adv.FLIBM: Advance FLIBM stock
In marchtaylor/FLIBM: Individual-based operating model for fisheries simulations

adv.FLIBM

R Documentation

Advance FLIBM stock

Description

Advance FLIBM stock

Usage

adv.FLIBM(obj, years = NULL, seasons = NULL, monitor = TRUE, purgeProb = 0.05)

Arguments

`obj`	object of class FLIBM
`years`	character vector. years to cycle for advancement. Defaults to full length of dimension. Vector should follow chronological order.
`seasons`	character vector. seasons to cycle for advancement. Defaults to full length of dimension. Vector should follow chronological order. If shorter than a full year, then the year argument should be for a single year.
`monitor`	logical. Should progression be printed.
`purgeProb`	probability of purging empty inds during time step (between 0 and 1)

Value

FLIBM object

Examples


stk <- create.FLIBM(years=ac(2000:2009))
stk$rec$params$season_wt[] <- c(0,0,0.25,1,0.25,0,0,0,0,0,0,0)
dimnames(stk$stock.l@stock.n)['year']
nrow(stk$inds)
stk$stock.a@stock.n[,'2000',,,,]

set.seed(1)
stk <- adv.FLIBM(obj = stk, years = ac(2000:2009))
plot(stk$stock.a@stock.n)

# plot length-frequency
DIM <- dim(stk$stock.l@catch.n)
DIMNAMES <- dimnames(stk$stock.l@catch.n)

lfq <- flquant2lfq(stk$stock.l@catch.n)

pal <- colorRampPalette(c("grey30",5,7,2), bias=1.5)
with(lfq, image(x=dates, y=midLengths, z=t(catch), col=pal(100)))


# numbers by age at start of the year
stk$stock.a@range[c("minfbar", "maxfbar")] <- c(2,4)
stk.yr <- simplifySeason(stk)
stk.yr <- stk.yr[2:dim(stk.yr)[1],] # removes age=0 class
plot(stk.yr)

# Biomass at age
plot(stk$stock.a@stock.n[,,,1,,]*stk$stock.a@stock.wt[,,,1,,])

# catch curve
tmp <- stk.yr@catch.n[,"2009"]
tmp
plot(1:6, log(c(tmp)))
df <- data.frame(logN = log(c(tmp))[1:4], age = 1:4)
fit <- lm(logN ~ age, df)
fit
abline(fit, col=2)

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