SSS {SAMtool} | R Documentation |
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 total 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), with no process error.
Usage
SSS(
x = 1,
Data,
dep = 0.4,
SR = c("BH", "Ricker"),
rescale = "mean1",
start = NULL,
prior = list(),
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 |
rescale |
A multiplicative factor that rescales the catch in the assessment model, which
can improve convergence. By default, |
start |
Optional named list of starting values. Entries can be expressions that are evaluated in the function:
|
prior |
A named list for the parameters of any priors to be added to the model. See details in |
silent |
Logical, passed to |
opt_hess |
Logical, whether the hessian function will be passed to |
n_restart |
The number of restarts (calls to |
control |
A named list of arguments for optimization to be passed to |
... |
Other arguments to be passed (not currently used). |
Details
In SAMtool, SSS is an implementation of SCA_Pope with fixed final depletion (in terms of total biomass, not spawning biomass) assumption.
Value
An object of class Assessment.
Author(s)
Q. Huynh
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
res <- SSS(Data = Red_snapper)
SSS_MP <- make_MP(SSS, HCR40_10, dep = 0.3) # Always assume depletion = 0.3