Conventions

This page summarizes the visual conventions used throughout the book.

Commands and output

This book mixes terminal commands with document source. Shell commands appear in syntax-highlighted blocks. A command the reader types is shown after a $ prompt; the prompt itself is not typed. Output appears on the following lines, without a prompt:

$ quarto --version
1.5.57

When a sequence of commands is shown without output, the prompts are omitted for readability:

quarto render report.qmd
quarto preview report.qmd

Inline commands, file names, and Quarto options are set in monospace. Quarto subcommands are named in full (quarto render, not merely render) so that they are unambiguous. Document source, including YAML front matter and executable cells, is shown in fenced blocks labeled by language:

title: 'Baseline summary'
format: html

Placeholders that the reader must replace with their own values are written in angle brackets, for example quarto render <file> or quarto publish <target>. The angle brackets are not typed.

Callouts

Three callout types appear:

Tip

A small practical recommendation.

A short question testing comprehension of the just-read material. Click to expand the answer.

Warning

A pitfall the reader may otherwise hit, most often a difference from R Markdown that silently changes behavior.

Comparisons with R Markdown

Because this book is a transition, we frequently place an R Markdown construct beside its Quarto equivalent. Such pairs are shown as two adjacent code blocks, the .Rmd form first and the .qmd form second, so that the reader can read the translation directly:

R Markdown:  ```{r, echo=FALSE}
Quarto:      ```{r}
             #| echo: false

These comparisons are the spine of the book; where a construct transfers unchanged, we say so explicitly.

Cross-references

Within this book, sections are referenced by their Quarto label (@sec-day1, @sec-crossrefs). These resolve to clickable links in HTML and section numbers in PDF. Figures and tables use the @fig- and @tbl- prefixes introduced on Day 3.

References to the companion volumes R for Biostatistics, Git and GitHub for Biostatistics, and the Biostatistics Practicum use prose pointers rather than Quarto cross-references, because cross-references do not resolve across separate books. For example: ‘see the publishing chapter of the companion Git and GitHub for Biostatistics volume’.

Chapter structure

Every content chapter follows the same five-section template:

  1. Learning objectives. What you will be able to do after the day.
  2. Lecture. The substantive content, with commands to run and documents to render in your own environment as you read.
  3. Worked example. A small but realistic authoring scenario that uses the day’s content end to end.
  4. Homework. Problems organized from easier to harder.
  5. Solutions. Worked solutions to all homework problems. Read only after attempting the problem.

Each chapter closes with a short What’s next pointer. The pattern repeats deliberately; by the third chapter you know where to find each component.