Applied Epidemiology in Aquaculture
A hands-on guide with R
Preface
Welcome to Applied Epidemiology in Aquaculture — a hands-on course in veterinary epidemiology written for the people who keep farmed fish and shrimp healthy, and taught entirely through R and real aquaculture problems.
Who this book is for
Fish-health vets, aquaculture health managers, diagnostic-lab staff, regulators, and graduate students. No prior coding is assumed: Chapter 2 sets up R from zero, and every method is shown as copy-paste code you can run on the book’s own datasets.
How the book is organised
The book follows a single spine — the five-level preventive framework for aquatic animal health (Mardones, Aquaculture Health Management, 2020), expressed as five plain-language phases of disease management:
| Phase | Prevention level | Question it answers |
|---|---|---|
| Anticipate | primordial | What raises risk before disease appears? |
| Prevent | primary | How do we stop outbreaks occurring? |
| Detect | secondary | How do we find disease early? |
| Respond | tertiary | How do we limit harm once it’s here? |
| Safeguard / Revisit | quaternary | How do we avoid the harms of control, and learn? |
Every chapter opens with a “Where this sits” box naming its phase, so you always know which layer of defence you are building. Pathogen genetics and host resistance cut across all five, which is why genetics (Chapter 16) threads through the whole book.
The two farms (and a shrimp pond)
Every example runs on three recurring operations: Aysén Salmon Co. (Atlantic salmon, cold marine cages + RAS), Lago Verde Tilapia (warm freshwater ponds), and Camarones del Golfo (whiteleg shrimp, brackish ponds). Their signature diseases — SRS, streptococcosis, and AHPND — appear throughout.
How to use it
Each chapter is a task-centred lab: an overview, a short Preparation block, a worked walkthrough with real code and output, an interpretation for the farm, and exercises. The datasets are small, simulated, and fully reproducible — every one is generated by a seeded R script in scripts/, and the figures quoted in the text were produced by running that code.
A note on the evidence
The methods are illustrated with real studies wherever possible, drawing on the published and forthcoming work of the author and collaborators on Piscirickettsia salmonis (SRS), sea lice, diagnostics, antimicrobial resistance, and transmission. Standard references — Dohoo, Martin & Stryhn’s Veterinary Epidemiologic Research, Thrusfield & Christley, and Stevenson — anchor the methods, and the format follows the spirit of the Epidemiologist R Handbook.
This book is a work in progress. Datasets are simulated for teaching and are not real farm records. Figures attributed to studies “in review” or “in preparation” reflect the authors’ forthcoming work and may change on publication.
Let’s begin where every investigation begins — with a population of fish.