Handbook of Capture-Recapture Analysis

List of Illustrations ix
List of Tables xi
Preface xvii

Chapter One: Introduction to the Handbook by Bryan F. J. Manly, Trent L. McDonald, and Steven C. Amstrup 1
1.1 Introduction 1
1.2 Overview of chapters 2 to 8 3
1.3 Maximum Likelihood with Capture-Recapture Methods 9
1.4 Model Selection Procedures 17
1.5 Notation 19

Chapter Two: Classical Closed-population Capture-Recapture Models by Anne Chao and Richard M. Huggins 22
2.1 Introduction 22
2.2 Structure of Capture-Recapture Experiments and Data 23
2.3 Early Models and Estimators 26
2.4 Limitations of Early Models and the Motivation for More General Models 34
2.5 Chapter Summary 35

Chapter Three: Classical Open-population Capture-Recapture Models by Kenneth H. Pollock and Russell Alpizar-Jara 36
3.1 Introduction 36
3.2 The Original Jolly-Seber Model 38
3.3 The Jolly-Seber Likelihood Components 44
3.4 Restrictions and Generalizations of the Jolly-Seber Model 45
3.5 Age-dependent Models 46
3.6 Goodness-of-Fit and Model Selection Issues 47
3.7 Examples 48
3.8 Conclusions 55
3.9 Chapter Summary 55

Chapter Four: Modern Closed-population Capture-Recapture Models by Anne Chao and Richard M. Huggins 58
4.1 Introduction 58
4.2 Discrete-time Models with Unequal Catchabilities 58
4.3 Continuous-time Models 78
4.4 Computing Considerations 85
4.5 Chapter Summary 86

Chapter Five: Modern Open-population Capture-Recapture Models by James D. Nichols 88
5.1 Introduction 88
5.2 Conditional Single-age Models 89
5.3 Conditional Multiple-age Models 102
5.4 Reverse-time Models 107
5.5 Unconditional Models 109
5.6 The Robust Design 116
5.7 Discussion 120
5.8 Chapter Summary 121

Chapter Six: Tag-recovery Models by John M. Hoenig, Kenneth H. Pollock, and William Hearn 124
6.1 Introduction 124
6.2 Assumptions of Brownie Models 128
6.3 Interpretation of the Tag-recovery Rate Parameter 128
6.4 Functional Linkage Between the Exploitation Rate and the Survival Rate 131
6.5 Instantaneous Rate Models for Estimating Harvest and Natural Mortality 131
6.6 Diagnostics and Tests of Assumptions 132
6.7 Preventing and Dealing with Failures of Assumptions 134
6.8 Chapter Summary 140

Chapter Seven: Joint Modeling of Tag-recovery and Live-resighting Data by Richard J. Barker 142
7.1 Introduction 142
7.2 Data Structure 144
7.3 Simple Models 145
7.4 More General Models 156
7.5 Model Fitting and Assessment 157
7.6 Tag Misreads and Tag Loss 161
7.7 Computing Considerations 161
7.8 Chapter Summary 163

Chapter Eight: Multistate Models by Carl J. Schwarz 165
8.1 Introduction 165
8.2 The Arnason-Schwarz Model 166
8.3 The Jolly-Seber Approach 177
8.4 Multisample Stratified Closed Populations 187
8.5 Multisample Stratified Open Populations 192
8.6 Chapter Summary 194

Chapter Nine: Examples by Trent L. McDonald, Steven C. Amstrup, Eric V. Regehr, and Bryan F. J. Manly 194
9.1 Introduction 196
9.2 Open-population Analyses of Data on the
European Dipper 198
9.3 The Huggins Closed-population Model Applied to the
European Dipper Data 231
9.4 Assessing Goodness-of-Fit 236
9.5 Horvitz-Thompson Open-population Size Estimates 241
9.6 A Multistate (Multistrata) Model 245
9.7 Polar Bears in the Southern Beaufort Sea 247
9.8 Dead Recoveries of Mallard Ducks 254
9.9 Chapter Summary 263

Chapter Ten: Capture-Recapture Methods in Practice by Bryan F. J. Manly, Steven C. Amstrup, and Trent L. McDonald 266
10.1 Introduction 266
10.2 Closed-population Models 266
10.3 Open-population Models 267
10.4 Tag-recovery Models 269
10.5 Other Models 270
10.6 Model Selection 271
10.7 Known Ages 272

Appendix 275
A.1 Capability Matrix for Common Capture-Recapture Software Packages 275
A.2 General and Contact Information for Common Capture-Recapture Software Packages Listed in Table A.1 277

References 281
Contributor's Notes 301
Index 303