Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence

0120887665......Page 1
Copyright page......Page 5
Table of Contents......Page 8
Preface......Page 14
Acknowledgments......Page 18
CHAPTER 1: Introduction......Page 20
1.1. OPERATIONAL DEFINITIONS......Page 21
1.2. SAMPLING ANIMAL POPULATIONS AND COMMUNITIES: GENERAL PRINCIPLES......Page 22
WHY?......Page 23
WHAT?......Page 24
HOW?......Page 26
GENERATION OF SYSTEM DYNAMICS......Page 31
STATICS AND PROCESS VS. PATTERN......Page 36
1.4. DISCUSSION......Page 39
CHAPTER 2: Occupancy in Ecological Investigations......Page 44
2.1. GEOGRAPHIC RANGE......Page 46
2.2. HABITAT RELATIONSHIPS AND RESOURCE SELECTION......Page 52
2.3. METAPOPULATION DYNAMICS......Page 54
INFERENCE BASED ON SINGLE-SEASON DATA......Page 55
INFERENCE BASED ON MULTIPLE-SEASON DATA......Page 59
2.4. LARGE-SCALE MONITORING......Page 60
INFERENCE BASED ON STATIC OCCUPANCY PATTERNS......Page 63
INFERENCE BASED ON OCCUPANCY DYNAMICS......Page 66
2.6. DISCUSSION......Page 68
CHAPTER 3: Fundamental Principles of Statistical Inference......Page 72
RANDOM VARIABLES, PROBABILITY DISTRIBUTIONS, AND THE LIKELIHOOD FUNCTION......Page 74
EXPECTED VALUES......Page 77
INTRODUCTION TO METHODS OF ESTIMATION......Page 79
PROPERTIES OF POINT ESTIMATORS......Page 80
Precision (Variance and Standard Error)......Page 81
COMPUTER-INTENSIVE METHODS......Page 82
MAXIMUM LIKELIHOOD ESTIMATORS......Page 83
PROPERTIES OF MAXIMUM LIKELIHOOD ESTIMATORS......Page 84
CONFIDENCE INTERVAL ESTIMATORS......Page 85
3.3. BAYESIAN METHODS OF ESTIMATION......Page 86
THEORY......Page 87
THE LOGIT LINK FUNCTION......Page 90
ESTIMATION......Page 92
BACKGROUND AND DEFINITIONS......Page 94
LIKELIHOOD RATIO TESTS......Page 95
3.6. MODEL SELECTION......Page 96
THE AKAIKE INFORMATION CRITERION (AIC)......Page 97
QUASI-AIC......Page 99
MODEL AVERAGING AND MODEL SELECTION UNCERTAINTY......Page 100
3.7. DISCUSSION......Page 101
CHAPTER 4: Single-species, Single-season Occupancy Models......Page 102
4.1. THE SAMPLING SITUATION......Page 103
4.2. ESTIMATION OF OCCUPANCY IF PROBABILITY OF DETECTION IS 1 OR KNOWN WITHOUT ERROR......Page 104
GEISSLER-FULLER METHOD......Page 106
AZUMA-BALDWIN-NOON METHOD......Page 108
NICHOLS-KARANTH METHOD......Page 109
BUILDING A MODEL......Page 111
ESTIMATION......Page 113
Constant Detection Probability Model......Page 114
Probability of Occupancy Given Species Not Detected at a Site......Page 116
EXAMPLE: BLUE-RIDGE TWO-LINED SALAMANDERS......Page 118
MISSING OBSERVATIONS......Page 120
COVARIATE MODELING......Page 122
VIOLATIONS OF MODEL ASSUMPTIONS......Page 123
ASSESSING MODEL FIT......Page 127
Pronghorn Antelope......Page 132
Mahoenui Giant Weta......Page 135
4.5. ESTIMATING OCCUPANCY FOR A FINITE POPULATION OR SMALL AREA......Page 141
PREDICTION OF UNOBSERVED OCCUPANCY STATE......Page 142
A BAYESIAN FORMULATION OF THE MODEL......Page 144
BLUE-RIDGE TWO-LINED SALAMANDERS REVISITED......Page 148
4.6. DISCUSSION......Page 150
CHAPTER 5: Single-species, Single-season Models with Heterogeneous Detection Probabilities......Page 152
GENERAL FORMULATION......Page 154
FINITE MIXTURES......Page 156
CONTINUOUS MIXTURES......Page 158
ABUNDANCE MODELS......Page 159
MODEL FIT......Page 160
5.2. EXAMPLE: BREEDING BIRD POINT COUNT DATA......Page 161
5.3. GENERALIZATIONS: COVARIATE EFFECTS......Page 163
