RStudio IDE and Quarto

Integrated Development Environment (IDE)

https://rafalab.dfci.harvard.edu/dsbook-part-1/productivity/reproducible-projects.html

• Posit provides a free IDE for R with RStudio
• Positron (newer and adapted to LLMs)

The panes

The Basics

• Open a new R script file. (example.R)
• Learn tab complete.
• Run commands while editing scripts.
• Run the entire script.
• Make a plot.
• Change options to never save workspace.
• Change IDE appearance.

Projects

• Start a new project in a new directory.
• Start a new project in an existing directory.
• Change projects.
• Use the File menu to create a new Quarto document

Type of editor

• we will be creating and editing markdown documents - mostly using the Quarto paradigm

• for Quarto you can use either a source view or a visual view:

  • Source - See the actual code (WYSIWYG)
  • Visual - Partial preview of final document.

Note: You can state your preference in the header:

title: RStudio IDE
keywords: "Productivity Tools"

editor: source

The header

• Start a new empty document.

• At the top you see:

---
title: "Untitled"
---

• The things between the --- are the YAML header.

• Quarto guide.

Quick Markdown Text formating

*italics* or _italics_ = italics

**bold** = bold

***bold italics*** = bold italics

~~strikethrough~~ = strikethrough

`code` = code

Code chunk

This:

```
line 1
line 2
```

shows a code chunk:

line 1
line 2

Headings

You can start sections and subsections like this:

# Header 1

## Header 2

### Header 3

Links

• Show the link: <https://quarto.org/docs/guide/>

• Add link to text: [Quarto Guide](https://quarto.org/docs/guide/)

Looks like this:

https://quarto.org/docs/guide/

Quarto Guide

Images

![Introductory Statistics with R](https://m.media-amazon.com/images/I/51gZOXbaNnL._AC_UF1000,1000_QL80_.jpg)

Shows the plot and caption:

Introductory Statistics with R

• The image can also be a local file (replacing the html link with the path to the image.)

Unordered Lists

Bullets:

-   bullet 1
    -   sub-bullet 1
    -   sub-bullet 2
-   bullet 2

Looks like this:

• bullet 1
  • sub-bullet 1
  • sub-bullet 2
• bullet 2

Ordered Lists

Ordered list:

1.  Item 1
2.  Item 2

Looks like this:

1. Item 1
2. Item 2

Equations

Note

Technical report often uses LaTeX for typesetting.

There are many online tutorials, like this one.

Equations using LaTeX.

Examples:

• Inline: $Y_i = \beta_0 + \beta_1 x_i + \varepsilon_i$ looks like this \(Y_i = \beta_0 + \beta_1 x_i + \varepsilon_i\)

• Display math:

$$
\mathbf{Y} = \mathbf{X\beta} + \mathbf{\varepsilon}
$$

looks like this:

\[ \mathbf{Y} = \mathbf{X\beta} + \mathbf{\varepsilon} \]

Code in Quarto document .qmd (or RMarkdown .rmd)

One can include and execute the code chunks in .qmd document by

```{r}
# R code here, e.g.
2+3
```

Note

To add an R chunks, type the shortcut key binding command-option-I on the Mac and Ctrl-Alt-I on Windows.

R Code Chuns

We can write something like this:

```{r}
x <- 1
y <- 2
x + y
```

It looks like this:

[1] 3

Note that it was evaluated and the result is shown.

Local control

• By default, the code and result will show up.

• control the behavior with #|

• For example, to avoid showing code in the final document, use echo: FALSE.

```{r}
#| echo: false
x <- 1
y <- 2
x + y
```

Other local controls

• There are many options

• to avoid executing the code use eval: FALSE.

• To avoid showing warnings warning: FALSE, to avoid showing messages message: FALSE.

Note

to apply an option globally, set them in the header.

execute:
  echo: false

Labeling a code chun is a good practice

• We recommend getting into the habit of labeling code chunks:

```{r}
#| label: one-plus-two
x <- 1
y <- 2
x + y
```

• Helps with debugging
• Helps reading the code

More on markdown

• RStudio’s tutorial: https://quarto.org/docs/get-started/hello/rstudio.html
• The knitR book: https://yihui.name/knitr/
• Pandoc’s Markdown in-depth documentation
• Guide for academic reports
• RMarkdwon Cheatsheet

Quarto render

• RStudio provided Render button to compile the document.

• quarto render filename.qmd in a terminal renders single qmd file.

• quarto render renders all qmd files.

• You can produce html, pdf, or word documents.

• You can specify the default in the YAML header using: format: html, format: pdf,format: docx, or format: gfm (GitHub flavored markdown).