponding to ICES Blim
# #Yr_Fmed = 1980 # First year for calculating median R/S
#)
#saveRDS(HD, file = "LRP/LRP_GoM_haddock.rds")
#
#plot_F(HD)
#plot_B(HD)
#plot_SR(HD)
#plot_Hist(HD)
#plot_SR_LRP(HD)
#plot_SP(HD)
# Southern New England yellowtail flounder
OM <- readRDS("OM/OM_sne_yt.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
SNEYT <- get_ref_pt(Hist, OM,
Year_assess = 2005, # Framework 42
Name = "SNE~yellowtail~flounder",
Yr_SRP = 1987, # Year corresponding to ICES Blim
Yr_SP = 1987,
#Yr_Fmed = 1980 # First year for calculating median R/S
Yr_Brecover = 1987
)
saveRDS(SNEYT, file = "LRP/LRP_sne_yt.rds")
# SA red porgy
OM <- readRDS(file = "OM/OM_SA_RedPorgy.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
RP <- get_ref_pt(Hist, OM,
Year_assess = 1992, # Amendment 4 (see SEDAR 60 report)
Name = "SA~red~porgy",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim
#Yr_Fmed = 1990 # First year for calculating median R/S
Yr_Brecover = NA
)
saveRDS(RP, file = "LRP/LRP_SA_RedPorgy.rds")
RP <- readRDS(file = "LRP/LRP_SA_RedPorgy.rds")
# SA gag grouper
OM <- readRDS(file = "OM/OM_SA_gag.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
gag <- get_ref_pt(Hist, OM,
Year_assess = OM@CurrentYr, #
Name = "SA~gag~grouper",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim
Yr_Fmed = 1976, # First year for calculating median R/S
Yr_SP = 2006,
Yr_Brecover = 1988
)
saveRDS(gag, file = "LRP/LRP_SA_gag.rds")
gag <- readRDS(file = "LRP/LRP_SA_gag.rds")
# Cowcod
OM <- readRDS(file = "OM/OM_SCB_cowcod.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
CC <- get_ref_pt(Hist, OM,
Year_assess = 2000, # Amendment 4 (see SEDAR 60 report)
Name = "SCB~cowcod",
Yr_SRP = NA, # Year corresponding to ICES Blim
#Yr_Fmed = 1983 # First year for calculating median R/S
Yr_Brecover = 1934
)
saveRDS(CC, file = "LRP/LRP_SCB_cowcod.rds")
CC <- readRDS(file = "LRP/LRP_SCB_cowcod.rds")
# NEA horse mackerel
OM <- readRDS(file = "OM/OM_NEA_hom.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
HOM <- get_ref_pt(Hist, OM,
Year_assess = 2020, #?
Name = "NEA~horse~mackerel",
Yr_SRP = 2017, # Year corresponding to ICES Blim
Yr_Fmed = 1982, # First year for calculating median R/S
Yr_Brecover = 1982
)
saveRDS(HOM, file = "LRP/LRP_NEA_hom.rds")
HOM <- readRDS(file = "LRP/LRP_NEA_hom.rds")
#local({
# HOM$RPts <- filter(HOM$RPts, Year >= 1983)
# plot_SR_LRP(HOM)
#})
# US Dark-blotched rockfish
OM <- readRDS(file = "OM/OM_WC_darkblotched.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
DB <- get_ref_pt(Hist, OM,
Year_assess = 2003, # Declared overfished
Name = "US~darkblotched~rockfish",
Yr_SRP = 2010, # Year corresponding to ICES Blim
Yr_Fmed = 1970, # First year for calculating median R/S
Yr_Brecover = NA
)
saveRDS(DB, file = "LRP/LRP_WC_darkblotched.rds")
DB <- readRDS(file = "LRP/LRP_WC_darkblotched.rds")
# US POP
#OM <- readRDS(file = "OM/OM_WC_pop.rds")
#Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
#
#POP <- get_ref_pt(Hist, OM,
# Year_assess = 2001, # Declared overfished
# Name = "U.S.~Pacific~ocean~perch",
# Yr_SRP = 1987, # Year corresponding to ICES Blim
# Yr_Fmed = 1965 # First year for calculating median R/S
#)
#
#saveRDS(POP, file = "LRP/LRP_WC_pop.rds")
#POP <- readRDS(file = "LRP/LRP_WC_pop.rds")
#
#local({
# POP$RPts <- filter(POP$RPts, Year != 2008)
# plot_SR_LRP(POP)
#})
#
#plot_F(POP)
#plot_B(POP)
