stockSim: Simulation of a stock
In marchtaylor/fishdynr: Fisheries science related population dynamics models

Description Usage Arguments Details Value References Examples

stockSim simulates a stock using variable fishing mortality and stock recruitment relationship

1	stockSim(params, nyears = 100, Ft = 0, env_at = 1, env_bt = 1)

`params`	List of parameters for the population. Applies a single cohort simulation for the initial population state using `cohortSim` function
`nyears`	number of years in the simulation
`Ft`	time series vector for fishing mortality. If a single value, then the function assumes a constant fishing mortality for the entire simulation (default=0)
`env_at`	time series vector for environmental effects to maximum recruitment (e.g. `srrFecBH_a` in `srrFecBH`) (default=1).
`env_bt`	time series vector for environmental effects to half maximum recruitment parameter (e.g. `srrFecBH_b` in `srrFecBH`) (default=1).

params list should contain the following parameters:

species Species name
growthFun Name of growth function (e.g. "growth_VB" is the von Bertalanffy growth function)
amax Maximum age
LWa Length-weight relationship parameter a (weight~a*length^b)
LWb Length-weight relationship parameter b (weight~a*length^b)
M Natural mortality
F Fishing mortality
N0 Number of individuals at time 0
matFun Name of maturity function (e.g. "pmat_w" is a logistic function that includes width, w, of quantiles)
selectFun Function to use for gear selection. Determines lengths vulnerable to fishing mortality (e.g. "gillnet" and "knife_edge" functions).
srrFun Stock-recruitment relationship function (e.g. "srrFecBH").
fec Number of eggs produced per weight [g] of mature female (For use in srrFecFun).
... Other parameters for growth, maturity, and selectivity functions.

For fitting an optimal time series of fishing mortalities, Ft, see optim.stockSim (Walters and Martell, 2004).

A list

Btc matrix. Stock biomass by time (rows) and cohort (columns).
Ytc matrix. Fishery yield by time (rows) and cohort (columns).
Bt vector. Stock biomass by time.
Yt vector. Fishery yield by time.
Nt vector. Stock size (in numbers) by time.
Ct vector. Fishery catch (in numbers) by time.

Walters, C. J., Martell, S. J., 2004. Fisheries ecology and management. Princeton University Press.

data(tilapia)
params <- tilapia
params$knife_edge_size <- 20
params$N0 <- 1e9
nyears <- 50
Ft <- rep(0.5, nyears)
set.seed(1)
env_at <- runif(nyears, min=0.5, max=1.5)
env_bt <- rep(1, nyears); env_bt[20:35] <- 0.5
tmp <- stockSim(Ft=Ft, params=params, nyears=nyears, env_at=env_at, env_bt=env_bt)
plot(tmp$Bt, t="l")
plot(tmp$Yt, t="l")
sum(tmp$Yt/1e6, na.rm=TRUE)