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| Preface | |
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| A brief outline of the book | |
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| The bare bones: Basic issues in the simplest context | |
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| The epidemic in a closed population | |
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| The questions (and the underlying assumptions) | |
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| Initial growth | |
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| The final size | |
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| The epidemic in a closed population: summary | |
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| Heterogeneity: The art of averaging | |
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| Differences in infectivity | |
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| Differences in infectivity and susceptibility | |
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| The pitfall of overlooking dependence | |
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| Heterogeneity: a preliminary conclusion | |
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| Stochastic modeling: The impact of chance | |
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| The prototype stochastic epidemic model | |
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| Two special cases | |
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| Initial phase of the stochastic epidemic | |
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| Approximation of the main part of the epidemic | |
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| Approximation of the final size | |
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| The duration of the epidemic | |
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| Stochastic modeling: summary | |
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| Dynamics at the demographic time scale | |
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| Repeated outbreaks versus persistence | |
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| Fluctuations around the endemic steady state | |
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| Vaccination | |
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| Regulation of host populations | |
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| Tools for evolutionary contemplation | |
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| Markov chains: models of infection in the ICU | |
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| Time to extinction and critical community size | |
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| Beyond a single outbreak: summary | |
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| Inference, or how to deduce conclusions from data | |
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| Introduction | |
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| Maximum likelihood estimation | |
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| An example of estimation: the ICU model | |
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| The prototype stochastic epidemic model | |
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| ML-estimation of � and � in the ICU model | |
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| The challenge of reality: summary | |
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| Structured populations | |
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| The concept of state | |
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| i-states | |
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| p-states | |
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| Recapitulation, problem formulation and outlook | |
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| The basic reproduction number | |
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| The definition of R<sub>0</sub> | |
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| NGM for compartmental systems | |
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| General h-state | |
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| Conditions that simplify the computation of R<sub>0</sub> | |
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| Sub-models for the kernel | |
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| Sensitivity analysis of R<sub>0</sub> | |
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| Extended example: two diseases | |
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| Pair formation models | |
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| Invasion under periodic environmental conditions | |
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| Targeted control | |
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| Summary | |
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| Other indicators of severity | |
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| The probability of a major outbreak | |
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| The intrinsic growth rate | |
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| A brief look at final size and endemic level | |
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| Simplifications under separable mixing | |
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| Age structure | |
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| Demography | |
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| Contacts | |
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| The next-generation operator | |
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| Interval decomposition | |
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| The endemic steady state | |
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| Vaccination | |
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| Spatial spread | |
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| Posing the problem | |
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| Warming up: the linear diffusion equation | |
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| Verbal reflections suggesting robustness | |
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| Linear structured population models | |
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| The nonlinear situation | |
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| Summary: the speed of propagation | |
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| Addendum on local finiteness | |
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| Macroparasites | |
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| Introduction | |
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| Counting parasite load | |
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| The calculation of R<sub>0</sub> for life cycles | |
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| A 'pathological' model | |
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| What is contact? | |
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| Introduction | |
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| Contact duration | |
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| Consistency conditions | |
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| Effects of subdivision | |
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| Stochastic final size and multi-level mixing | |
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| Network models (an idiosyncratic view) | |
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| A primer on pair approximation | |
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| Case studies on inference | |
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| Estimators of R<sub>0</sub> derived from mechanistic models | |
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| Introduction | |
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| Final size and age-structured data | |
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| Estimating R<sub>0</sub> from a transmission experiment | |
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| Estimators based on the intrinsic growth rate | |
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| Data-driven modeling of hospital infections | |
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| Introduction | |
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| The longitudinal surveillance data | |
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| The Markov chain bookkeeping framework | |
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| The forward process | |
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| The backward process | |
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| Looking both ways | |
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| A brief guide to computer intensive statistics | |
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| Inference using simple epidemic models | |
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| Inference using 'complicated' epidemic models | |
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| Bayesian statistics | |
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| Markov chain Monte Carlo methodology | |
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| Large simulation studies | |
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| Elaborations | |
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| Elaborations for Part I | |
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| Elaborations for Chapter 1 | |
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| Elaborations for Chapter 2 | |
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| Elaborations for Chapter 3 | |
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| Elaborations for Chapter 4 | |
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| Elaborations for Chapter 5 | |
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| Elaborations for Part II | |
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| Elaborations for Chapter 7 | |
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| Elaborations for Chapter 8 | |
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| Elaborations for Chapter 9 | |
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| Elaborations for Chapter 10 | |
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| Elaborations for Chapter 11 | |
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| Elaborations for Chapter 12 | |
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| Elaborations for Part III | |
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| Elaborations for Chapter 13 | |
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| Elaborations for Chapter 15 | |
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| Bibliography | |
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| Index | |