6  R Markdown - A very brief introduction

6.1 What is R Markdown?

R Markdown is a file format that combines R code with Markdown, a simple formatting syntax for authoring HTML, PDF, and MS Word documents.

This means you can embed R code into a report, run it, and then display the results. It’s a really useful way to present both the process of analysis, and its results.

6.2 Getting Started

You need to have:

  1. R installed

  2. RStudio installed

  3. The rmarkdown package installed. If not, install it with:

install.packages("rmarkdown")

6.3 Creating an R Markdown Document

  1. Open RStudio.

  2. Go to File > New File > R Markdown...

  3. A dialogue box will pop up. For now, keep the default options (HTML output) and click OK.

You’ll see a template document.

6.4 Basic Syntax

R Markdown uses Markdown syntax. Here are some basics:

  • Headers are created using hash symbols: # Header 1, ## Header 2, ### Header 3

  • Lists are created with dashes: - item 1, - item 2, * item 3

  • Bold is created with two asterixes: **bold**

  • Italics are created with a single asterix: *italic*

  • Links can be embedded: [Google](https://www.google.com)

Activity 1: In a new section, create a header called “Introduction”, write a brief intro about your favourite sport, and include a link to its official website.

6.5 Embedding R Code

This is the key strength of R Markdown for our purposes. You can embed chunks of R code. You begin by typing {r}, then your code, then to close the chunk.

Including the text above will produce the following output:

# This is an R code chunk

summary(mtcars$mpg)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  10.40   15.43   19.20   20.09   22.80   33.90

When the report is rendered, it will show both the code and its output.

Activity 2: Create a new code chunk and calculate the mean and median of the mpg column in the mtcars dataset.

6.6 Including Plots

You can also include visualisation data within your report:

library(ggplot2)
data(mtcars)

ggplot(mtcars, aes(x=mpg, y=wt)) + geom_point() + ggtitle("Scatterplot of MPG vs Weight")

Activity 3: Use the mtcars dataset to create a histogram of the mpg column.

6.7 Knitting

Once your R Markdown document is ready, it’s time to “knit” it, turning it into a report.

Click the “Knit” button in the script editor panel’s toolbar. Choose the desired output format, and RStudio will render your document.

Activity 4: Knit your document.