How to use this book

We begin with a short orientation. In this chapter we set out the daily cadence, the chapter template, and the conventions used throughout, so that the reader knows what to expect.

The daily cadence

Each day has the same shape:

  • Lecture content (~1 hour). Read the chapter, running each command and rendering each document in your own environment as you encounter it. Do not skip the renders; the chapter is designed to be read with a terminal open and a scratch project at hand.
  • Homework (~2 hours). Five to eight problems, with worked solutions at the end of the chapter. Attempt each problem before checking the solution.

The cadence assumes one chapter per day for five consecutive days. The workshop may be compressed (two chapters per day across two-and-a-half days) or expanded (one chapter per week across a month) depending on the reader’s other commitments; we leave the choice to the reader.

Chapter template

Each chapter follows a five-section template, and we shall keep to it consistently:

  1. Learning objectives. A bulleted list of what the reader should be able to do by the end of the day.
  2. Lecture. The substantive content for the day, with commands to run and documents to render.
  3. Worked example. A small but realistic authoring scenario that uses the day’s content end to end, most often translating or extending a familiar R Markdown document.
  4. Homework. Problems organized from easier to harder.
  5. Solutions. Worked solutions to all homework problems. Read only after attempting the problem.

There are no quizzes, no examinations, and no tests in this book. Self-assessment proceeds entirely through the homework solutions.

A note on the two tools

The book concerns two related but distinct things:

  • R Markdown is the authoring system the reader already knows. It couples the knitr engine to Pandoc and renders .Rmd documents. We treat it as the starting point, not the subject.
  • Quarto is the newer system the reader is moving to. It is a standalone command-line tool that renders .qmd documents, shares R Markdown’s knitr engine, and adds a uniform model for many output formats and project types. Quarto is the subject of every chapter.

Keeping the distinction clear from the outset prevents a common confusion in which the two are treated as one, or in which Quarto is assumed to be an R package rather than an independent tool.

Conventions

The visual cues used throughout the book are described on the Conventions page. In brief:

  • Commands you type follow a $ prompt; output has no prompt.
  • Placeholders you replace are written in <angle-brackets>.
  • Document source is shown in fenced blocks labeled by language.
  • Command lines and file listings are wrapped at 78 characters.

Companion volumes

This workshop sits within the rgtlab curriculum sequence. The two preparatory boot camps precede it, and two follow-on volumes extend it:

The end of Chapter 5 describes how the publishing material here connects to Git and GitHub for Biostatistics and how the reproducibility thread continues into Reproducible Research for the Health Sciences.