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 in your own terminal as you encounter it. Do not skip the commands; the chapter is designed to be read with a terminal open and a scratch repository 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 boot camp 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 student’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 student should be able to do by the end of the day.
  2. Lecture. The substantive content for the day, with commands to run.
  3. Worked example. A small but realistic biostatistical scenario that uses the day’s content end to end, most often placing an R analysis script under version control.
  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 teaches two related but distinct tools:

  • Git is the version-control system. It runs on your own machine and records the history of your files. Git is the subject of Days 1 through 3.
  • GitHub is a website that hosts Git repositories and adds collaboration features (issues, pull requests, review). GitHub is not Git; it is one of several services that host Git repositories. GitHub is the subject of Days 4 and 5, operated from the terminal with the official gh command-line tool.

Keeping the distinction clear from the outset prevents a common beginner confusion in which the two are treated as a single thing.

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>.
  • GitHub operations use the gh command-line tool.
  • Command lines and file listings are wrapped at 78 characters.

Companion volumes

This boot camp is the version-control half of a two-part preparation; the R half is R for Biostatistics. After both, the reader may continue with the four follow-on volumes:

The end of Chapter 5 describes how the Practicum picks up the version-control thread and extends it into a full reproducible pipeline.