#plot_SR(POP)
#plot_Hist(POP)
#
#plot_SR_LRP(POP)
#plot_SP(POP)
#
# sGSL cod
OM <- readRDS(file = "OM/OM_sGSL_cod.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
GSLC <- get_ref_pt(Hist, OM,
Year_assess = 1993, # See 2005 SAR
Name = "sGSL~cod",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim
Yr_Fmed = 1971, # First year for calculating median R/S,
Yr_SP = 1992,
Yr_Brecover = 1975
)
#GSLC$RPts$FMSY <- GSLC$RPts$SB0 <- GSLC$RPts$
saveRDS(GSLC, file = "LRP/LRP_sGSL_cod.rds")
GSLC <- readRDS(file = "LRP/LRP_sGSL_cod.rds")
# sGSL herring
OM <- readRDS(file = "OM/OM_sGSL_herring.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
# Update hist for change in SR rel
rp <- sapply(1:OM@nyears, function(y) {
opt2 <- optimize(SAMtool:::yield_fn_SCA, interval = c(1e-4, 4),
M = Hist@SampPars$Stock$M_ageArray[1, , y],
mat = Hist@SampPars$Stock$Mat_age[1, , y],
weight = Hist@SampPars$Stock$Wt_age[1, , y],
vul = Hist@SampPars$Fleet$V_real[1, , y],
SR = "Ricker",
Arec = ifelse(y >= 15, 8.48, 19.89),
Brec = ifelse(y >= 15, 9.7e-6, 1.21e-5),
catch_eq = "Baranov")
opt3 <- SAMtool:::yield_fn_SCA(opt2$minimum,
M = Hist@SampPars$Stock$M_ageArray[1, , y],
mat = Hist@SampPars$Stock$Mat_age[1, , y],
weight = Hist@SampPars$Stock$Wt_age[1, , y],
vul = Hist@SampPars$Fleet$V_real[1, , y],
SR = "Ricker",
Arec = ifelse(y >= 15, 8.48, 19.89),
Brec = ifelse(y >= 15, 9.7e-6, 1.21e-5),
catch_eq = "Baranov",
opt = FALSE)
FMSY <- opt2$minimum
MSY <- -1 * opt2$objective
SBMSY <- opt3["E"]
unfished <- SAMtool:::yield_fn_SCA(0,
M = Hist@SampPars$Stock$M_ageArray[1, , y],
mat = Hist@SampPars$Stock$Mat_age[1, , y],
weight = Hist@SampPars$Stock$Wt_age[1, , y],
vul = Hist@SampPars$Fleet$V_real[1, , y],
SR = "Ricker",
Arec = ifelse(y >= 15, 8.48, 19.89),
Brec = ifelse(y >= 15, 9.7e-6, 1.21e-5),
catch_eq = "Baranov",
opt = FALSE)
SB0 <- unfished["E"]
c("FMSY" = FMSY, "SBMSY" = SBMSY, "SB0" = SB0)
})
Hist@Ref$ByYear$FMSY[1, 1:OM@nyears] <- rp[1, ]
Hist@Ref$ByYear$SSBMSY[1, 1:OM@nyears] <- rp[2, ]
Hist@Ref$ByYear$SSB0[1, 1:OM@nyears] <- rp[3, ]
GSLH <- get_ref_pt(Hist, OM,
Year_assess = 2002, #identified to be below LRP
Name = "sGSL~herring",
Yr_SRP = NA, # Year corresponding to ICES Blim
#Yr_Fmed = 1983 # First year for calculating median R/S
Yr_Brecover = 1981,
Yr_SP = 1980
)
saveRDS(GSLH, file = "LRP/LRP_sGSL_herring.rds")
GSLH <- readRDS(file = "LRP/LRP_sGSL_herring.rds")
# NAFO plaice
OM <- readRDS(file = "OM/OM_NAFO_plaice.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
# Calculate reference points with M = 0.2 in years where population M = 0.53 (temporary)
for(y in 1:OM@nyears) {
if(any(OM@cpars$M_ageArray[1, , y] > 0.2)) {
MSYs <- local({
OM@cpars$M_ageArray[1, , y] <- OM@cpars$M_ageArray[1, , 1]
optMSY_eq(1,
M_ageArray = OM@cpars$M_ageArray,
Wt_age = OM@cpars$Wt_age,
Mat_age = OM@cpars$Mat_age,
Fec_age = OM@cpars$Mat_age * OM@cpars$Wt_age,
V = OM@cpars$V,
maxage = OM@maxage,
R0 = OM@cpars$R0,
SRrel = OM@SRrel,
hs = OM@cpars$hs,
SSBpR = Hist@SampPars$Stock$SSBpR,
yr.ind = y,
plusgroup = 1,
StockPars = list(relRfun = function(...) NULL,
SRRpars = list(data.frame())))
})
Fcalc <- local({
OM@cpars$M_ageArray[1, , y] <- OM@cpars$M_ageArray[1, , 1]
boundsF <- c(1E-3, 3)
F_search <- exp(seq(log(min(boundsF)), log(max(boundsF)), length.out = 50))
Ref_search <- MSEtool:::Ref_int_cpp(F_search,
M_at_Age = OM@cpars$M_ageArray[1, , y],
