Creating an R Markdown notebook

In RStudio, go to File -> New File -> R Markdown. It will ask you what you want to call the file - leave the output as HTML for now.

You should see a file open with a lot of text and code already there. This is the default R Markdown document and comes with a lot of pointers about how to do things. For now, save the file as example.Rmd, and hit the “Knit” button.

If everything went well, you should see a nicely formatted webpage/ report pop up in RStudio’s built-in browser. Congratulations, you’ve made your first report!

Basic formatting

Now that we know everything’s working, let’s start from scratch and learn how R Markdown works step-by-step. The first thing we should do is delete everything except for the following:

---
title: "test"
author: "Jeff Stafford"
date: "August 20, 2017"
output: html_document
---

The stuff between the ---s is called YAML - it’s a markup format that describes what kind of document to make, who wrote it, and other technical bits that’s not actual content in your report. If you want, you can modify it, but let’s leave it be for now.

At the bottom of the document, let’s start typing some text. Everything that follows is example markdown output and syntax:

Normal characters result in normal text.

 *this makes italics*

 **big bad bold text** 

 ***italic AND bold***

# A header

Three backticks makes
a block of text 
look the same way.

Including code, data, and plots

To include code in a report, we just change the “code” styling slightly. Add a {r} after the triple backticks to have that block of text get treated as R code. The top of the code header should look like this: ```{r}

In practice, it looks something like this:

5 + 6

## [1] 11

print("The code output gets put directly below")

## [1] "The code output gets put directly below"

If you want to display data, you have a couple options. The first, is just to print out data the way you normally would.

library(gapminder)
head(gapminder)

## # A tibble: 6 x 6
##   country     continent  year lifeExp      pop gdpPercap
##   <fctr>      <fctr>    <int>   <dbl>    <int>     <dbl>
## 1 Afghanistan Asia       1952    28.8  8425333       779
## 2 Afghanistan Asia       1957    30.3  9240934       821
## 3 Afghanistan Asia       1962    32.0 10267083       853
## 4 Afghanistan Asia       1967    34.0 11537966       836
## 5 Afghanistan Asia       1972    36.1 13079460       740
## 6 Afghanistan Asia       1977    38.4 14880372       786

However, there is a special function knitr::kable() that inserts a nice-looking table into your report. Depending on what your output format is, it sometimes is even interactive!

knitr::kable(head(gapminder))

You can put code inline in text by just typing “r some code” in backtics.

Plots are done the same way as code:

library(ggplot2)
ggplot(gapminder, aes(x=year, y=lifeExp, group=year)) +
    geom_boxplot()

You can use R markdown to create HTML reports, Word documents, PDFs, and even websites. For instance, this entire lesson website was created using R markdown.