Conventions

This page summarizes the visual conventions used throughout the book.

Commands and output

This book is command-line first. 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:

$ git --version
git version 2.45.2

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

git add analysis.R
git commit -m 'Add baseline analysis'

Inline commands, file names, and Git objects are set in monospace. Git subcommands are named in full (git commit, not merely commit) so that they are unambiguous. GitHub operations use the official gh command-line tool, shown the same way:

$ gh repo view --web
Opening github.com/rgt47/trial-analysis in your browser.

Placeholders that the reader must replace with their own values are written in angle brackets, for example git clone <url> or gh repo create <name>. 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 an operation that discards work irrecoverably.

Diagrams of history

Commit history is drawn as a left-to-right graph, with each node a commit labeled by a short hash and time flowing rightward. Branch and tag names are pointers attached to commits:

        main
         |
A -- B -- C

Here C is the most recent commit and main points to it. These diagrams are conceptual; the real hashes are the forty-character identifiers Git assigns.

Cross-references

Within this book, sections are referenced by their Quarto label (@sec-day1, @sec-merge-conflicts). These resolve to clickable links in HTML and section numbers in PDF.

References to the companion volumes R for Biostatistics and Biostatistics Practicum use prose pointers rather than Quarto cross-references, because cross-references do not resolve across separate books. For example: ‘see the Docker chapter of the companion Biostatistics Practicum 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 in your own terminal as you read.
  3. Worked example. A small but realistic biostatistical 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.