war.FLIBM: Calculate width at recruitment (WAR) of a single cohort

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

Calculate width at recruitment (WAR) of a single cohort

Description

The function 'war.FLIBM' simulates a single cohort (i.e. spawning year) and estimates the width of the cohort length distribution through time (width between defined quantiles). The width at recruitment ('$war') is then the width of the cohort when the lower quantile surpasses the length of recruitment to the fishery ('L50'). Results provide a way of estimating the 'MA' setting that should be used within the function lfqRestructure of the TropFishR package.

Usage

war.FLIBM(
  obj = NULL,
  ssbfec = 1e+06,
  FM = 0.2,
  years = dimnames(obj$stock.a)$year,
  qs = c(0.05, 0.95),
  minN = 100,
  monitor = FALSE,
  plot = TRUE
)

Arguments

obj	FLIBM object
ssbfec	numeric value. Single value describing constant spawning stock biomass (or fecundity), used in determining recruitment with obj$rec during the first year of simulation.
FM	numeric value ofmaximum fishing mortality to be applied (Default: 'FM = 0.2').
years	character vector. Years to use in simulation (from dimnames(obj$stock.a@stock.n) )
qs	numeric vector of length. Definesthe lower and upper quantiles to use in calculating 'war' (Default: 'qs = c(0.05, 0.95)')
minN	numeric value. Defines the minimum number of individuals required to estimate quantiles at a given time.
monitor	logical. Should progression be printed.
plot	logical. Should summary plot be drawn.

Value

list. Contains a summary data.frame with statistics over time over time ('$df'), and estimates of width at recruitment ('$war'), moving average ('MA'), and length at first capture ('L50').

Examples

## load data
data(stkMed)
stkMed$rec$params$rmax <- 1e4

## war analysis
set.seed(1111)
res <- war.FLIBM(obj = stkMed, qs = c(0.1, 0.9),
  FM = 0.2, years = ac(1980:1985),
  monitor = TRUE, plot = TRUE)

## estimated values
res$war # width at recruitment
res$MA # moving average setting given current bin size
res$L50 # length at first capture

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