MSEtool (version 2.0.1)

SSS: Simple Stock Synthesis

Description

A simple age-structured model (SCA_Pope) fitted to a time series of catch going back to unfished conditions. Terminal depletion (ratio of current biomass to unfished biomass) is by default fixed to 0.4. Selectivity is fixed to the maturity ogive, although it can be overridden with the start argument. The sole parameter estimated is R0 (unfished recruitment).

Usage

SSS(
  x = 1,
  Data,
  dep = 0.4,
  SR = c("BH", "Ricker"),
  rescale = "mean1",
  start = NULL,
  silent = TRUE,
  opt_hess = FALSE,
  n_restart = ifelse(opt_hess, 0, 1),
  control = list(iter.max = 2e+05, eval.max = 4e+05),
  ...
)

Arguments

x

A position in the Data object (by default, equal to one for assessments).

Data

An object of class Data

dep

Depletion value to use in the model. Can be an expression that will be evaluated inside the function.

SR

Stock-recruit function (either "BH" for Beverton-Holt or "Ricker").

rescale

A multiplicative factor that rescales the catch in the assessment model, which can improve convergence. By default, "mean1" scales the catch so that time series mean is 1, otherwise a numeric. Output is re-converted back to original units.

start

Optional named list of starting values. Entries can be expressions that are evaluated in the function:

• R0 - unfished recruitment

• vul_par - a length-two vector for the age of 95% and 50% fleet selectivity. Fixed to maturity otherwise.

silent

Logical, passed to MakeADFun, whether TMB will print trace information during optimization. Used for dignostics for model convergence.

opt_hess

Logical, whether the hessian function will be passed to nlminb during optimization (this generally reduces the number of iterations to convergence, but is memory and time intensive and does not guarantee an increase in convergence rate).

n_restart

The number of restarts (calls to nlminb) in the optimization procedure, so long as the model hasn't converged. The optimization continues from the parameters from the previous (re)start.

control

A named list of agruments for optimization to be passed to nlminb.

...

Other arguments to be passed (not currently used).

References

Cope, J.M. 2013. Implementing a statistical catch-at-age model (Stock Synthesis) as a tool for deriving overfishing limits in data-limited situations. Fisheries Research 142:3-14.

Examples

# NOT RUN {
res <- SSS(1, Data = Red_snapper)

SSS_MP <- make_MP(SSS, HCR40_10, dep = 0.3) # Always assume depletion = 0.3
# }