Text formatting

You can italicize text by placing it inside of a single set of asterisks (*) or underscores (_).

You can bold text by placing it inside of a double set of asterisks (**) or underscores(__).

Headers are created by starting a line with a specific number of pound or hash signs (#) that corresponds with the level of your header. For example:

Second-level header

Lists

An unordered list (with bullet points) can be created by typing an asterisk and space (*) at the beginning of each line. Second-level sub-bullets can be created by typing tab twice and then typing a hyphen and a space (-) at the beginning of each line. (I think on some computers sub-bullets may work if you type tab once, but it doesn’t on my Mac!)

• Bullet 1
  • Sub-bullet 1
  • Sub-bullet 2
• Bullet 2
• Bullet 3

Please note: You’ll need to leave a blank line in your .Rmd file before the first bullet or it won’t output properly.

An ordered list (with numbers) can be created by typing a number, period, and space (e.g., 1.) at the beginning of each line. Second-level sub-bullets can be created by typing tab twice and then typing “i”, a right parenthesis, and a space (i)) at the beginning of each line. (With each new line, you’ll increase your “i”s as this is written in lowercase Roman numerals.)

1. Number 1
   1. Sub-bullet 1
   2. Sub-bullet 2
2. Number 2
3. Number 3

Equations

You can add equations to your R Markdown file by including them either between single dollar signs (for inline equations within your text) or double dollar signs (for a separate equation section below your text–often used to highlight formulas in papers). This is based on something called LaTeX notation.

Here is an example of an inline equation: \(y_i = \alpha + \beta x_i + e_i\).

Here is a displayed formula:

\[\frac{1}{1+\exp(-x)}\]

Hyperlinks

You can add a hyperlink by typing the text you’d like to link in brackets followed by the URL in parentheses with no space between them. Here is an example.

Images

The code to include an image is similar to that for a hyperlink. You’ll type an exlamation point, followed by the image caption in brackets, followed by the image location (either a URL or a path to the image’s location on your computer) with no spaces between them. The image here is a bit large, so you’ll see that RMarkdown pushed it to the next page in the knitted PDF document.

Butler Library

Quotes

Quotes can be included by typing a greater-than sign and space at the beginning of each line (>).

To be, or not to be, that is the question: Whether ’tis nobler in the mind to suffer The slings and arrows of outrageous fortune…

Tables

Basic tables can be included using the following notation:

You can also include tables within code chunks, which will be illustrated in the next section.

Code chunks

Most of the time, you’ll use code chunks within R Markdown to run your code. Here is an example code chunk. (I’ve also created some dummy data here we’ll use to demonstrate functions in subsequent code chunks.)

```r
x <- c(1, 2, 4, 4, 5, 5, 5, 7, 9, 9)
y <- 1:10
df <- data.frame(x, y)
x
```

```
##  [1] 1 2 4 4 5 5 5 7 9 9
```

To insert an R code chunk, you can type it manually or use the shortcut key (Ctrl-Alt-I on PC; Cmd-Option-I on Mac). This will produce the following code chunk:

Inline code

Inline code can be included by placing your code in and starting it with r and a space. (If you’re viewing this in the PDF, see the .Rmd file for the code.) Inline code can be a really helpful way to pull out a datapoint and include it in your text. For example, here is the second value in our vector x : 2.

Tables (from code chunks)

You can create a table of a dataframe by placing the dataframe name within the kable() function.

kable(df)

Plots

Images generated by knitr are saved in a figures folder.

hist(x)

ggplot(data = df, aes(x = x, y = y)) +
  geom_point()

Code chunk options

There are a wide range of code chunk options, which you can find listed in this helpful cheat sheet. We highlight some of the most common here.

```r
# We included the eval = FALSE option at the beginning of this chunk
y <- 0
```


```r
# We can check here and see that the change in the previous chunk was not made to y
# because the code wasn't evaluated.
y
```

```
##  [1]  1  2  3  4  5  6  7  8  9 10
```

```r
for (i in 1:5000) {
    lm((i+1)~i)
}
```

```r
plot(x)
```

<img src="intro-to-rmarkdown_files/figure-html/unnamed-chunk-6-1.png" width="288" />

plot(x)