Part 1: Why Reproducibility?

The foundation of reliable research

What is Reproducibility?

At its core, reproducibility means:

Same data + same code = same results

But it’s not just about allowing others to verify your work. It’s about being able to reproduce your own analysis — whether that’s next week, next month, or when Reviewer 2 asks for changes six months from now.

Ask yourself

Can you reproduce your own analysis from 6 months ago? Do you remember which version of the data you used? Which script ran in which order?

Common Problems

These scenarios might sound familiar:

Scenario Root Cause
“Table 1 doesn’t match the text” — your advisor Manual copy-paste
final_v3_FINAL.docx — which is the real final? No version control
Can’t reproduce your 3-month-old results Code and data separated, no documentation
“Just change X” leads to hours of work Manual workflow, no automation
The common thread

All these problems share a root cause: manual work. Every time you copy a number, rename a file manually, or try to remember what you did, you are prone to make errors. This is inevitable, as we all make mistakes as humans.

Today’s Core Message

Three principles for reproducible research:

  1. Automate — Generate outputs from code, not copy-paste
  2. Integrate — Keep code and text together in one place
  3. Track — Version control everything with Git

This workshop will show you how to do this in practice.

❌ Before

project/
├── analysis_v1.docx
├── analysis_v2.docx
├── analysis_v3_FINAL.docx
├── analysis_v3_FINAL_revised.docx  ← ?
└── figures/
    ├── fig1_old.png
    ├── fig1_new.png
    └── fig1_FINAL.png

✅ After

project/
├── analysis.qmd  ← Single source
├── _quarto.yml
└── .git/         ← Full history

↓ quarto render
report.html / .docx / .pdf
Principle Tools
Automate gtsummary, ggplot2, R functions
Integrate Quarto (.qmd files)
Track Git + GitHub

Why Plain Text?

All the tools we’ll use today work with plain text files (.qmd, .R, .yml). This matters because:

  • Git-Friendly — Plain text shows exactly what changed between versions. Binary formats just show “file changed.”
  • AI-Friendly — AI tools can read, understand, and help you write plain text code
  • Future-Proof — Plain text will always be readable. Can you open a 1995 Word document?

Part 2: Project Setup →