Package: SPoRC 0.1.0

Setup Model Dimensions | Setup Recruitment Dynamics | Setup Biological Dynamics | Setup Movement and Tagging | Setup Catch and Fishing Mortality | Setup Fishery Indices and Compositions | Setup Survey Indices and Compositions | Setting up Fishery Selectivity and Catchability | Setting up Survey Selectivity and Catchability | Setup Model Weighting | Fit Model and Plot

Define Operating Model | Define Management Options | Define Estimation Model | Define and Run Closed-Loop Simulation

Reference Points | Single Region | Spawning Potential Ratio | Maximum Sustainable Yield (Beverton-Holt) | Multi-Region | Independent | Global | Local | Deriving Catch Advice and Projections | Code Demonstration | Getting Reference Points | Multi Region | Conducting Catch Projections to Derive Catch Advice (Deterministic Recruitment) | Conducting Stochastic Population Projections | References

Overview | Estimation Model | Projection Options | Functions to Determine Catch | Management Procedures | Simulation Loop (Single Replicate) | Simulation Loop (Parrallelized) | Condition Closed Loop Simulation | Run Simulations | Process Results | Visualize

Data Inputs for Defining Model Dimensions | Data Inputs for Defining Recruitment Processes | Data Inputs for Defining Biological Processes | Data Inputs for Defining Movement Processes | Data Inputs for Defining Tagging Processes | Data Inputs for Defining Catch and Fishing Mortality Processes | Data Inputs for Defining Fishery Indices and Compositions | Data Inputs for Defining Survey Indices and Compositions | Data Inputs for Defining Fishery Selectivity and Catchability | Data Inputs for Defining Survey Selectivity and Catchability | Data Inputs for Defining Model Weighting

Process Equations | Population Initialization | Recruitment Processes | Population Projection | Observation Equations | Fishery Observation Model | Survey Observation Model | Tagging Observation Model | Fishery and Survey Selectivity | Likelihoods | Observation Likelihoods | Fishery Catches | Fishery and Survey Indices | Fishery and Survey Compositions | Structuring Compositions and Ageing Error | Tagging | Parameter Priors and Process Error Penalties | Parameter Priors | Natural Mortality | Fishery and Survey Catchability | Steepness | Recruitment Proportions | Movement | Tag Reporting Rates | Process Error Penalties | Initial Age Deviations | Recruitment Deviations | Fishing Mortality Deviations | Joint Likelihood | References

Simulation Settings | Population, Recruitment, and Biological Processes | Fishery Processes | Survey Processes | Tagging

Setup Model Dimensions | Setup Recruitment Dynamics | Setup Biological Dynamics | Setup Movement and Tagging Dynamics | Setup Catch and Fishing Mortality | Setup Index and Composition Data (Fishery and Survey) | Setup Selectivity and Catchability (Fishery and Survey) | Setup Model Weighting | Fit Model and Plot

Simulation Cross-Testing in SPoRC | Define Model Dimensions | Fishing Processes | Survey Processes | Biological Dynamics | Tagging and Movement | Recruitment | Run the Operating Model | Define Estimation Model | Run Cross-Test Analysis | Self Testing

Load data and packages | Setup model | Setup Recruitment Dynamics | Setup biological dynamics | Setup Movement and Tagging | Setup Catch and Fishing Mortality | Setup Fishery Indices and Compositions | Setup Survey Indices and Compositions | Setup Fishery Selectivity and Catchability | Setup Survey Selectivity and Catchability | Setup Model Weighting | Fit model | Fit model (Without Francis) | Fit model (With Francis) | Check Model Results | Convergence | Time Series Results | Catch and Index Fits | Composition Fits | Fishery Ages | Fishery Lengths | Survey Ages | Retrospectives | Retrospectives (Without Francis) | Retrospectives (With Francis) | Likelihood Profiles | Jitter Analysis | MCMC | Reference Points and Projections | Reference Points | Projections | Spawning Biomass Projections | Catch Projections | Catch Advice under $F_{40%}$ | Fishing Mortality Projections

Fishery Removals | Fishery Selectivity | Fishery Catchability | Fishery Composition Likelihoods | Survey Selectivity | Survey Catchability | Survey Composition Likelihoods | Natural Mortality | Recruitment | Movement | Tagging

Biological Processes | Fishery Processes | Survey Processes | Tagging Processes | Likelihoods | Parameter Deviations | Derived Quantities

Setup Model Dimensions | Setup Recruitment Dynamics | Setup Biological Dynamics | Setup Movement and Tagging Dynamics | Setup Catch and Fishing Mortality | Setup Index and Composition Data (Fishery and Survey) | Setup Selectivity and Catchability (Fishery and Survey) | Setup Model Weighting | Fit Model and Plot

Starting Values | Mapping | Fixing Parameters | Sharing Parameters

Steepness | Natural Mortality | Catchability | Selectivity | Movement | Tag Reporting Rates | Recruitment Proportions