| |
| |
| Preface | |
| |
| |
| Acknowledgments | |
| |
| |
| |
| Modeling | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Why Individual-based Modeling and Ecology? | |
| |
| |
| |
| Linking Individual Traits and System Complexity: Three Examples | |
| |
| |
| |
| Individual-based Ecology | |
| |
| |
| |
| Early IBMs and Their Research Programs | |
| |
| |
| |
| What Makes a Model an IBM? | |
| |
| |
| |
| Status and Challenges of the Individual-based Approach | |
| |
| |
| |
| Conclusions and Outlook | |
| |
| |
| |
| A Primer to Modeling | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Heuristics for Modeling | |
| |
| |
| |
| The Modeling Cycle | |
| |
| |
| |
| Summary and Discussion | |
| |
| |
| |
| Pattern-oriented Modeling | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Why Patterns, and What Are Patterns? | |
| |
| |
| |
| The Tasks of Pattern-oriented Modeling | |
| |
| |
| |
| Discussion | |
| |
| |
| |
| Individual-based Ecology | |
| |
| |
| |
| Theory in Individual-based Ecology | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Basis for Theory in IBE | |
| |
| |
| |
| Goals of IBE Theory | |
| |
| |
| |
| Theory Structure | |
| |
| |
| |
| Theory Development Cycle | |
| |
| |
| |
| Example: Development of Habitat Selection Theory for Trout | |
| |
| |
| |
| Summary and Discussion | |
| |
| |
| |
| A Conceptual Framework for Designing Individual-based Models | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Emergence | |
| |
| |
| |
| Adaptive Traits and Behavior | |
| |
| |
| |
| Fitness | |
| |
| |
| |
| Prediction | |
| |
| |
| |
| Interaction | |
| |
| |
| |
| Sensing | |
| |
| |
| |
| Stochasticity | |
| |
| |
| |
| Collectives | |
| |
| |
| |
| Scheduling | |
| |
| |
| |
| Observation | |
| |
| |
| |
| Summary and Conclusions | |
| |
| |
| |
| Conceptual Design Checklist | |
| |
| |
| |
| Examples | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Group and Social Behavior | |
| |
| |
| |
| Population Dynamics of Social Animals | |
| |
| |
| |
| Movement: Dispersal and Habitat Selection | |
| |
| |
| |
| Regulation of Hypothetical Populations | |
| |
| |
| |
| Comparison with Classical Models | |
| |
| |
| |
| Dynamics of Plant Populations and Communities | |
| |
| |
| |
| Structure of Communities and Ecosystems | |
| |
| |
| |
| Artificially Evolved Traits | |
| |
| |
| |
| Summary and Conclusions | |
| |
| |
| |
| The Engine Room | |
| |
| |
| |
| Formulating Individual-based Models | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Contents of an IBM Formulation | |
| |
| |
| |
| Formulating an IBM's Spatial Elements | |
| |
| |
| |
| Formulating Logical and Probabilistic Rules | |
| |
| |
| |
| Formulating Adaptive Traits | |
| |
| |
| |
| Controlling Uncertainty | |
| |
| |
| |
| Using Object-oriented Design and Description | |
| |
| |
| |
| Using Mechanistic and Discrete Mathematics | |
| |
| |
| |
| Designing Superindividuals | |
| |
| |
| |
| Summary and Conclusions | |
| |
| |
| |
| Software for Individual-based Models | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| The Importance of Software Design for IBMs | |
| |
| |
| |
| Software Terminology and Concepts | |
| |
| |
| |
| Software Platforms | |
| |
| |
| |
| Software Testing | |
| |
| |
| |
| Moving Software Development Forward | |
| |
| |
| |
| Important Implementation Techniques | |
| |
| |
| |
| Some Favorite Software Myths | |
| |
| |
| |
| Summary and Conclusions | |
| |
| |
| |
| Analyzing Individual-based Models | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Steps in Analyzing an IBM | |
| |
| |
| |
| General Strategies for Analyzing IBMs | |
| |
| |
| |
| Techniques for Analyzing IBMs | |
| |
| |
| |
| Statistical Analysis | |
| |
| |
| |
| Sensitivity and Uncertainty Analysis | |
| |
| |
| |
| Robustness Analysis | |
| |
| |
| |
| Parameterization | |
| |
| |
| |
| Independent Predictions | |
| |
| |
| |
| Summary and Conclusions | |
| |
| |
| |
| Communicating Individual-based Models and Research | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Types of IBE Work to Communicate | |
| |
| |
| |
| Complete and Efficient Model Description | |
| |
| |
| |
| Common Review Comments | |
| |
| |
| |
| Visual Communication of Executable Models | |
| |
| |
| |
| Communicating Software | |
| |
| |
| |
| Summary and Conclusions | |
| |
| |
| |
| Conclusions and Outlook | |
| |
| |
| |
| Using Analytical Models in Individual-based Ecology | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Classifications of Ecological Models | |
| |
| |
| |
| Benefits of Analytical Models | |
| |
| |
| |
| Analytical Approximation of IBMs | |
| |
| |
| |
| Using Analytical Models to Understand and Analyze IBMs | |
| |
| |
| |
| Summary and Discussion | |
| |
| |
| |
| Conclusions and Outlook for Individual-based Ecology | |
| |
| |
| |
| Introduction | |
| |
| |
| |
| Why Do We Need IBE? | |
| |
| |
| |
| How Is IBE Different From Traditional Ecology? | |
| |
| |
| |
| What Can Ecology Contribute to the Science of Complex Systems? | |
| |
| |
| |
| A Visit to the Individual-based Ecology Laboratory | |
| |
| |
| Glossary | |
| |
| |
| References | |