The Reproducible Student Researcher

The only question is when, and how much of it you get back. Eight months into a project you need to regenerate Figure 3 with one more data point. There are four scripts with promising names, two of them called something like analysis_final, and neither produces the numbers in your draft.

Download the A4 edition (PDF, 471 KB)Download the 6 × 9 print edition (PDF, 503 KB)

Free · 134 pages (A4) · 173 pages (6 × 9) · DRM-free PDF

The Reproducible Student Researcher full paperback cover with back, spine, and front — Paperback wrap: back cover, spine, and front cover.

Nothing was deleted. Nothing was corrupted. You simply have no record of what you did, and that turns out to be the same thing as not having done it.

This is the practical subset of reproducible research, written for a student with a project and a deadline. Not Docker images and continuous integration. Six habits, none taking more than an afternoon, that between them close every way a project falls apart.

What this book helps you do

Why raw data is read-only, and how to enforce it at the filesystem level

Git in seven commands, without the branching mythology

One command that rebuilds every figure and number from raw data

The environment file everybody skips, and why silent version changes hurt most

Assertions and seeds: the tiny subset of testing that pays for itself

A project template, a Git card, and a checklist built to be photocopied

What is inside

The downloadable editions include the complete chapters and toolkit listed below.

Why Work Disappears

The Week You Lost
What Reproducible Actually Means
The Five Artefacts

Files and Records

Naming Things
A Project Layout That Survives
Raw Data Is Read-Only
The Digital Lab Notebook
Backups, and the 3-2-1 Rule

Version Control

Git Without the Mythology
The Seven Commands You Need
Branches, and Whether You Need One
What Never Goes in a Repository

Code That Runs Again

Scripts, Not Sessions
One Command Rebuilds Everything
The Environment Is Part of the Result
Seeds and Determinism
Notebooks: Where They Help and Where They Hurt

Analysis and Outputs

Every Figure Made by Code
Numbers That Trace Back
Checking Analysis Code
Documenting for Your Future Self

The README That Makes It Usable
Licences, DOIs, and Archives
The Handover

Toolkit

The Project Template
Git Command Card
The Reproducibility Checklist
README and Statement Templates
Environment Recipes by Language
Ten Failures, and What Would Have Prevented Them

Two PDF editions are included

Both layouts are free to download from this page. Use the 6 × 9 edition when you want the paperback reading experience or a compact printout. Use the A4 edition for a larger screen page and easier home or office printing.

A4 screen edition

PDF · 134 pages · 471 KB

A larger page for reading on screen, and the easier one to print at home or in an office.

Download this edition

6 × 9 print edition

PDF · 173 pages · 503 KB

The paperback proportions, best when you want a compact printout or the book reading experience.