Open Research Workflow
A practical guide to reproducible research using Quarto, Positron, GitHub, and Zenodo
Open Research Workflow
A step-by-step guide to making your research reproducible, citable, and open — from day one of your project to final publication.
Quarto Positron GitHub Zenodo renv R
Why this guide?
Open and reproducible research is increasingly expected — not just encouraged — by journals, funding agencies, and the scientific community. But the practicalities of how to do it are rarely taught explicitly during a PhD.
This guide documents a complete workflow that takes you from setting up a new project on Day 1 through to archiving your code and data permanently when a paper is accepted. It uses realistic placeholder data from a freshwater ecology study so you can follow along with a real example.
This guide focuses on a two-file Quarto approach: an analysis.qmd for all your R code, and an index.qmd for your clean manuscript. This keeps your analysis fully transparent while your manuscript stays readable. It is designed for use in Positron, the modern successor to RStudio.
It’s not just organisation, either: Quarto renders PDF through LaTeX, so you get proper academic typesetting immediately, and a one-line csl: swap reformats every citation to match any journal’s house style — no manual reference wrangling. More on both in chapter 1.
The workflow at a glance
⚙️
1. Project Setup
Create your folder structure, initialise Git in Positron, push to GitHub, connect to Zenodo, and set up renv — all on Day 1.
📄
2. Quarto Flow
How to use analysis.qmd and index.qmd together — analysis feeds manuscript, both tracked in version control.
🔀
3. Version Control
Commit habits, what to track, what to ignore, and how to use the Source Control panel in Positron effectively.
🗄️
4. Zenodo
Reserve a DOI before submission, keep it unlocked during review, and publish permanently at acceptance.
📬
5. During Review
Give reviewers access to your code and data via GitHub without locking the version yet.
✅
6. After Acceptance
Create a GitHub release, publish your Zenodo record, and update your data availability statement.
The tools
| Tool | Purpose | Cost |
|---|---|---|
| Quarto | Write manuscript and analysis together | Free |
| Positron | IDE with built-in Git and Quarto support | Free |
| Git | Track every change locally | Free |
| GitHub | Host code publicly, give reviewers access | Free |
| renv | Record exact R package versions | Free |
| Zenodo | Permanent archive with a citable DOI | Free |
Quarto and Positron both support Python as a first-class language — {python} code chunks work the same way {r} chunks do, and the two-file structure, Git/GitHub habits, and Zenodo archiving are entirely language-agnostic. The one R-specific piece is renv; swap it for venv/requirements.txt, conda/environment.yml, or Poetry to get the same locked-dependency guarantee.
Get the starter template
Skip the blank-page problem. This is a working Quarto project — folder structure, analysis.qmd, index.qmd, placeholder data — that renders out of the box. Every file marks exactly what to replace with FILL IN comments.
⬇ Download the .zip Use the GitHub template →
Not sure what you’d actually get? See the manuscript this template renders — HTML · PDF · Word
Who is this for?
This guide is for anyone doing research who:
- Uses R and Quarto for analysis and writing
- Wants to make their research reproducible without a steep learning curve
- Is preparing to submit to journals that require data availability statements
- Wants a citable DOI for their code and data
The workflow itself is field-agnostic — it’s just Quarto, Git, GitHub, renv, and Zenodo. The worked examples throughout use freshwater ecology data because that’s the author’s own research, but nothing about the setup is ecology-specific.
About this guide
This guide was written by Olivier V. Raven as part of his PhD research on kōura (Paranephrops planifrons) ecology and habitat restoration in Aotearoa New Zealand.
The guide itself follows the workflow it describes — it is written in Quarto, version controlled on GitHub, and archived on Zenodo.
License: CC BY 4.0 — feel free to adapt and reuse with attribution.
Cite as: Raven, O.V. (2026). Open Research Workflow: A practical guide to reproducible research using Quarto, Positron, GitHub, and Zenodo. DOI pending — will be archived on Zenodo.