6 Steps Towards Reproducible Research

• July 17, 2024

By Heidi Seibold

Overview

Reproducible research is crucial for advancing science, allowing others to verify results and build upon previous work. This guide outlines six impactful steps to make your research reproducible and open. It is structured to help you implement these steps gradually, depending on your current practices and goals.

1. Get Your Files and Folders in Order

The Importance of Organization

A well-organized file and folder structure is fundamental for managing complex research projects. It helps you and your collaborators find files quickly, reduces redundancy, and prevents errors.

Suggested Folder Structure

Here is a basic template for organizing your research project:

.
└── project-name
    ├── analysis       # Data analysis files
    ├── src            # Source files and functions
    ├── comm           # Communication documents
    │   ├── internal-comm
    │   └── journal-comm
    ├── data
    │   ├── data_clean
    │   └── data_raw   # Untouched raw data
    ├── dissemination  # Manuscripts, posters, presentations
    ├── documentation  # Documentation files
    └── misc           # Miscellaneous files

This structure can be tailored to fit the specific needs of your project.

Your Tasks

• Review and reorganize your current projects using a similar structure.
• Discuss with collaborators and adjust the structure based on feedback.

2. Use Good Names

The Power of Naming

Good naming conventions for files, folders, and functions can significantly improve the clarity and usability of your project.

Examples of Bad and Good Names

Bad:

• Myabstract.docx
• figure 1.png

Good:

• 2024-07-08_abstract-for-conference.docx
• Fig01_scatterplot-talk-length-vs-interest.png

Naming Guidelines

• Machine readable: Avoid spaces and special characters.
• Human readable: Use descriptive names.
• Consistent: Stick to a naming convention throughout your project.
• Default ordering: Use dates in YYYY-MM-DD format.

Your Tasks

• Audit and improve naming conventions in your current project.
• Establish and adhere to a naming convention.

3. Document with Care

Importance of Documentation

Proper documentation ensures that others (and your future self) can understand and reproduce your work.

Key Documentation Practices

• README: Include a README file in each project outlining its purpose, involved parties, and key information.
• Code Documentation: Use literate programming or clear comments to explain your code.
• Metadata: Document information about your data, including its origin, content, and licensing.

Your Tasks

• Create or update the README file in your current project.
• Start or improve code commenting practices.
• Ensure metadata is documented.

4. Version Control

Why Version Control?

Version control is essential for tracking changes, collaborating with others, and maintaining a history of your work.

Using Git

Git is the most popular version control system, allowing you to track changes, collaborate, and revert to previous versions easily.

Steps to Get Started

1. Install Git.
2. Create an account on GitHub or GitLab.
3. Initialize a repository and start committing your changes.

Your Tasks

• Set up Git for your current project.
• Learn Git through tutorials or workshops.

5. Stabilize Your Computing Environment and Software

Avoiding Environment Issues

Stabilizing your computing environment ensures that your code runs consistently over time, regardless of updates to software or operating systems.

Strategies

1. Record your computing environment: Document software versions using tools like sessionInfo() in R.
2. Virtual Machines: Use virtual machines to encapsulate your environment.
3. Containers: Utilize Docker or Apptainer for portable and shareable environments.

Your Tasks

• Choose a method for stabilizing your environment.
• Implement this method in your current project.

6. Publish Your Research Outputs

Sharing Your Work

Publishing your research outputs ensures that others can access and build on your work.

Options for Publishing

• General purpose repositories: Zenodo, Open Science Framework.
• Institutional repositories: University-specific services.
• Field-specific repositories: Discipline-focused platforms.

If Data Cannot Be Shared Openly

Consider publishing metadata, synthetic data, or sharing data with specific researchers if your data is sensitive.

Your Tasks

• Identify suitable repositories for your field.
• Start publishing your data and code in these repositories.

Conclusion

Reproducible research enhances the credibility and impact of your work. By implementing these six steps, you can make your research more transparent and accessible. Remember, improving reproducibility is a gradual process—take it one step at a time and continuously seek to enhance your practices.

Seibold, H. (2024). 6 Steps Towards Reproducible Research. Zenodo. https://zenodo.org/records/12744715