Overall file structure | Setting up a new operating model | Forecast file modifications | Starter file modifications | Control file modifications | Data file modifications | Setting up a new estimation model | Testing the new estimation model

Overview | Stock Synthesis | Installation | Installing | Installing Stock Synthesis | Installing dependent R packages | Scenarios | File structure | Input file structure | Simulation file structure | Example simulations | Setting up the example | Fishing mortality | Composition data | Survey index of abundance | Estimating parameters | Visualizing the results | Self test to check for bias | Setup self test | Run self-test | Checking output | Beautiful output | .csv files | Post-processing of results | Calculate the relative error (RE) | Merge scalar and time series | Separate the deterministic from the stochastic runs | Boxplots | Stochasticity | Generating observation error | calculate_data_units() | Distributional assumptions for observation error | Indices of abundance | Effective sample sizes | Age and length compositions | Sampling with overdispersion | Structure of data bins | Mean length at age | Conditional age at length | Generating process error | Reproducibility | Detailed features | Time-varying parameters in the OM | Parallel computing | References

Modifying the OM and EM models included with ss3sim