Society for Medical Decision Making

Session Summary

This beginner-friendly workshop focuses on using R and Git/GitHub to manage the full lifecycle of a scientific project, with a strong emphasis on version control and collaborative working. Participants will learn how to set up projects, manage dependencies, ensure reproducibility, and prepare code for publication, all within a collaborative framework that simulates real-world scientific teamwork. The course combines theoretical concepts with practical, hands-on exercises to build a foundational understanding of managing projects in an open-source environment.

Learning Objectives

• Begin projects in R using best practices for file organization and setup, integrating Git from the outset to track changes and manage contributions.
• Fluency with Git operations such as branching, merging, resolving conflicts, and using remote repositories to facilitate collaboration among multiple contributors.
• Fluency with collaborative features of GitHub, including pull requests, code reviews, and using issues for communication, to enhance team cooperation and project transparency.
• Utilize R’s package managers to handle project dependencies correctly, ensuring that your projects are portable and reproducible across different environments.
• Implement reproducibility checks and techniques, such as using RMarkdown and Docker, to ensure that analyses are repeatable and can be run on any computer.
• Recognize how to package your research projects using R packages, publish your code on GitHub, and archive final versions on platforms like Zenodo for broader dissemination.

Pre-Course Preparation

Pre-course setup materials will be distributed 2 weeks in advance of the course date. These materials will include a short video and pre-work designed to take less than 30 minutes.

Time Allocation & Topic Outline

Time allocation ~3.5hrs
1 hour- Introduction to Git + GitHub
1 hour- Collaborative workflow for scientific teams
30 minutes- Project management and best practices
30 minutes- Dependency management and reproducibility
30 minutes- Packaging your project and archiving your programs

Faculty Background & Qualifications

Jacob Jameson, M.S.
Jacob Jameson is a Ph.D. student in Health Policy/Decision Sciences at Harvard University and holds an M.S. in Computer Science from The University of Chicago. He has taught a version of this short course at both the 2023 and 2024 SMDM Annual Meetings.

Madison Coots, M.S.
Madison Coots is a Ph.D. student in Public Policy at Harvard University and holds an M.S. in Computer Science from Stanford University. She co-taught this course at the 2024 SMDM Annual Meeting.

COI
No proprietary software.