Using R Markdown

Key terms

• Document: A Markdown file where you type stuff

• Chunk: A piece of R code that is included in your document. It looks like this:

  ```{r}
  # Code goes here
  ```

  There must be an empty line before and after the chunk. The final three backticks must be the only thing on the line—if you add more text, or if you forget to add the backticks, or accidentally delete the backticks, your document will not knit correctly.

• Knit: When you “knit” a document, R runs each of the chunks sequentially and converts the output of each chunk into Markdown. R then runs the knitted document through pandoc to convert it to HTML or PDF or Word (or whatever output you’ve selected). We will always use PDF for this course.

  You can knit by clicking on the “Knit” button at the top of the editor window, or by pressing ⌘⇧K on macOS or control + shift + K on Windows.

  

Add chunks

There are three ways to insert chunks:

• Press ⌘⌥I on macOS or control + alt + I on Windows

• Click on the “Insert” button at the top of the editor window

  

• Manually type all the backticks and curly braces (don’t do this)

Chunk names

You can add names to chunks to make it easier to navigate your document. If you click on the little dropdown menu at the bottom of your editor in RStudio, you can see a table of contents that shows all the headings and chunks. If you name chunks, they’ll appear in the list. If you don’t include a name, the chunk will still show up, but you won’t know what it does.

To add a name, include it immediately after the {r in the first line of the chunk. Names cannot contain spaces, but they can contain underscores and dashes. All chunk names in your document must be unique.

```{r name-of-this-chunk}
# Code goes here
```

Chunk options

There are a bunch of different options you can set for each chunk. You can see a complete list in the RMarkdown Reference Guide or at knitr’s website.

Options go inside the {r} section of the chunk:

```{r name-of-this-chunk, warning=FALSE, message=FALSE}
# Code goes here
```

The most common chunk options are these:

• fig.width=5 and fig.height=3 (or whatever number you want): Set the dimensions for figures
• echo=FALSE: The code is not shown in the final document, but the results are
• message=FALSE: Any messages that R generates (like all the notes that appear after you load a package) are omitted
• warning=FALSE: Any warnings that R generates are omitted
• include=FALSE: The chunk still runs, but the code and results are not included in the final document. Don’t use this on your labs as we need to see your work, but do use this for your final project when the output is to be polished and clean.

You can also set chunk options by clicking on the little gear icon in the top right corner of any chunk:

Inline chunks

You can also include R output directly in your text, which is really helpful if you want to report numbers from your analysis. To do this, use `r r_code_here`.

It’s generally easiest to calculate numbers in a regular chunk beforehand and then use an inline chunk to display the value in your text. For instance, this document…

```{r find-avg-mpg, echo=FALSE}
avg_mpg <- mean(mtcars$mpg)
```

The average fuel efficiency for cars from 1974 was `r round(avg_mpg, 1)` miles per gallon.

… would knit into this:

The average fuel efficiency for cars from 1974 was 20.1 miles per gallon.

Output formats

You can specify what kind of document you create when you knit in the YAML front matter.

title: "My document"
output:
  html_document: default
  pdf_document: default
  word_document: default

You can also click on the down arrow on the “Knit” button to choose the output and generate the appropriate YAML. If you click on the gear icon next to the “Knit” button and choose “Output options”, you change settings for each specific output type, like default figure dimensions or whether or not a table of contents is included.

The first output type listed under output: will be what is generated when you click on the “Knit” button or press the keyboard shortcut (⌘⇧K on macOS; control + shift + K on Windows). If you choose a different output with the “Knit” button menu, that output will be moved to the top of the output section.

The indentation of the YAML section matters, especially when you have settings nested under each output type. Here’s what a typical output section might look like:

---
title: "My document"
author: "My name"
date: "January 13, 2020"
output: 
  html_document: 
    toc: yes
    fig_caption: yes
    fig_height: 8
    fig_width: 10
  pdf_document: 
    latex_engine: xelatex  # More modern PDF typesetting engine
    toc: yes
  word_document: 
    toc: yes
    fig_caption: yes
    fig_height: 4
    fig_width: 5
---