stkMed: stkMed dataset

In marchtaylor/FLIBM: Individual-based operating model for fisheries simulations

stkMed dataset

Description

The stkMed 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(stkMed)
plot(stkMed$stock.a@stock.n)


set.seed(42) # for reproducibility

stkMed <- create.FLIBM(
  length = seq(0,70,2), age = 0:10,
  year = ac(1980:2099), season = ac(1:12),
  n.units = "1e3", wt.units = "kg"
)

### SRR

# pulsed recruitment (March-May)
stkMed$rec$params$season_wt[] <- 0
stkMed$rec$params$season_wt[3:5] <- c(0.25, 1, 0.25)

# SRR params
stkMed$rec$params['rmax'] <- 1e4
stkMed$rec$params['beta'] <- 1

# addl. variability
# add log-normal noise to rec covar (one value per year)
stkMed$rec$covar[] <- rlnorm(n = dim(stkMed$rec$covar)[2],
  meanlog = 0, sdlog = 0.5)



### Growth
stkMed$growth$params$popLinf <- 64.6
stkMed$growth$params$Linf.cv <- 0.1
stkMed$growth$params$popK <- 0.21
stkMed$growth$params$K.cv <- 0.1
stkMed$growth$params$LWa <- 0.018
stkMed$growth$params$LWb <- 2.895
stkMed$growth$params$Lmat <- 34
stkMed$growth$params$Lmat_w <- 6.8

### Mortality
stkMed$m$model <- function (length) {return(0.32)}
stkMed$harvest$params$L50 <- 11
stkMed$harvest$params$wqs <- 2.2
stkMed$harvest$params$FM <- 0.16


# Fbar ages
# range(stkMed$stock.a)[c("minfbar", "maxfbar")] <- c(1,3)

# Spin-up
stkMed <- spinup.FLIBM(obj = stkMed, nyearsmax = 30, nyearsslope = 5)

# Advance first 20 years
stkMed <- adv.FLIBM(obj = stkMed, years = ac(1980:1999))

# plot stock numbers
plot(stkMed$stock.a@stock.n[,ac(1980:1999)])
plot(stkMed$stock.a@harvest[,ac(1980:1999)])

# save(stkMed, file = "data/stkMed.rda")

marchtaylor/FLIBM documentation built on Jan. 19, 2025, 10:56 p.m.