21. Reproducible Workflow

From Analysis to Transparent Reporting

1 Introduction

A sound analysis is not complete until it is transparent, traceable, and reproducible. Reproducibility links data, code, model output, interpretation, and communication into one workflow.

2 Key Concepts

The chapter closes the sequence by foregrounding these principles.

• Reproducibility means the analysis can be traced and rerun from source.
• Transparent workflow keeps data, code, output, and interpretation connected.
• Documented decisions make analyses easier to evaluate and revise.
• Quarto and scripts support literate, inspectable analysis.
• Reporting limitations and diagnostics is part of reproducible science, not an optional extra.

3 Core Principles

• distinguish exploratory from confirmatory work,
• keep code and narrative together,
• document decisions,
• report diagnostics and limitations,
• make figures and tables reproducible from source.

4 Practical Tools

In this module, reproducibility is supported primarily through:

• R scripts,
• Quarto documents,
• stable project structure,
• explicit reporting of analytical choices.

5 Source

This chapter expands the placeholder material in:

• 26-reproducible-workflow.qmd