Ecological Modeling

  1. The Modeling Cycle: From Concept to Application
    1. Step 1: Problem Formulation and Objectives
      1. Defining the Question
        1. Identifying Research Goals
          1. Identifying Management Goals
            1. Stakeholder Engagement
            2. Identifying the System and its Boundaries
              1. System Components and Interactions
                1. Temporal Boundaries
                  1. Spatial Boundaries
                  2. Determining the Required Output
                    1. Model Outputs and Performance Metrics
                      1. Precision Requirements
                        1. Time Horizons
                      2. Step 2: Model Conceptualization
                        1. Identifying Key Variables and Processes
                          1. State Variables
                            1. Parameters and Drivers
                              1. Forcing Functions
                              2. Creating a Conceptual Diagram
                                1. Flowcharts
                                  1. Stock-and-Flow Diagrams
                                    1. Influence Diagrams
                                    2. Making Assumptions and Justifications
                                      1. Rationale for Simplifications
                                        1. Implications of Assumptions
                                          1. Assumption Documentation
                                        2. Step 3: Mathematical Formulation
                                          1. Choosing the Model Type
                                            1. Selection Criteria
                                              1. Trade-off Analysis
                                              2. Writing Equations
                                                1. Formulation of Model Equations
                                                  1. Dimensional Analysis
                                                    1. Conservation Laws
                                                    2. Defining Variables and Parameters
                                                      1. State Variables
                                                        1. Parameters
                                                          1. Driving Variables
                                                            1. Initial Conditions
                                                              1. Boundary Conditions
                                                            2. Step 4: Parameterization
                                                              1. Parameter Classification
                                                                1. Fixed Parameters
                                                                  1. Variable Parameters
                                                                    1. Uncertain Parameters
                                                                    2. Sources of Parameter Values
                                                                      1. Literature Review
                                                                        1. Field Experiments
                                                                          1. Laboratory Experiments
                                                                            1. Expert Knowledge
                                                                              1. Estimation from Data
                                                                              2. Parameter Estimation Methods
                                                                                1. Least Squares Fitting
                                                                                  1. Maximum Likelihood Estimation
                                                                                    1. Bayesian Parameter Estimation
                                                                                  2. Step 5: Model Implementation
                                                                                    1. Choosing a Software Environment
                                                                                      1. Programming Languages
                                                                                        1. Modeling Platforms
                                                                                          1. Specialized Software
                                                                                          2. Numerical Methods
                                                                                            1. Analytical Solutions
                                                                                              1. Numerical Solutions
                                                                                                1. Time-Stepping Methods
                                                                                                  1. Spatial Discretization
                                                                                                  2. Coding and Documentation
                                                                                                    1. Code Structure
                                                                                                      1. Documentation Standards
                                                                                                        1. Version Control
                                                                                                          1. Error Checking
                                                                                                            1. Debugging Strategies
                                                                                                          2. Step 6: Model Verification and Analysis
                                                                                                            1. Verification Procedures
                                                                                                              1. Code Testing
                                                                                                                1. Unit Testing
                                                                                                                  1. Integration Testing
                                                                                                                  2. Sensitivity Analysis
                                                                                                                    1. Local Sensitivity Analysis
                                                                                                                      1. Global Sensitivity Analysis
                                                                                                                        1. Parameter Ranking
                                                                                                                        2. Uncertainty Analysis
                                                                                                                          1. Parameter Uncertainty
                                                                                                                            1. Model Structure Uncertainty
                                                                                                                              1. Scenario Uncertainty
                                                                                                                                1. Uncertainty Propagation
                                                                                                                              2. Step 7: Calibration and Validation
                                                                                                                                1. Calibration Techniques
                                                                                                                                  1. Manual Calibration
                                                                                                                                    1. Automated Calibration
                                                                                                                                      1. Multi-objective Calibration
                                                                                                                                      2. Validation Approaches
                                                                                                                                        1. Split-Sample Validation
                                                                                                                                          1. Cross-Validation
                                                                                                                                            1. Independent Data Validation
                                                                                                                                            2. Goodness-of-Fit Measures
                                                                                                                                              1. Statistical Measures
                                                                                                                                                1. Visual Assessment
                                                                                                                                                  1. Pattern-Based Validation
                                                                                                                                                2. Step 8: Application and Interpretation
                                                                                                                                                  1. Scenario Development
                                                                                                                                                    1. Baseline Scenarios
                                                                                                                                                      1. Alternative Scenarios
                                                                                                                                                        1. Extreme Scenarios
                                                                                                                                                        2. Model Output Analysis
                                                                                                                                                          1. Statistical Analysis
                                                                                                                                                            1. Trend Analysis
                                                                                                                                                              1. Threshold Detection
                                                                                                                                                              2. Result Interpretation
                                                                                                                                                                1. Ecological Interpretation
                                                                                                                                                                  1. Management Implications
                                                                                                                                                                    1. Policy Recommendations
                                                                                                                                                                    2. Communication and Reporting
                                                                                                                                                                      1. Uncertainty Communication
                                                                                                                                                                        1. Visualization Techniques
                                                                                                                                                                          1. Stakeholder Engagement

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                                                                                                                                                                      5. Core Models in Population Ecology