Applied Hierarchical Modeling in Ecology
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TableofContentsPart1.PreludeChapter1.Distribution,Abundance,andSpeciesRichnessinEcology1.1.PointProcesses,Distribution,Abundance,andSpeciesRichness1.2.Meta-populationDesigns1.3.StateandRateParameters1 ...
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- Part 1. Prelude
- Chapter 1. Distribution, Abundance, and Species Richness in Ecology
- 1.1. Point Processes, Distribution, Abundance, and Species Richness
- 1.2. Meta-population Designs
- 1.3. State and Rate Parameters
- 1.4. Measurement Error Models in Ecology
- 1.5. Hierarchical Models for Distribution, Abundance, and Species Richness
- 1.6. Summary and Outlook
- Exercises
- Chapter 2. What Are Hierarchical Models and How Do We Analyze Them?
- 2.1. Introduction
- 2.2. Random Variables, Probability Density Functions, Statistical Models, Probability, and Statistical Inference
- 2.3. Hierarchical Models (HMs)
- 2.4. Classical Inference Based on Likelihood
- 2.5. Bayesian Inference
- 2.6. Basic Markov Chain Monte Carlo (MCMC)
- 2.7. Model Selection and Averaging
- 2.8. Assessment of Model Fit
- 2.9. Summary and Outlook
- Exercises
- Chapter 3. Linear Models, Generalized Linear Models (GLMs), and Random Effects Models: The Components of Hierarchical Models
- 3.1. Introduction
- 3.2. Linear Models
- 3.3. Generalized Linear Models (GLMs)
- 3.4. Random Effects (Mixed) Models
- 3.5. Summary and Outlook
- Exercises
- Chapter 4. Introduction to Data Simulation
- 4.1. What Do We Mean by Data Simulation, and Why Is It So Tremendously Useful?
- 4.2. Generation of a Typical Point Count Data Set
- 4.3. Packaging Everything in a Function
- 4.4. Summary and Outlook
- Exercises
- Chapter 5. Fitting Models Using the Bayesian Modeling Software BUGS and JAGS
- 5.1. Introduction
- 5.2. Introduction to BUGS Software: WinBUGS, OpenBUGS, and JAGS
- 5.3. Linear Model with Normal Response (Normal GLM): Multiple Linear Regression
- 5.4. The R Package rjags
- 5.5. Missing values (NAs) in a Bayesian Analysis
- 5.6. Linear Model with Normal Response (Normal GLM): Analysis of Covariance (ANCOVA)
- 5.7. Proportion of Variance Explained (R2)
- 5.8. Fitting a Model with Nonstandard Likelihood Using the Zeros or the Ones Tricks
- 5.9. Poisson GLM
- 5.10. GoF Assessment: Posterior Predictive Checks and the Parametric Bootstrap
- 5.11. Binomial GLM (Logistic Regression)
- 5.12. Moment-Matching in a Binomial GLM to Accommodate Underdispersion
- 5.13. Random-Effects Poisson GLM (Poisson GLMM)
- 5.14. Random-Effects Binomial GLM (Binomial GLMM)
- 5.15. General Strategy of Model Building with BUGS
- 5.16. Summary and Outlook
- Exercises
- Chapter 1. Distribution, Abundance, and Species Richness in Ecology
- Part 2. Models for Static Systems
- Chapter 6. Modeling Abundance with Counts of Unmarked Individuals in Closed Populations: Binomial N-mixture Models
- 6.1. Introduction to the Modeling of Abundance
- 6.2. An Exercise in Hierarchical Modeling: Derivation of Binomial N-mixture Models from First Principles
- 6.3. Simulation and Analysis of the Simplest Possible N-mixture Model
- 6.4. A Slightly More Complex N-mixture Model with Covariates
- 6.5. A Very General Data Simulation Function for N-mixture Models: simNmix
- 6.6. Study Design, Bias, and Precision of the Binomial N-mixture Model Estimator
- 6.7. Study of Some Assumption Violations Using Function simNmix
- 6.8. Goodness-of-Fit (GoF)
- 6.9. Abundance Mapping of Swiss Great Tits with unmarked
- 6.10. The Issue of Space, or: What Is Your Effective Sample Area?
