stk1: stk1 dataset
| stk1 | R Documentation |
stk1 dataset
Description
The stk1 data generated with the with FLIBM.
The stock has a seasonal recruitment pattern, with interannual
variation in recruitment strength.
See example for script used to generate data.
Usage
data(stk1)
Format
FLIBM class object
Examples
library(FLIBM)
# to load and plot
data(stk1)
plot(stk1$stock.a@stock.n)
# data generation
set.seed(42)
stk1 <- create.FLIBM(
length = 0:85, age = 0:6,
year = ac(1960:2000), season = ac(1:12),
n.units = "1e3", wt.units = "kg"
)
# pulsed recruitment (March-May)
stk1$rec$params$season_wt[] <- 0
stk1$rec$params$season_wt[3:5] <- c(0.25, 1, 0.25)
# SRR params
stk1$rec$params['rmax'] <- 1e4
# add log-normal noise to rec covar (one value per year)
stk1$rec$covar[] <- rlnorm(n = dim(stk1$rec$covar)[2],
meanlog = 0, sdlog = 0.5)
# Fbar ages
range(stk1$stock.a)[c("minfbar", "maxfbar")] <- c(1,3)
# historical F
yrs <- 1960:2000
steepness <- 0.25
FMmax <- 1
FMs <- FMmax / (1 + exp(-steepness * (yrs - 1990) ))
plot(yrs, FMs)
# Advance
for(yr in seq(yrs)){
stk1$harvest$params$FM <- FMs[yr]
stk1 <- adv.FLIBM(obj = stk1, years = ac(yrs[yr]))
}
# plot stock numbers
plot(stk1$stock.a@stock.n)
# trim
summary(stk1)
ymin <- 1980
ymax <- 1999
stk1$stock.a <- trim(stk1$stock.a, year = 1980:1999)
stk1$stock.l <- trim(stk1$stock.l, year = 1980:1999)
stk1$length.a <- trim(stk1$length.a, year = 1980:1999)
stk1$age.l <- trim(stk1$age.l, year = 1980:1999)
# plot stock numbers
plot(stk1$stock.a@stock.n)
# plot yearly object
stkYr <- simplifySeason(stk1)
stkYr <- stkYr[ac(1:range(stkYr)["max"]),] # remove age 0
plot(stkYr)
# save(stk1, file = "data/stk1.rda")
