Where Do I Start?
This book can be read cover to cover, but most readers arrive with a specific question about their fish. This page is a map: find the question closest to yours, and it points you to the chapter, the framework phase, and the online Epivet Tools calculator that answer it. You do not need to read the chapters in order — each is self-contained, and the foundations (Chapters 1–3) are here whenever you need them.
Find your question
| Your question on the farm | Start at | Phase | Calculator |
|---|---|---|---|
| “I’m new to this / how do I set up R?” | Ch 1–3 Foundations | enabling layer | — |
| “How much disease is there? Is it going up?” | Ch 4 Prevalence & incidence | Detect | ci-prop, true-prev |
| “Can I trust this test? The PCR doesn’t match the clinic.” | Ch 6 Diagnostic tests | Detect | dx-test, true-prev |
| “What is raising the risk of disease?” | Ch 5 → Ch 9 Association & causation | Anticipate | assoc-2x2 |
| “How many fish should I sample? Can I prove freedom?” | Ch 7 → 8, then Ch 12 | Anticipate / Detect | ss-estimate, ss-detect, sys-sens |
| “Does my vaccine work? Can vaccination stop it?” | Ch 10 Vaccines, R₀, herd immunity | Prevent | vaccine-herd |
| “Does my antibiotic work? Is resistance rising?” | Ch 11 Antibiotics & AMR | Respond / Safeguard | chi-trend |
| “There’s an outbreak right now — what do I do?” | Ch 13 → Ch 14 Outbreak & spread | Respond | — |
| “Where is it spreading? Which farms are high-risk?” | Ch 14 Spatial & network | Respond / Anticipate | moran |
| “What does all the evidence say?” | Ch 15 Systematic review & meta-analysis | Safeguard | meta-rr |
| “Can we breed resistant fish? Which strain is it?” | Ch 16 Genetics & molecular epi | Prevent (cross-cutting) | herit |
Three ways to use this book
- By question — use the map above; jump straight to what you need today.
- By phase — follow the spine Anticipate → Prevent → Detect → Respond → Safeguard, reading the chapters tagged to each phase (every chapter opens with a “Where this sits” box).
- As a course — read Chapters 1–16 in order, doing the exercises; by the end you will have investigated an outbreak from first principles.
A quick orientation. If you are unsure which phase your question belongs to, ask when in the life of a disease you are acting. Before it appears → Anticipate. To stop it appearing → Prevent. To find it early → Detect. To limit harm once it’s here → Respond. To avoid the harms of control and learn for next time → Safeguard.