Chapter 1 R Markdown

Watch this video before beginning.

1.1 Introduction to Markdown

Markdown is a lightweight markup language which emphasizes ease of writing and reading content and can easily be converted into HTML. Markdown was invented by John Gruber with significant contributions from Aaron Swartz. R Markdown extends markdown to include R code results including tables and visualizations. The rmarkdown package can create web pages, PDFs, and slide presentations from R Markdown documents. The real power of R Markdown is the ability to intertwine natural language and code. This approach is known as literate programming.

1.2 Basic Markdown Syntax

Below are a few examples of Markdown’s syntax. You can find a comprehensive syntax guide on RStudio’s website. Headers

# I'm huge!
## I'm still large
### I'm a reasonable size Prose

It was the best of times, it was the worst of times, it was the age of wisdom, 
it was the age of foolishness, it was the epoch of belief, it was the epoch of 
incredulity, it was the season of Light, it was the season of Darkness, it was 
the spring of hope, it was the winter of despair, we had everything before us, 
we had nothing before us, we were all going direct to Heaven, we were all going 
direct the other way – in short, the period was so far like the present period, 
that some of its noisiest authorities insisted on its being received, for good 
or for evil, in the superlative degree of comparison only. Bold and italic



***bold and italic*** Lists


- an item
- another item
- a third item


1. an item
2. another item
3. a third item Images

![A seagull]( Quoted Text

> Good night, Mrs. Calabash, wherever you are. Code

# Code from Hadley Wickham's purr package

reduce <- function(.x, .f, ..., .init) {
  .f <- as_function(.f, ...)

  f <- function(x, y) {
    .f(x, y, ...)

  Reduce(f, .x, init = .init)
} Inline Code

You can use the `c()` function to make vectors.

1.3 Putting the R in R Markdown

If you want to insert R code into an R Markdown document you can use the following syntax:

# Write some R code here!
x <- rnorm(10)

The results of computing x^2 and the graph produced by plot(x) will both be displayed under this chunk of R code once you render this R Markdown file into a web page, a PDF, or a presentation. There are several options that are useful for customizing these R code chunks which we’ll discuss in a later section.

1.4 Writing and Rendering Documents

Open up a new file in a plain text editor and have your R console ready. I highly recommend using RStudio since it nicely combines a plain text editor, an R console, and a file browser. Write some markdown in your plain text editor, or copy and paste the R Markdown below:

title: "Simulation in R"
author: Brian Caffo
date: July 28, 2016

## Simple Simulation in R

Welcome to my tutorial on doing very simple simulations in R. The first
simulation we're going to try is flipping a coin, which can result in the
the coin landing heads up or tails up. We can simulate flipping one coin by
running the `flip_one_coin()` function defined below:

flip_one_coin <- function(){
  sample(c("H", "T"), 1)

## Simulation 1

Let's test the simple result of performing one coin flip:


## Flip Many Coins

Instead of flipping one coin at a time, we can define a function that will flip
a specified number of coins:

flip_coins <- function(n){
  sample(c("H", "T"), n, replace = TRUE)

## Coin Filling Results

Let's take a look at the results of flipping 100 coins with a bar graph:


One feature of R Markdown that is different from regular Markdown is the presence of yaml front matter at the beginning of the file. Yaml is a simple medium for providing metadata about the document that you’re writing. The yaml front matter is written in-between a pair of three hyphens (---) at the beginning of the document. In the Rmd file above I’ve specified a title, author, and date for this document which will be placed at the beginning of the document.

Save your R Markdown document in your current working directory as simple_sim.Rmd. In order to render this document into a webpage first install the rmarkdown package if you haven’t already with install.packages("ramrkdown"). Once the package is installed you can load the rmarkdown package with library(rmarkdown). You can then render your R Mardown into a webpage by entering render("simple_sim.Rmd") into the R console. After the HTML document has been produced you can view your new document by entering browseURL("simple_sim.html") into the R console. Congratulations on creating your first data product!

If you want to create a PDF instead of an HTML document you need to provide different arguments to the render() function. Enter render("simple_sim.Rmd", output_format = pdf_document()) into the R console in order to create a PDF.

There are several advantages and disadvantages between distributing HTML or PDF documents. HTML allows your data product to be distributed as a website which allows you to embed interactive visualizations, some of which will we talk about creating in a later chapter. PDF documents are more self-contained compared to HTML, although they are static documents - they’re not responsive like a webpage can be. In general, if you want others to build upon your data product

1.5 Creating Presentations in R Markdown

In addition to creating webpages and PDFs from R Markdown, you can also create slide presentations. Use the R Markdown document from the previous section and enter render("simple_sim.Rmd", output_format = ioslides_presentation()) into the R console. Now open up the slide deck with browseURL("simple_sim.html"). As you can see this is still a webpage, except your document has been rendered as a slide deck!

Each slide is demarcated in your R markdown file with two pound signs ## followed by the title of the slide. The fields specified in the yaml front matter create the first slide. If you’d rather produce PDF slides, you can enter render("simple_sim.Rmd", output_format = beamer_presentation()) into the R console in order to create PDF slides with the LaTeX Beamer framework.

1.6 Sharing R Markdown Documents

We recommend the following websites for sharing the HTML files that you produce from R Markdown documents. If you’ve taken The Data Scientist’s Toolbox then you should be familiar with GitHub Pages. If you’re familiar with Git and you haven’t used it before their documentation for creating a site is very straightforward. If you’re not familiar with Git and you’re using RStudio you should take advantage of RPubs, which is perhaps the easiest way to share an HTML document from RStudio. You can find simple instructions for using RPubs here. If you’re looking for a site that will host any HTML file for free, including HTML files that are generated by R Markdown, you should check out NeoCities.

1.7 Closing Thoughts

With R Markdown you can intertwine code from many programming languages, including R, with prose, tables, and graphics. From the source of one Rmd file you can produce several different kinds of data products including websites, PDFs, and even ebooks. For more information about R Markdown we encourage you to visit