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Methods in R: A topic reference for biomedical research and peer review

Welcome!

Methods in R cover Welcome to “Methods in R: A Topic Reference for Biomedical Research and Peer Review”.

This book is shaped for two readers it expects to serve in the same week: the author who has data in front of them and needs to pick a method, run it in R, and write the Methods paragraph; and the peer reviewer who has a manuscript on their desk and needs to know what a competent application of that method looks like, which diagnostics should have been reported, and what red flags to flag.

The body covers sixteen topic areas — from foundations and inference through regression, survival, Bayesian methods, machine learning, bioinformatics, and study design — with hands-on labs that consolidate the methods of each area into a single runnable file. Every method page ends with a For Reviewers section: the misapplications, the missing diagnostics, the red flags in tables and figures, and the things to verify against the authors’ references and arithmetic. A final part, Reporting Templates, gives copy-paste Methods and Results paragraphs tagged by STROBE / CONSORT / TRIPOD-AI / PRISMA / ARRIVE.

The book is not a textbook of statistics. It assumes you can read an R session and follow a method already named to you. Where it differs from the existing biostatistics shelf is in being optimised for lookup, not linear reading, and in pairing every method with a concrete review checklist.


Open Source Repository

This book has been built using {rmarkdown} and {bookdown}. Formulas are rendered using MathJax. All source files are available on GitHub: https://github.com/r-heller/methods-in-r. You are free to fork, share, and reuse the contents under the CC BY-SA 4.0 license.


How To Use The Guide

  • Linear vs. lookup. If you already know the method, jump to its chapter. If not, start at Chapter 1 and follow the decision tree.
  • Where the code lives. Code in each method page and lab is display-only in the rendered book; copy it into an R session with the packages cited in that section attached. Reusable helpers are kept in R/helpers.R in the source repository.
  • Per-chapter PDFs. Every chapter has a Download this chapter (PDF) button at the top of its page; the full set is also available at pdf-chapters/.
  • Whole-book PDF and EPUB. Use the navbar Download menu for a single-file PDF or EPUB.
  • Corrections and suggestions. Open an issue at https://github.com/r-heller/methods-in-r/issues.


Contributing

Issues and pull requests are welcome — see CONTRIBUTING.md.


Citation

The suggested citation is:

Heller, R. (2026). Methods in R: A Topic Reference for Biomedical Research and Peer Review (Version 1.0.0). Self-published via GitHub Pages. https://r-heller.github.io/methods-in-r/.

Download the reference as BibTeX or .ris.


This book was built by the bookdown R package.