Introduction to Quarto

The theme of this lesson is good management of your files and data. In part two of this week’s coursework you will learn how to identify folders and paths, and create Quarto documents.

Principles of Reproducibility

File Management

As boring as it sounds, file management is arguably one of the most important skills a data scientist should have. The reproducibility of a project depends just as much on the way in which the project was stored as the computing tools used. While using R and Quarto make an important step in creating a reproducible analysis, there are other pieces that are arguably just as important—such as file management.

Believe it or not, your computer has multiple locations** where files can be stored. There has been a bit of a generational shift as computers have evolved: the “file system” metaphor itself is outdated because no one uses physical files anymore.

[This article]((https://futurism.com/the-byte/gen-z-kids-file-systems) makes the argument that with modern search capabilities, most people use their computers as a laundry hamper instead of as a nice, organized filing cabinet. However, the laundry hamper approach doesn’t play nicely with working in R and creating Quarto documents.

A good programmer will store files according to the Project TIER protocol. More specifically, you will have:

  • a “Stat 250” folder in your Documents folder, containing all your materials associated with STAT 250
  • a sub-folder for each week (e.g., Week 1, Week 2)
  • separate folders within each week for each assignment (e.g., Practice Activity, Lab)

Reproducible Documents

Over the last ten years, science has experienced a “reproducibility” crisis. Meaning, a substantial portion of scientific findings were unable to be recreated because people didn’t sufficiently document the processes they used. As such, a foundational aspect of scientific research is using tools which allow others to reproduce your findings.

Enter Quarto—a dynamic document that allows us to interweave R code and written text in the same document. Gone are the days of copying and pasting the results of your R code into a Word document—breaking the connection between your analysis and your report. Quarto is here to save the day!

Introduction to Quarto

HTML Documents

We will exclusively use HTML documents in this course. If you are interested in learning more about formatting options for Quarto HTML documents, I would recommend checking out:

Getting in the Details of Quarto

The following video goes into the details about the ways to adopt and work with Quarto documents to produce reproducible analyses.