emLab Standard Operating Procedures

Standard operating procedures for emLab projects:

https://emlab-ucsb.github.io/SOP/

Table of Contents

1. File Structure
   • Google Shared Drive
   • GRIT Data Storage Space
   • GitHub Structure
2. Data
   • Data File Naming
   • Metadata
   • Accessing emLab Data in R
   • Tidy Data
   • Data Formats
   • Data Use Agreements and Confidential Data
3. Code
   • Code Styling
   • Code Documentation
   • Functional Programming
   • Package Reproducibility
   • Pipeline Reproducibility
   • Code Review
   • Exploratory Data Analysis
4. Git and GitHub
   • Getting Set Up
   • Repository Organization
   • Version Control with Commits
   • Using Issues
   • Working with Branches
   • Pull Requests
   • Rulesets
   • Effective Workflows
   • Public Repositories for Publications
   • GitHub Extensions in Positron and VS Code
   • AI Coding Assistants
5. Quarto
   • Chunk Best Practices
   • Figures, Tables, and References
   • Citations and Bibliography
   • Caching
   • Targets Integration
   • Themes and Dark Mode
   • Publishing
   • Presentations
6. High Performance Computing
   • Resources and Software
   • Getting Set Up
   • Using Sequoia
   • Using Quebracho
   • Best Practices and Resource Allocation
   • Accessing Data
   • Accessing Code
7. Reports and Publications
   • Affiliation and Authorship
   • Reports
   • Publishing Data
   • Sharing on Website

Contributing

The website is built using Quarto. To contribute:

1. Pull the latest updates from main.
2. Create a new branch.
3. Make your edits.
4. Open a pull request against main.
5. Tag a reviewer and address their feedback.
6. Once approved and merged, a GitHub Actions workflow will automatically render and publish the site to GitHub Pages.