Cover -- Title -- Copyright -- Contents -- Preface -- Acknowledgments -- PART 1. MODELING -- Chapter 1. Introduction -- 1.1 Why Individual-based Modeling and Ecology? -- 1.2 Linking Individual Traits and System Complexity: Three Examples -- 1.3 Individual-based Ecology -- 1.4 Early IBMs and Their Research Programs -- 1.5 What Makes a Model an IBM? -- 1.6 Status and Challenges of the Individual-based Approach -- 1.7 Conclusions and Outlook -- Chapter 2. A Primer to Modeling -- 2.1 Introduction -- 2.2 Heuristics for Modeling -- 2.3 The Modeling Cycle -- 2.4 Summary and Discussion -- Chapter 3. Pattern-oriented Modeling -- 3.1 Introduction -- 3.2 Why Patterns, and What Are Patterns? -- 3.3 The Tasks of Pattern-oriented Modeling -- 3.4 Discussion -- PART 2. INDIVIDUAL-BASED ECOLOGY -- Chapter 4. Theory in Individual-based Ecology -- 4.1 Introduction -- 4.2 Basis for Theory in IBE -- 4.3 Goals of IBE Theory -- 4.4 Theory Structure -- 4.5 Theory Development Cycle -- 4.6 Example: Development of Habitat Selection Theory for Trout -- 4.7 Summary and Discussion -- Chapter 5. A Conceptual Framework for Designing Individual-based Models -- 5.1 Introduction -- 5.2 Emergence -- 5.3 Adaptive Traits and Behavior -- 5.4 Fitness -- 5.5 Prediction -- 5.6 Interaction -- 5.7 Sensing -- 5.8 Stochasticity -- 5.9 Collectives -- 5.10 Scheduling -- 5.11 Observation -- 5.12 Summary and Conclusions -- 5.13 Conceptual Design Checklist -- Chapter 6. Examples -- 6.1 Introduction -- 6.2 Group and Social Behavior -- 6.3 Population Dynamics of Social Animals -- 6.4 Movement: Dispersal and Habitat Selection -- 6.5 Regulation of Hypothetical Populations -- 6.6 Comparison with Classical Models -- 6.7 Dynamics of Plant Populations and Communities -- 6.8 Structure of Communities and Ecosystems -- 6.9 Artificially Evolved Traits -- 6.10 Summary and Conclusions.

PART 3. THE ENGINE ROOM -- Chapter 7. Formulating Individual-based Models -- 7.1 Introduction -- 7.2 Contents of an IBM Formulation -- 7.3 Formulating an IBM's Spatial Elements -- 7.4 Formulating Logical and Probabilistic Rules -- 7.5 Formulating Adaptive Traits -- 7.6 Controlling Uncertainty -- 7.7 Using Object-oriented Design and Description -- 7.8 Using Mechanistic and Discrete Mathematics -- 7.9 Designing Superindividuals -- 7.10 Summary and Conclusions -- Chapter 8. Software for Individual-based Models -- 8.1 Introduction -- 8.2 The Importance of Software Design for IBMs -- 8.3 Software Terminology and Concepts -- 8.4 Software Platforms -- 8.5 Software Testing -- 8.6 Moving Software Development Forward -- 8.7 Important Implementation Techniques -- 8.8 Some Favorite Software Myths -- 8.9 Summary and Conclusions -- Chapter 9. Analyzing Individual-based Models -- 9.1 Introduction -- 9.2 Steps in Analyzing an IBM -- 9.3 General Strategies for Analyzing IBMs -- 9.4 Techniques for Analyzing IBMs -- 9.5 Statistical Analysis -- 9.6 Sensitivity and Uncertainty Analysis -- 9.7 Robustness Analysis -- 9.8 Parameterization -- 9.9 Independent Predictions -- 9.10 Summary and Conclusions -- Chapter 10. Communicating Individual-based Models and Research -- 10.1 Introduction -- 10.2 Types of IBE Work to Communicate -- 10.3 Complete and Efficient Model Description -- 10.4 Common Review Comments -- 10.5 Visual Communication of Executable Models -- 10.6 Communicating Software -- 10.7 Summary and Conclusions -- PART 4. CONCLUSIONS AND OUTLOOK -- Chapter 11. Using Analytical Models in Individual-based Ecology -- 11.1 Introduction -- 11.2 Classifications of Ecological Models -- 11.3 Benefits of Analytical Models -- 11.4 Analytical Approximation of IBMs -- 11.5 Using Analytical Models to Understand and Analyze IBMs -- 11.6 Summary and Discussion.

Chapter 12. Conclusions and Outlook for Individual-based Ecology -- 12.1 Introduction -- 12.2 Why Do We Need IBE? -- 12.3 How Is IBE Different From Traditional Ecology? -- 12.4 What Can Ecology Contribute to the Science of Complex Systems? -- 12.5 A Visit to the Individual-based Ecology Laboratory -- Glossary -- References -- Index.