Writing with code

An introduction to Literate Programming with R and Quarto

Dr. Jerid Francom

Jan 19, 2024

Overview

Literate Programming
Quarto
Lab 00: Writing with code

Literate Programming

Literate programming is an approach to programming in which code, documentation, and results are all interwoven into a single document.

Encourages stating the problem and solution in plain language
Encourages writing code that is easy to read and understand
Includes more explicit documentation than traditional code comments
Facilitates reproducible research

Quarto

Quarto is a document generation system that supports literate programming. It is designed to support a wide range of document types (HTML, PDF, Word, etc.) and programming languages (R, Python, Julia, etc.).

---
title: "My First Quarto Document"
format: html
---

## Intro to Quarto

This is a code block which simply prints a message.

```{r}
#| label: example-code

print("My name is Quarto")
```

Quarto + Markdown

In Quarto, prose is written in Markdown. Markdown is a lightweight markup language that is easy to read and write.

Markdown	HTML
`# Heading`	Heading
`bold`	bold
`footnote^[Footnote info...]`	footnote¹
`- bullets`	- bullets
`[links](https://quarto.org)`	links

Quarto + R

Code blocks in Quarto introduce sections where code can be executed.

```{r}
#| label: fig-example-plot
#| fig-cap: A simple plot

ggplot(
  data,
  aes(x = cat, y = passive)
) +
  geom_col() +
  labs(
    x = "Categories",
    y = "Passives (count)"
  )
```

The code here generates the plot in Figure 1.

Lab 00: Writing with code

Setup

In lab 00, you will create a basic Quarto document and explore some of the features of Quarto.

Clone the lab
Complete the lab

Copy the clone URL for the lab 00 repository
Open RStudio (with Docker Desktop running)
Create a new project from version control
Paste the clone URL into the repository URL field

Follow the instructions in the README.md file

Footnotes

Footnote info…