8. Project Documentation with write_readme()

Introduction

Consistent project documentation is crucial for reproducibility and collaboration. rUM automatically creates a README file and a dated progress notes file. The README file has information that someone would read first to learn about a project. The dated progress notes holds a template for keeping track of changes. rUM also includes a write_readme() function which can be used to add these files to an existing project.

Getting Started

To add documentation to an existing project, type:

rUM::write_readme()

This creates two files in your project directory:

1. README.md: A comprehensive project documentation template
2. dated_progress_notes.md: A progress tracker

The README Template

The generated README.md includes structured sections for:

# Project Name

## Description
- Study Name: 
- Principal Investigator: 
- Author: 

## Project Setup
[Steps for project reproduction]

## File Descriptions
[Details about key project files]

## Directory Structure
[Overview of project organization]

## Miscellaneous
[Additional project notes]

Progress Tracking

The dated_progress_notes.md file automatically starts with:

# Add project updates here
Dec 3, 2024: project started

This file serves as a chronological log of project developments and milestones.

Handling Existing Files

If a README file already exists, write_readme() will provide an interactive prompt:

> rUM::write_readme()
#> ℹ **CAUTION!!**
#> README.md found in project level directory! Overwrite?

This ensures you won’t accidentally overwrite existing documentation.

Best Practices

1. Update the README.md immediately after project creation
2. Keep the dated_progress_notes.md current with significant changes
3. Use consistent formatting in your documentation
4. Include enough detail for others to understand and reproduce your work

Conclusion

The write_readme() function provides a foundation for thorough project documentation. By starting with well-structured templates and maintaining regular updates, you can ensure your projects remain accessible and reproducible.

Whether you’re working solo or collaborating with a team, good documentation practices make your research more valuable and easier to build upon.