lfqGen: Generate length frequency data from a synthetic fish...
In marchtaylor/fishdynr: Fisheries science related population dynamics models

Description Usage Arguments Value References Examples

See dt_growth_soVB for information on growth function. The model creates variation in growth based on a mean phi prime value for the population, which describes relationship between individual Linf and K values. See Vakily (1992) for more details.

lfqGen(tincr = 1/12, K.mu = 0.5, K.cv = 0.1, Linf.mu = 80,
  Linf.cv = 0.1, ts = 0, C = 0.85, LWa = 0.01, LWb = 3,
  Lmat = 0.5 * Linf.mu, wmat = Lmat * 0.2, rmax = 10000, beta = 1,
  repro_wt = c(0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0), M = 0.7,
  harvest_rate = M, L50 = 0.25 * Linf.mu, wqs = L50 * 0.2,
  bin.size = 1, timemin = 0, timemax = 20,
  timemin.date = as.Date("1980-01-01"), N0 = 10000,
  fished_t = seq(17, 19, tincr), lfqFrac = 1, progressBar = TRUE)

`tincr`	time increment for simulation (default = 1/12; i.e. 1 month)
`K.mu`	mean K (growth parameter from von Bertalanffy growth function)
`K.cv`	coefficient of variation on K
`Linf.mu`	mean Linf (infinite length parameter from von Bertalanffy growth function)
`Linf.cv`	coefficient of variation on Linf
`ts`	summer point (range 0 to 1) (parameter from seasonally oscillating von Bertalanffy growth function)
`C`	strength of seasonal oscillation (range 0 to 1) (parameter from seasonally oscillating von Bertalanffy growth function)
`LWa`	length-weight relationship constant 'a' (W = a*L^b). Model assumed length in cm and weight in kg.
`LWb`	length-weight relationship constant 'b' (W = a*L^b). Model assumed length in cm and weight in kg.
`Lmat`	length at maturity (where 50% of individuals are mature)
`wmat`	width between 25% and 75% quantiles for Lmat
`rmax`	parameter for Beverton-Holt stock recruitment relationship (see `srrBH`)
`beta`	parameter for Beverton-Holt stock recruitment relationship (see `srrBH`)
`repro_wt`	weight of reproduction (vector of monthly reproduction weight)
`M`	natural mortality
`harvest_rate`	Fishing mortality (i.e. 'F')
`L50`	minimum length of capture (in cm). Where selectivity equals 0.5. Assumes logistic ogive typical of trawl net selectivity.
`wqs`	width of selectivity ogive (in cm)
`bin.size`	resulting bin size for length frequencies (in cm)
`timemin`	time at start of simulation (in years). Typically set to zero.
`timemax`	time at end of simulation (in years).
`timemin.date`	date corresponding to timemin (of "Date" class)
`N0`	starting number of individuals
`fished_t`	times when stock is fished
`lfqFrac`	fraction of fished stock that are sampled for length frequency data (default = 1).
`progressBar`	Logical. Should progress bar be shown in console (Default=TRUE)

a list containing growth parameters and length frequency object

Vakily, J.M., 1992. Determination and comparison of bivalve growth, with emphasis on Thailand and other tropical areas. WorldFish.

Munro, J.L., Pauly, D., 1983. A simple method for comparing the growth of fishes and invertebrates. Fishbyte 1, 5-6.

Pauly, D., Munro, J., 1984. Once more on the comparison of growth in fish and invertebrates. Fishbyte (Philippines).

res <- lfqGen()
names(res)

op <- par(mfcol=c(2,1), mar=c(4,4,1,1))
plot(N ~ dates, data=res$pop, t="l")
plot(B ~ dates, data=res$pop, t="l", ylab="B, SSB")
lines(SSB ~ dates, data=res$pop, t="l", lty=2)
par(op)

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