Reproducible Research

MATH-7360 Data Analysis

rm(list = ls()) # clean-up workspace

Announcement

• HW1 keys will be posted on Next Monday

• Wednesday class uncertainty

• Office hour by appointment

• Play with Git and GitHub

  • Read the error message

  • Google your error message (reliable solution source: stackoverflow)

Reproducible Research

Definition

In computational sciences this means:

the data and code used to make a finding are available and they are sufficient for an independent researcher to recreate the finding.

Christopher Gandrud

Why

• Science is about accumulating knowledge and reproducibility is the foundation.

• Greater research impact. Note: “a study can be reproducible and still be wrong.”

• Better work habits

  • avoid thinking ‘no one was looking’

  • communicate with future-you

• Better teamwork

  • communicate with another person. For example, your instructor with your HWs.

Tools for reproducible research

• Version control: Git+GitHub.

• Distribute method implementation, e.g., R/Python/Julia packages, on GitHub or bitbucket.

• Dynamic document: RMarkdown for R or Jupyter for Julia/Python/R.

• Docker container for reproducing a computing environment.

• Cloud computing tools.

• We are going to practice reproducible research now. That is to make your homework reproducible using Git, GitHub, and RMarkdown.