| Preface | p. ix |
| Introduction | p. 1 |
| Models in Context | p. 3 |
| Complexity and Obscurity in Nature and in Models | p. 3 |
| Making the Connections: Data, Inference, and Decision | p. 5 |
| Two Elements of Models: Known and Unknown | p. 13 |
| Learning with Models: Hypotheses and Quantification | p. 19 |
| Estimation versus Forward Simulation | p. 23 |
| Statistical Pragmatism | p. 24 |
| Model Elements: Application to Population Growth | p. 27 |
| A Model and Data Example | p. 27 |
| Model State and Time | p. 30 |
| Stochasticity for the Unknown | p. 42 |
| Additional Background on Process Models | p. 44 |
| Elements of Inference | p. 45 |
| Point Estimation: Maximum Likelihood and the Method of Moments | |
| Introduction | p. 47 |
| Likelihood | p. 47 |
| A Binomial Model | p. 53 |
| Combining the Binomial and Exponential | p. 54 |
| Maximum Likelihood Estimates for the Normal Distribution | p. 56 |
| Population Growth | p. 57 |
| Application: Fecundity | p. 60 |
| Survival Analysis Using Maximum Likelihood | p. 62 |
| Design Matrixes | p. 68 |
| Numerical Methods for MLE | p. 71 |
| Moment Matching | p. 71 |
| Common Sampling Distributions and Dispersion | p. 74 |
| Assumptions and Next Steps | p. 76 |
| Elements of the Bayesian Approach | p. 77 |
| The Bayesian Approach | p. 78 |
| The Normal Distribution | p. 84 |
| Subjective Probability and the Role of the Prior | p. 91 |
| Confidence Envelopes and Prediction Intervals | p. 93 |
| Classical Interval Estimation | p. 95 |
| Bayesian Credible Intervals | p. 115 |
| Likelihood Profile for Multiple Parameters | p. 120 |
| Confidence Intervals for Several Parameters: Linear Regression | p. 122 |
| Which Confidence Envelope to Use | p. 130 |
| Predictive Intervals | p. 133 |
| Uncertainty and Variability | p. 141 |
| When Is It Bayesian? | p. 142 |
| Model Assessment and Selection | p. 143 |
| Using Statistics to Evaluate Models | p. 143 |
| The Role of Hypothesis Tests | p. 144 |
| Nested Models | p. 144 |
| Additional Considerations for Classical Model Selection | p. 151 |
| Bayesian Model Assessment | p. 154 |
| Additional Thoughts on Bayesian Model Assessment | p. 159 |
| Larger Models | p. 161 |
| Computational Bayes: Introduction to Tools Simulation | p. 163 |
| Simulation to Obtain the Posterior | p. 163 |
| Some Basic Simulation Techniques | p. 164 |
| Markov Chain Monte Carlo Simulation | p. 173 |
| Application: Bayesian Analysis for Regression | p. 189 |
| Using MCMC | p. 202 |
| Computation for Bayesian Model Selection | p. 205 |
| Priors on the Response | p. 209 |
| The Basics Are Now Behind Us | p. 212 |
| A Closer Look at Hierarchical Structures | p. 213 |
| Hierarchical Models for Context | p. 213 |
| Mixed and Generalized Linear Models | p. 216 |
| Application: Growth Responses to CO2 | p. 230 |
| Thinking Conditionally | p. 235 |
| Two Applications to Trees | p. 241 |
| Noninformative Priors in Hierarchical Settings | p. 249 |
| From Simple Models to Graphs | p. 249 |
| More Advance Methods | p. 251 |
| Time | |
| Why Is Time Important? | p. 253 |
| Time Series Terminology | p. 254 |
| Descriptive Elements of Time Series Models | p. 255 |
| The Frequency Domain | p. 264 |
| Application: Detecting Density Dependence in Population Time Series | p. 264 |
| Bayesian State Space Models | p. 272 |
| Application: Black Noddy on Heron Island | p. 282 |
| Nonlinear State Space Models | p. 289 |
| Lags | p. 297 |
| Regime Change | p. 298 |
| Constraints on Time Series Data | p. 300 |
| Additional Sources of Variablity | p. 301 |
| Alternatives to the Gibbs Sampler | p. 302 |
| More on Longitudinal Data Structures | p. 302 |
| Intervention and Treatment Effects | p. 309 |
| Capture-Recapture Studies | p. 318 |
| Structured Models as Matrixes | p. 329 |
| Structure as Systems of Difference Equations | p. 336 |
| Time Series, Population Regulation, and Stochasticity | p. 347 |
| Space-Time | p. 353 |
| A Deterministic Model for a Stochastic Spa | |
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