The SS2OM function is used to import an operating model from SS3 output to an OM object in openMSE.
The SS2OM function requires an argument specifying the location of the SS3 output:
SSdir <- 'C:/SS_examples/Simple_discard'Then SS2OM is used to create the OM object from the SS3 output:
OM <- SS2OM(SSdir)## -- Using function SS_output of package r4ss version 1.43.0 to extract
## data from SS file structure --## Reading directory: G:/Shared drives/BM shared/4.
## Resources/9_SS_examples/Simple_discard## -- End of r4ss operations --## Converting SS output to MOM...## 2 - sex and 1 - fleet model detected.## Converting MOM to OM...You will notice the SS2OM function first creates an MOM object from the SS3 output, and then converts the MOM object to an OM object.
If there are multiple fleets in the SS3 model, the aggregate fleet characteristics are calculated for the OM object. If there are multiple stocks (e.g., male and female) in the SS3 model, the average stock values are used in the OM object. See Converting MOM to OM for more details.
See ?SS2OM for details on additional optional arguments for the SS2OM function.
Simulate OM
The historical fishery can be simulated in the usual way:
Hist <- Simulate(OM)Compare OM and SS3 Output
The fishery dynamics generated by the OM object can be compared to those predicted by the SS3 output with the plot_SS2OM function:
plot_SS2OM(Hist, SSdir)This function generates a HTML report with plots of stock and fishery dynamics (e.g., numbers, biomass, catch) from the OM. For example, the OM comparison report for the above example is available here.
If the SS3 model has multiple stocks with sexual dimorphism, there may be a discrepancy between some of the values predicted by SS3 (e.g., spawning biomass) and those generated by the single-stock OM.