sophiazzw7 / computing-bootcamp-2018

Materials for the DSS Computing Bootcamp, 2018

DSS Computing Bootcamp

This is a 3 hour computing bootcamp for incoming PhD and MS students to the Department of Statistical Science at Duke University.

The workshop will cover the following topics:

Introduction to Reproducible Research

• Recognize the problems that reproducible research helps address, featuring brief discussion of case studies case studies of (lack of) reproducibility gone wrong.
• Identify pain points in getting your analysis to be reproducible.
• The role of documentation, sharing, automation, and organization in making your research more reproducible. Introducing some tools to solve these problems, specifically R/RStudio/RMarkdown.

Organizing your project to facilitate Reproducible Research

• Organize projects and folders to enable reproducibility and reusability
• Understand the structure of data files and the importance of documenting all changes made
• Using these practices, create a reproducible project workflow using R/RStudio/RMarkdown.

Version control

• Introduction to git/GitHub as a version control tool.
• Practice initiating a project directory, making / committing / pushing changes, and creating a pull request to someone else's remote repository.
• Discuss the role of version control in reproducibility of one's own project as well as in collaborative projects.

Introduction to the department computing eco-system

• Account activation and access to departmental servers.
• Discussion of how to responsibly use distributed computing resources.

Acknowledgments

• Reproducible Science Curriculum Hackathon

• GitHub's ssh help pages

• Software Carpentry Project

• Karl Broman - Wisc's Tools4RR

• Karl Broman - Reproducible Research

• Grolemund and Wickham - R for Data Science

• Case studies:

  • Science retracts gay marriage paper without agreement of lead author, http://news.sciencemag.org/policy/2015/05/science-retracts-gay-marriage-paper-without-lead-author-s-consent
  • Seizure study retracted after authors realize data got "terribly mixed", http://retractionwatch.com/2013/02/01/seizure-study-retracted-after-authors-realize-data-got-terribly-mixed/
  • Bad spreadsheet merge kills depression paper, quick fix resurrects it, http://retractionwatch.com/2014/07/01/bad-spreadsheet-merge-kills-depression-paper-quick-fix-resurrects-it/