Welcome to Using R Markdown

Now that you’re hopefully becoming more confident in your R skills, we can start thinking about how to integrate code and text to make a more coherent document.

Opening up an R Markdown Script

• Once you’re in R Studio, you can open up an R markdown by clicking this icon

• You do not need to download anything additional if you want to knit to an HTML file.

• If you would like to knit to a pdf, you need to install MiKTex for Windows or MacTex for Macs. You can download both of these here.

• It is not recommended that you knit to a Word document.

Setting up your document

Markdown is an easy way of displaying code, output, and text all contained in the same file.

• Headers are started with a ‘#’ sign
• Text is anything outside of an R chunk
• R chunks look like this: {r} #example R chunk.

There are several useful commands that help you be flexible in displaying your output. Some include: - include: tells R whether to include the R code and the corresponding output - echo: tells R whether to include the R code - eval: tells R whether to evaluate the code in the chunk

• All of these commands are entered when you start the R chunk.

• R markdown automatically includes a setup R chunk (below).
  • This allows all of your chunks to be set in the same way.
  • If you need to change a specific chunk you can override this default in the chunk.

knitr::opts_chunk$set(echo = TRUE, fig.width = 4, fig.height = 4)

Your GSI’s and Google are great resources!

R Markdown

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. Here is an example of outputing the summary statistics of the cars dataset contained in base R:

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Including Math Symbols

Install the mat2tex package using install.packages('mat2tex')

Note: This package is not available for R 3.5.1. To check the version of R that you are using type version into the console.

• Vector notation \(\mathbf{x}\)

• Matrix notation \(\mathbb{X}\)

• Centering an Equation \[ \mathbf{\hat\beta} = (\mathbb{X}^\mathrm{T}\mathbb{X})^{-1}\mathbb{X}^\mathrm{T}\mathbf{Y} \]

• Aligning Multiple Equations: \[ \begin{aligned} \mathbf{\hat\beta} = (\mathbb{X}^\mathrm{T}\mathbb{X})^{-1}\mathbb{X}^\mathrm{T} \mathbf{Y}\\ \mathbf{b} = (\mathbb{X}^\mathrm{T}\mathbb{X})^{-1}\mathbb{X}^\mathrm{T}\mathbf{y} \end{aligned} \]

Some Helpful Documents

Some helpful starter documents are Markdown Basics and Markdown Intro