Wt_at_Age = OM@cpars$Wt_age[1, , y],
Mat_at_Age = OM@cpars$Mat_age[1, , y],
Fec_at_Age = OM@cpars$Wt_age[1, , y] * OM@cpars$Mat_age[1, , y],
V_at_Age = OM@cpars$V[1, , y],
maxage = OM@maxage,
relRfun = function(...) NULL,
SRRpars = data.frame(),
plusgroup = 1)
RPS <- Ref_search[3,]
SSB <- Hist@TSdata$SBiomass[1, , ] %>% rowSums()
R <- Hist@AtAge$Number[1, 1, , ] %>% rowSums()
Fmed <- MSEtool:::LinInterp_cpp(RPS, F_search, xlev = median(R/SSB))
Fmed
})
Hist@Ref$ByYear$FMSY[1, y] <- MSYs["F"]
Hist@Ref$ByYear$SSBMSY[1, y] <- MSYs["SB"]
Hist@Ref$ByYear$SSB0[1, y] <- MSYs["SB0"]
Hist@Ref$ByYear$Fmed[1, y] <- Fcalc
}
}
PL <- get_ref_pt(Hist, OM,
Year_assess = 1994, # Fishing moratorium
Name = "NAFO~plaice",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim
#Yr_Fmed = 1960, # First year for calculating median R/S
Yr_SP = 1993,
Yr_Brecover = 1976
)
saveRDS(PL, file = "LRP/LRP_NAFO_plaice.rds")
PL <- readRDS(file = "LRP/LRP_NAFO_plaice.rds")
#plot_F(PL)
#plot_B(PL)
#plot_SR(PL)
#ggsave("SR_plaice.png", height = 4, width = 5)
#plot_Hist(PL)
#plot_SR_LRP(PL)
#plot_SP(PL)
# NAFO cod
OM <- readRDS(file = "OM/OM_NAFO_cod.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
NAFOcod <- get_ref_pt(Hist, OM,
Year_assess = 1994, # Fishing moratorium
Name = "NAFO~cod",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim
#Yr_Fmed = 1960, # First year for calculating median R/S
Yr_SP = 1991,
Yr_Brecover = 1976
)
saveRDS(NAFOcod, file = "LRP/LRP_NAFO_cod.rds")
NAFOcod <- readRDS(file = "LRP/LRP_NAFO_cod.rds")
#plot_F(NAFOcod)
#plot_B(NAFOcod)
#plot_SR(NAFOcod)
#ggsave("SR_plaice.png", height = 4, width = 5)
#plot_Hist(NAFOcod)
#plot_SR_LRP(NAFOcod)
#plot_SP(NAFOcod)
# GoM cod
OM <- readRDS(file = "OM/OM_GoM_cod.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
GoM_cod <- get_ref_pt(Hist, OM,
Year_assess = 2005, # Framework 42
Name = "GM~cod",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim
#Yr_Fmed = 1960, # First year for calculating median R/S
Yr_SP = 2011,
Yr_Brecover = 1994
)
saveRDS(GoM_cod, file = "LRP/LRP_GoM_cod.rds")
GoM_cod <- readRDS(file = "LRP/LRP_GoM_cod.rds")
# BET
OM <- readRDS(file = "OM/OM_ICCAT_BET.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
BET <- get_ref_pt(Hist, OM,
Year_assess = 2018, # ICCAT resolutions and lobbying
Name = "Atlantic~bigeye~tuna",
Yr_SRP = 2011, # Year corresponding to ICES Blim
Yr_Fmed = 1973, # First year for calculating median R/S
Yr_Brecover = NA
)
saveRDS(BET, file = "LRP/LRP_ICCAT_BET.rds")
BET <- readRDS(file = "LRP/LRP_ICCAT_BET.rds")
# WCVI herring
OM <- readRDS(file = "OM/OM_WCVI_herring.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
WCVI <- get_ref_pt(Hist, OM,
Year_assess = 2005, # close fishery
Name = "WCVI~Pacific~herring",
Yr_SRP = "hockey_stick", # Year corresponding to ICES Blim
Yr_Fmed = 1951, # First year for calculating median R/S
Yr_SP = 2005,
Yr_Brecover = 1968
)
saveRDS(WCVI, file = "LRP/LRP_WCVI_herring.rds")
# EBS cod
OM <- readRDS(file = "OM/OM_EBS_cod.rds")
Hist <- SubCpars(OM, 1:2) %>% runMSE(Hist = TRUE, silent = TRUE)
EBScod <- get_ref_pt(Hist, OM,
Year_assess = 2019, # zero catch advised https://doi.org/10.17895/ices.advice.4747
Name = "EBS~cod",
Yr_SRP = 2012, # Year corresponding to ICES Blim
Yr_Fmed = 1946, # First year for calculating median R/S
Yr_SP = 2012,
Yr_Brecover = 1960
)
saveRDS(EBScod, file = "LRP/LRP_EBS_cod.rds")