5.4. EXAMPLE: ANURAN CALLING SURVEY DATA......Page 165
5.5. ON THE IDENTIFIABILITY OF ψ......Page 167
5.6. DISCUSSION......Page 170
CHAPTER 6: Design of Single-season Occupancy Studies......Page 174
6.1. DEFINING A “SITE”......Page 176
6.2. SITE SELECTION......Page 177
6.3. DEFINING A “SEASON”......Page 179
6.4. CONDUCTING REPEAT SURVEYS......Page 180
6.5. ALLOCATION OF EFFORT: NUMBER OF SITES VS. NUMBER OF SURVEYS......Page 184
No Consideration of Cost......Page 186
Including Survey Cost......Page 189
DOUBLE SAMPLING DESIGN......Page 192
REMOVAL SAMPLING DESIGN......Page 194
6.6. DISCUSSION......Page 198
CHAPTER 7: Single-species, Multiple-season Occupancy Models......Page 202
7.1. BASIC SAMPLING SCHEME......Page 203
7.2. AN IMPLICIT DYNAMICS MODEL......Page 205
7.3. MODELING DYNAMIC CHANGES EXPLICITLY......Page 206
MODELING DYNAMIC PROCESSES WHEN DETECTION PROBABILITY IS 1......Page 208
CONDITIONAL MODELING OF DYNAMIC PROCESSES......Page 209
UNCONDITIONAL MODELING OF DYNAMIC PROCESSES......Page 211
MISSING OBSERVATIONS......Page 214
INCLUDING COVARIATE INFORMATION......Page 216
ALTERNATIVE PARAMETERIZATIONS......Page 217
EXAMPLE: HOUSE FINCH EXPANSION IN NORTH AMERICA......Page 220
7.4. INVESTIGATING OCCUPANCY DYNAMICS......Page 222
MARKOVIAN, RANDOM AND NO CHANGES IN OCCUPANCY......Page 224
EQUILIBRIUM......Page 227
EXAMPLE: NORTHERN SPOTTED OWL......Page 228
7.5. VIOLATIONS OF MODEL ASSUMPTIONS......Page 231
7.6. MODELING HETEROGENEOUS DETECTION PROBABILITIES......Page 233
7.7. STUDY DESIGN......Page 234
TIME INTERVAL BETWEEN “SEASONS”......Page 235
SAME VS. DIFFERENT SITES EACH SEASON......Page 237
MORE SITES VS. MORE SEASONS......Page 238
MORE ON SITE SELECTION......Page 240
7.8. DISCUSSION......Page 241
CHAPTER 8: Occupancy Data for Multiple Species: Species Interactions......Page 244
8.1. DETECTION PROBABILITY AND INFERENCES ABOUT SPECIES CO-OCCURRENCE......Page 245
GENERAL SAMPLING SITUATION......Page 250
STATISTICAL MODEL......Page 251
REPARAMETERIZING THE MODEL......Page 253
INCORPORATING COVARIATE INFORMATION......Page 256
MISSING OBSERVATIONS......Page 257
8.3. ADDRESSING BIOLOGICAL HYPOTHESES......Page 258
8.4. EXAMPLE: TERRESTRIAL SALAMANDERS IN GREAT SMOKY MOUNTAINS NATIONAL PARK......Page 259
8.5. STUDY DESIGN ISSUES......Page 261
8.6. EXTENSION TO MULTIPLE SEASONS......Page 263
8.7. DISCUSSION......Page 266
CHAPTER 9: Occupancy in Community-level Studies......Page 268
9.1. INVESTIGATING THE COMMUNITY AT A SINGLE SITE......Page 269
FRACTION OF SPECIES PRESENT IN A SINGLE SEASON......Page 271
CHANGES IN THE FRACTION OF SPECIES PRESENT OVER TIME......Page 272
9.2. INVESTIGATING THE COMMUNITY AT MULTIPLE SITES......Page 273
SINGLE-SEASON STUDIES: MODELING OCCUPANCY AND DETECTION......Page 274
SINGLE-SEASON STUDIES: SPECIES RICHNESS ESTIMATION......Page 275
EXAMPLE: AVIAN POINT COUNT DATA......Page 279
MULTIPLE-SEASON STUDIES......Page 281
9.3. DISCUSSION......Page 283
CHAPTER 10: Future Directions......Page 286
10.1. MULTIPLE OCCUPANCY STATES......Page 287
10.2. INTEGRATED MODELING OF HABITAT AND OCCUPANCY......Page 292
10.3. INCORPORATING INFORMATION ON MARKED ANIMALS......Page 298
10.4. INCORPORATING COUNT AND OTHER DATA......Page 299
10.5. RELATIONSHIP BETWEEN OCCUPANCY AND ABUNDANCE......Page 300
10.6. DISCUSSION......Page 301
APPENDIX: Some Important Mathematical Concepts......Page 304
References......Page 312
Index......Page 332