In ben-mhamed/biodynsls: Biomass dynamic model for short-lived species

Mediterrannée

rm(list = ls())
dat <- read.csv2(file = "/home/ben-mhamed/INRH/Working Groups/Crevette/data_Med.csv",sep=",")
dat <- transform(dat,log_CPUE=log(cpue))
data <- as.list(dat)[-2]
data$n <- nrow(dat)
params <- c("AobsErr","AprocErr","r","K","q","b","B","AACPUE_pred")
l <- biodynsls(data = data,params = params,type = "A")
plotIndex(l =l ,data = data)
plotDiag(l = l,data = data)
refPoints(l = l,data = data)

l <- biodynsls(data = data,params = params,type = "Std")
plotIndex(l =l ,data = data)
plotDiag(l = l,data = data)
refPoints(l = l,data = data)

l <- biodynsls(data = data,params = params,type = "SR")
plotIndex(l =l ,data = data)
plotDiag(l = l,data = data)
refPoints(l = l,data = data)

Atlantique

rm(list = ls())
data <- read.csv2(file = "/home/ben-mhamed/INRH/Working Groups/Crevette/data_Atl.csv",sep=",")
dat <- transform(dat,log_CPUE1=log(cpue1),log_CPUE2=log(cpue2),log_CPUE3=log(cpue3))
data <- as.list(dat)[c(-2,-4,-6)]
data$n <- 15
params <- c("AobsErr","AprocErr","r","K","q","b","B","AACPUE_pred")
l <- biodynsls2(data = data,params = params,type = "A")
l <- fit(data = data,params = params,type = "A",n.index = 3,n.adapt = 20000,n.iter = 100000,thin = 20)
plotIndex3(l = l,data = data)
plotDiag(l = l,data = data)
refPoints3(l = l,data = data)

l <- biodynsls2(data = data,params = params,type = "Std")
plotIndex2(l = l,data = data)
plotDiag(l = l,data = data)
refPoints2(l = l,data = data)

Atlantique avec indice d'Hauturier seul

rm(list = ls())
dat <- read.csv2(file = "/home/ben-mhamed/INRH/Working Groups/Crevette/data_Atl (indice Hauturier).csv",sep=",")
dat <- transform(dat,log_CPUE=log(cpue))
data <- as.list(dat)[-2]
data$n <- nrow(dat)
params <- c("AobsErr","AprocErr","r","K","q","b","B","AACPUE_pred")
l <- biodynsls(data = data,params = params,type = "A",n.adapt = 20000,n.iter = 100000,thin = 20)
plotIndex1(l =l ,data = data)
plotDiag(l = l,data = data)
refPoints1(l = l,data = data)

l <- biodynsls(data = data,params = params,type = "Std",n.adapt = 20000,n.iter = 100000,thin = 20)
plotIndex(l =l ,data = data)
plotDiag(l = l,data = data)
refPoints(l = l,data = data)

l <- biodynsls(data = data,params = params,type = "SR")
plotIndex(l =l ,data = data)
plotDiag(l = l,data = data)
refPoints(l = l,data = data)

Atlantique Last one

rm(list = ls())
data <- read.csv2(file = "/home/ben-mhamed/INRH/Working Groups/Crevette/data_Atl.csv",sep=",")
params <- c("AobsErr","AprocErr","r","K","q","b","B","AACPUE_pred")
l <- fit(data = data,params = params,type = "Std",n.index = 1,n.adapt = 20000,n.iter = 100000,thin = 20)
plotIndex(l = l,data = data)
plotDiag(l = l,data = data)
refPoints(l = l,data = data)

l <- biodynsls2(data = data,params = params,type = "Std")
plotIndex2(l = l,data = data)
plotDiag(l = l,data = data)
refPoints2(l = l,data = data)