A function that uses the file location of a fitted SS3 model including input files to population the various slots of an operating model with MLE parameter estimates. The function mainly populates the Stock and Fleet portions of the operating model; the user still needs to parameterize most of the observation and implementation portions of the operating model.
SS2OM(SSdir, nsim = 48, proyears = 50, reps = 1, maxF = 3,
seed = 1, Obs = DLMtool::Generic_Obs, Imp = DLMtool::Perfect_Imp,
import_mov = TRUE, gender = 1,
Name = "OM generated by SS2OM function",
Source = "No source provided", Author = "No author provided", ...)A folder with Stock Synthesis input and output files in it.
The number of simulations to take for parameters with uncertainty (for OM@cpars custom parameters).
The number of projection years for MSE
The number of stochastic replicates within each simulation in the operating model.
The maximum allowable F in the operating model.
The random seed for the operating model.
The observation model (class Obs).
The implementation model (class Imp).
Logical, whether to import movement matrix from the assessment.
An integer index for the sex for which life history values are importing (1 = female, 2 = male).
The name of the operating model
Reference to assessment documentation e.g. a url
Who did the assessment
Arguments to pass to SS_output.
An object of class OM.
The function generally uses values from the terminal year of the assessment for most life history parameters (maturity, M, etc). This function does detect time-varying growth in the assessment and uses annual length/weight-at-age for historical years. Selectivity is derived from the F-at-age matrix.