- 6.11. Bayesian Modeling of Swiss Great Tits with BUGS
- 6.12. Time-for-Space Substitution
- 6.13. The Royle-Nichols Model and Other Nonstandard N-mixture Models
- 6.14. Multiscale N-mixture Models
- 6.15. Summary and Outlook
- Exercises
- Chapter 7. Modeling Abundance Using Multinomial N-Mixture Models
- 7.1. Introduction
- 7.2. Multinomial N-Mixture Models in Ecology
- 7.3. Simulating Multinomial Observations in R
- 7.4. Likelihood Inference for Multinomial N-Mixture Models
- 7.5. Example 1: Bird Point Counts Based on Removal Sampling
- 7.6. Bayesian Analysis in BUGS Using the Conditional Multinomial (Three-Part) Model
- 7.7. Building Custom Multinomial Models in unmarked
- 7.8. Spatially Stratified Capture-Recapture Models
- 7.9. Example 3: Jays in the Swiss MHB
- 7.10. Summary and Outlook
- Exercises
- Chapter 8. Modeling Abundance Using Hierarchical Distance Sampling
- 8.1. Introduction
- 8.2. Conventional Distance Sampling
- 8.3. Bayesian Conventional Distance Sampling
- 8.4. Hierarchical Distance Sampling (HDS)
- 8.5. Bayesian HDS
- 8.6. Summary
- Exercises
- Chapter 9. Advanced Hierarchical Distance Sampling
- 9.1. Introduction
- 9.2. Distance Sampling (DS) with Clusters, Groups, or Other Individual Covariates
- 9.3. Time-Removal and DS Combined
- 9.4. Mark-Recapture/Double-Observer DS
- 9.5. Open HDS Models: Temporary Emigration
- 9.6. Open HDS Models: Implicit Dynamics
- 9.7. Open HDS Models: Modeling Population Dynamics
- 9.8. Spatial Distance Sampling: Modeling Within-Unit Variation in Density
- 9.9. Summary
- Exercises
- Chapter 10. Modeling Static Occurrence and Species Distributions Using Site-occupancy Models
- 10.1. Introduction to the Modeling of Occurrence—Including Species Distributions
- 10.2. Another Exercise in Hierarchical Modeling: Derivation of the Site-Occupancy Model
- 10.3. Simulation and Analysis of the Simplest Possible Site-Occupancy Model
- 10.4. A Slightly More Complex Site-Occupancy Model with Covariates
- 10.5. A General Data Simulation Function for Static Occupancy Models: simOcc
- 10.6. A Model with Lots of Covariates: Use of R Function model.matrix with BUGS
- 10.7. Study Design, and Bias and Precision of Site-Occupancy Estimators
- 10.8. Goodness-of-Fit
- 10.9. Distribution Modeling and Mapping of Swiss Red Squirrels
- 10.10. Multiscale Occupancy Models
- 10.11. Space-for-Time Substitution
- 10.12. Models for Data along Transects: Poisson, Exponential, Weibull, and Removal Observation Models
- 10.13. Occupancy Modeling of a Community of Species
- 10.14. Modeling Wiggly Covariate Relationships: Penalized Splines in Hierarchical Models
- 10.15. Summary and Outlook
- Exercises
- Chapter 11. Hierarchical Models for Communities
- 11.1. Introduction
- 11.2. Simulation of a Metacommunity
- 11.3. Metacommunity Data from the Swiss Breeding Bird Survey MHB
- 11.4. Overview of Some Models for Metacommunities
- 11.5. Community Models That Ignore Species Identity
- 11.6. Community Models that Fully Retain Species Identity
- 11.7. The Dorazio/Royle (DR) Community Occupancy Model with Data Augmentation (DA)
- 11.8. Inferences Based on the Estimated Z Matrix: Similarity among Sites and Species
- 11.9. Species Richness Maps and Species Accumulation Curves
- 11.10. Community N-mixture (or Dorazio/Royle/Yamaura - DRY) Models
- 11.11. Summary and Outlook
- Exercises
- Chapter 6. Modeling Abundance with Counts of Unmarked Individuals in Closed Populations: Binomial N-mixture Models
- Summary and Conclusion
- References
- Author Index
- Subject Index
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