How to use this book

This short orientation chapter explains the chapter template, the cross-references, and the conventions used throughout the book. It is the same template inherited from the sister volumes, with two adjustments specific to this book.

Chapter template

Every content chapter follows the same nine-section structure:

  1. Learning objectives. A bulleted list of capabilities the reader should have after working through the chapter.
  2. Orientation. Two to four paragraphs of prose framing: what the chapter is, why it matters, how it relates to adjacent chapters.
  3. The researcher’s contribution. A front-loaded section articulating the judgements at the centre of the chapter that no large language model can make on the reader’s behalf. Three to five paragraphs, each leading with a bold-tag judgement followed by elaboration.
  4. Content sections. The chapter’s substantive material, broken into sections with descriptive headings. Collapsible Check your understanding callouts appear at natural pauses.
  5. Worked example. A concrete worked example, ideally biomedical, that exercises the chapter’s tools end to end.
  6. Collaborating with an LLM on topic. Three prompt patterns paired with what to watch for and how to verify, specific to the chapter’s content.
  7. Principle in use. Three habits that define defensible work in this area.
  8. Exercises. Five exercises ranging from short conceptual checks to extended applied work.
  9. Further reading. Canonical, modern applied, and package-documentation pointers.

Adjustments specific to this book

Three adjustments distinguish this volume from the introductory and advanced sister volumes:

  • No prerequisites quiz. The introductory volume opens each chapter with a pre-flight quiz to surface missing prerequisites; this volume assumes the prerequisite material is in place and skips the quiz.
  • No practice test. The introductory volume closes with a self-administered practice test; this volume treats the exercises as the equivalent assessment.
  • Researcher-centred framing. The sister volumes address the biostatistician explicitly. This volume, whose audience extends across health-sciences research (clinicians, biostatisticians, epidemiologists, pharmacists, public-health researchers), refers to the researcher: whoever is running the analysis and signing the report. Where a chapter contains a worked example with an explicit role, the role is named (clinical fellow, pharmacoepidemiologist, biostatistician); the surrounding prose stays role-neutral.

Cross-references

References to chapters in this volume use @sec- labels: for example, @sec-agents-mcp resolves to Chapter 7. References to chapters in the sister volumes use full URLs, since the volumes deploy as separate Quarto sites: SCAI lives at https://scai.rgtlab.org, the advanced volume at https://scai-advanced.rgtlab.org, and the practicum at https://practicum.rgtlab.org.

Conventions

Visual cues used throughout the book are described on the Conventions page. Code blocks default to R; Python and shell snippets are labelled. LLM prompts are shown in fenced blocks with the prompt text and, where relevant, the literal verbatim model response.

Companion repositories

The book repository at https://github.com/rgt47/applied-genai contains:

  • docs/syllabi-survey.md, the curriculum survey that shaped the chapter list.
  • docs/mollick-digest.md, the 24-month One Useful Thing digest used to test the TOC for contemporariness.
  • references.bib, the working bibliography.

Both companion documents are intended as audit-trail artefacts; they explain why the book is shaped the way it is and will be updated as the field evolves.