The figure illustrates a roadmap for developing a dynamic and reproducible research article using Quarto and RStudio. The process is categorized into three levels of reproducibility: Minimal, Proper, and Full. Each level integrates specific tools and practices to enhance the reproducibility of the research.

This proposal is published in the following OSF project: https://osf.io/njdq5/
Shared in the following GitHub repository: https://github.com/phdpablo/article-template
Exemplified in the following URL address: https://phdpablo.github.io/article-template/

Minimal Reproducibility

1. Use this template: Start by utilizing the provided template, which is pre-configured with the TIER Protocol 4.0. This protocol helps organize research projects in a systematic manner.
2. Edit READMEs: Customize the README files to reflect the details and conclusions of your research. These README files help document the project structure and contents.
3. Share on OSF: Share the project on the Open Science Framework (OSF) to ensure accessibility and transparency. This can be done at the beginning, during, or at the end of the research process.

Proper Reproducibility

In addition to the steps mentioned above, the following steps are added:

1. Quarto settings: Adjust the Quarto configuration to fit the needs of your project. This includes modifying the _quarto.yml file for different themes and output formats.
2. Develop your narrative: Write the research narrative using Quarto’s .qmd files within RStudio. This narrative forms the main body of your article and integrates text, code, and outputs seamlessly.
3. Environment control: Implement environment control using the renv package. This ensures that the R environment is consistent and reproducible. The renv folder captures the exact versions of R packages used in the project.
4. Share dynamic article: Render and share the dynamic document via GitHub Pages. The Quarto-generated HTML files (docs folders) are hosted on GitHub Pages, making the research accessible and interactive.

Full Reproducibility

Building on the proper reproducibility steps, full reproducibility adds:

1. Use Docker: Employ Docker for operating system-level environment control. A Docker container encapsulates the entire project environment, ensuring that the research can be replicated exactly, regardless of the local machine setup.

Tools Utilized

• TIER Protocol 4.0: Provides a framework for organizing and documenting research projects.
• OSF: A platform for sharing research outputs and ensuring open science practices.
• Quarto: A tool for creating dynamic documents that integrate text, code, and outputs.
• RStudio: An integrated development environment (IDE) for R, facilitating data analysis and reproducible research.
• Git/GitHub: Version control systems that track changes and manage project versions.
• renv: An R package for managing and reproducing consistent R environments.
• GitHub Pages: A service for hosting static websites directly from a GitHub repository.
• Docker: A platform for containerizing applications to ensure consistent environments across different systems.

Summary

This template guides researchers through creating a reproducible and dynamic article using Quarto and RStudio. It starts with basic project setup and documentation, progresses through developing the research narrative with environment control, and culminates in full reproducibility with Docker. This structured approach ensures that research is well-documented, versioned, and easily shareable, promoting open science practices.