Individual-based Modeling And Ecology

by Grimm, Volker

• ISBN13: 9780691096650
• ISBN10: 0691096651
• Format: Hardcover
• Copyright: 2005-07-18
• Publisher: Princeton Univ Pr

Summary

Individual-based models are an exciting and widely used new tool for ecology. These computational models allow scientists to explore the mechanisms through which population and ecosystem ecology arises from how individuals interact with each other and their environment. This book provides the first in-depth treatment of individual-based modeling and its use to develop theoretical understanding of how ecological systems work, an approach the authors call "individual-based ecology." Grimm and Railsback start with a general primer on modeling: how to design models that are as simple as possible while still allowing specific problems to be solved, and how to move efficiently through a cycle of pattern-oriented model design, implementation, and analysis. Next, they address the problems of theory and conceptual framework for individual-based ecology: What is "theory"? That is, how do we develop reusable models of how system dynamics arise from characteristics of individuals? What conceptual framework do we use when the classical differential equation framework no longer applies? An extensive review illustrates the ecological problems that have been addressed with individual-based models. The authors then identify how the mechanics of building and using individual-based models differ from those of traditional science, and provide guidance on formulating, programming, and analyzing models. This book will be helpful to ecologists interested in modeling, and to other scientists interested in agent-based modeling.

Author Biography

Steven F. Railsback is a consulting scientist and Adjunct Professor of Mathematics at Humboldt State University.

Table of Contents

Preface	xi
Acknowledgments	xv
PART 1. MODELING	1	(50)
Chapter 1. Introduction	3	(19)
1.1 Why Individual-based Modeling and Ecology?	3	(2)
1.2 Linking Individual Traits and System Complexity: Three Examples	5	(4)
1.3 Individual-based Ecology	9	(2)
1.4 Early IBMs and Their Research Programs	11	(2)
1.5 What Makes a Model an IBM?	13	(2)
1.6 Status and Challenges of the Individual-based Approach	15	(4)
1.7 Conclusions and Outlook	19	(3)
Chapter 2. A Primer to Modeling	22	(16)
2.1 Introduction	22	(2)
2.2 Heuristics for Modeling	24	(3)
2.3 The Modeling Cycle	27	(9)
2.4 Summary and Discussion	36	(2)
Chapter 3. Pattern-oriented Modeling	38	(13)
3.1 Introduction	38	(2)
3.2 Why Patterns, and What Are Patterns?	40	(1)
3.3 The Tasks of Pattern-oriented Modeling	41	(7)
3.4 Discussion	48	(3)
PART 2. INDIVIDUAL-BASED ECOLOGY	51	(194)
Chapter 4. Theory in Individual-based Ecology	53	(18)
4.1 Introduction	53	(2)
4.2 Basis for Theory in IBE	55	(1)
4.3 Goals of IBE Theory	56	(2)
4.4 Theory Structure	58	(2)
4.5 Theory Development Cycle	60	(3)
4.6 Example: Development of Habitat Selection Theory for Trout	63	(5)
4.7 Summary and Discussion	68	(3)
Chapter 5. A Conceptual Framework for Designing Individual-based Models	71	(51)
5.1 Introduction	71	(2)
5.2 Emergence	73	(6)
5.3 Adaptive Traits and Behavior	79	(5)
5.4 Fitness	84	(7)
5.5 Prediction	91	(4)
5.6 Interaction	95	(3)
5.7 Sensing	98	(3)
5.8 Stochasticity	101	(4)
5.9 Collectives	105	(4)
5.10 Scheduling	109	(7)
5.11 Observation	116	(1)
5.12 Summary and Conclusions	117	(2)
5.13 Conceptual Design Checklist	119	(3)
Chapter 6. Examples	122	(123)
6.1 Introduction	122	(3)
6.2 Group and Social Behavior	125	(20)
6.3 Population Dynamics of Social Animals	145	(18)
6.4 Movement: Dispersal and Habitat Selection	163	(15)
6.5 Regulation of Hypothetical Populations	178	(9)
6.6 Comparison with Classical Models	187	(12)
6.7 Dynamics of Plant Populations and Communities	199	(19)
6.8 Structure of Communities and Ecosystems	218	(16)
6.9 Artificially Evolved Traits	234	(8)
6.10 Summary and Conclusions	242	(3)
PART 3. THE ENGINE ROOM	245	(118)
Chapter 7. Formulating Individual-based Models	247	(23)
7.1 Introduction	247	(1)
7.2 Contents of an IBM Formulation	248	(1)
7.3 Formulating an IBM's Spatial Elements	249	(4)
7.4 Formulating Logical and Probabilistic Rules	253	(2)
7.5 Formulating Adaptive Traits	255	(5)
7.6 Controlling Uncertainty	260	(2)
7.7 Using Object-oriented Design and Description	262	(2)
7.8 Using Mechanistic and Discrete Mathematics	264	(2)
7.9 Designing Superindividuals	266	(3)
7.10 Summary and Conclusions	269	(1)
Chapter 8. Software for Individual-based Models	270	(42)
8.1 Introduction	270	(3)
8.2 The Importance of Software Design for IBMs	273	(1)
8.3 Software Terminology and Concepts	274	(5)
8.4 Software Platforms	279	(9)
8.5 Software Testing	288	(6)
8.6 Moving Software Development Forward	294	(7)
8.7 Important Implementation Techniques	301	(5)
8.8 Some Favorite Software Myths	306	(2)
8.9 Summary and Conclusions	308	(4)
Chapter 9. Analyzing Individual-based Models	312	(37)
9.1 Introduction	312	(1)
9.2 Steps in Analyzing an IBM	313	(2)
9.3 General Strategies for Analyzing IBMs	315	(4)
9.4 Techniques for Analyzing IBMs	319	(8)
9.5 Statistical Analysis	327	(8)
9.6 Sensitivity and Uncertainty Analysis	335	(1)
9.7 Robustness Analysis	336	(5)
9.8 Parameterization	341	(4)
9.9 Independent Predictions	345	(1)
9.10 Summary and Conclusions	346	(3)
Chapter 10. Communicating Individual-based Models and Research	349	(14)
10.1 Introduction	349	(1)
10.2 Types of IBE Work to Communicate	350	(1)
10.3 Complete and Efficient Model Description	351	(3)
10.4 Common Review Comments	354	(2)
10.5 Visual Communication of Executable Models	356	(2)
10.6 Communicating Software	358	(1)
10.7 Summary and Conclusions	359	(4)
PART 4. CONCLUSIONS AND OUTLOOK	363	(28)
Chapter 11. Using Analytical Models in Individual-based Ecology	365	(15)
11.1 Introduction	365	(1)
11.2 Classifications of Ecological Models	366	(2)
11.3 Benefits of Analytical Models	368	(1)
11.4 Analytical Approximation of IBMs	369	(3)
11.5 Using Analytical Models to Understand and Analyze IBMs	372	(7)
11.6 Summary and Discussion	379	(1)
Chapter 12. Conclusions and Outlook for Individual-based Ecology	380	(11)
12.1 Introduction	380	(1)
12.2 Why Do We Need IBE?	381	(1)
12.3 How Is IBE Different From Traditional Ecology?	382	(5)
12.4 What Can Ecology Contribute to the Science of Complex Systems?	387	(1)
12.5 A Visit to the Individual-based Ecology Laboratory	388	(3)
Glossary	391	(4)
References	395	(26)
Index	421