Quarto 1: Introduction

The Quarto format (.qmd) is a multi-functional format, which is especially useful for scientific coding and analyses. Quarto documents can be used both to save and execute code as well as generating reports in various output formats. This is done by mixing markdown and so-called code chunks in the same document (we have course materials for markdown if you are unfamiliar with this format). The code itself as well as the output it generates can be included in the final report.

Quarto makes your analysis more reproducible by connecting your code, figures and descriptive text. You can use it to make reproducible reports, rather than e.g. copy-pasting figures into a Word document. You can also use it as a notebook, in the same way as lab notebooks are used in a wet lab setting (or as we utilise Jupyter notebooks in the tutorial after this one). Quarto itself does not require any particular programming language to be installed - any language you want to use can be installed separately. The currently supported languages are R, Python, Julia and Observable. Quarto is fully compatible with both R Markdown and Jupyter documents.

This tutorial depends on files from the course GitHub repo. Take a look at the setup for instructions on how to set it up if you haven’t done so already. Place yourself in the workshop-reproducible-research/tutorials/quarto/ directory, activate your quarto-env Conda environment and start your text editor or IDE of choice.

A note on R Markdown
Quarto is an evolution of the R Markdown Links to an external site. format, which was previously used in this course. While R Markdown is a widely-used and excellent software for code and reports, Quarto is most easily thought of as “R Markdown 2.0”. If you’re familiar with R Markdown, you will find Quarto to be highly similar. The creators of both Quarto and R Markdown (Posit Links to an external site.) have stated that R Markdown is not going to be deprecated, but most newer features will only come to Quarto. This means that if you’ve used R Markdown in the past now is a good time to make the switch, but you don’t have to. You can check out the Quarto website Links to an external site. for more in-depth discussions regarding Quarto/R Markdown (dis-)similarities.