How to use this book
The book is organised around method topics, not courses. There are sixteen topic chapters, plus Chapter 0 (the decision tree), five reporting-template chapters, and five appendices.
0.1 Three reading modes
As an author with data. Open 1. Answer the question “what are you trying to do?” until you land on a method. Read the method page top to bottom: the R Implementation block runs; the Output & Results section tells you what to read off; the Reporting Templates part has a paragraph you can paste into the Methods section of your paper.
As a peer reviewer. Search for the method by name and jump straight to the For Reviewers section at the bottom of the page. It tells you what should be in the Methods paragraph, which diagnostics should have been reported, and where the typical failures live. Then skim Theory and Assumptions to confirm the application is sound.
As a learner.
Each topic chapter has labs under chapters/<topic>/labs/. Labs follow
Hypothesis → Visualise → Assumptions → Conduct → Conclude. Work
through them in order; the methods they exercise live in the same
chapter and are linked from the labs.
0.2 Conventions
- All examples are R. The R Implementation block runs as written when
the listed packages are installed. Seeds are pinned (
set.seed(2026)for tutorials,set.seed(42)for some labs) so numbers reproduce. - Every method page has the same ten sections, in this order: Introduction · Prerequisites · Theory · Assumptions · R Implementation · Output & Results · Interpretation · Practical Tips · Reporting · For Reviewers.
- The Reporting Templates part is the only place with copy-paste Methods + Results prose. The reporting block on each method page links to the corresponding template entry.