This is a tutorial for R markdown. It also serves as a sample R markdown code. Please check the source code of this document.

# What is R markdown?

• Think of it as a source code for creating a webpage that can embed R code
• You write a source code and “compile” it to create a webpage

# Creating an R markdown document

In RStudio, click File -> New File -> R Markdown….

RStudio will create a skeleton file with some basic explanations. Read those.

You can compile the source code into HTML or PDF. I recommend HTML because it can adjust fontsize, linebreak, etc. according to the device.

# LaTeX

If you know LaTeX, a popular language for writing academic documents, you can use it in R markdown.

R markdown understands LaTeX syntax — just write them.

For the class, we use it to write math symbols and equations, which we discuss below.

# Writing math symbols and equations

Please check the source code of this document to see how to write math equations.

### Examples - read the source code!

Pythagorean theorem.

$a^2 + b^2 = c^2$

Arithmetic mean $$\geq$$ Geometric mean $$\geq$$ Harmonic mean.

$\frac{1}{n}\sum_{i=1}^N X_i \geq \left( \prod_{i=1}^N X_i \right)^{1/N} \geq \frac{1}{\sum_{i=1}^N 1/X_i}.$

Greek letters, plain texts and multiple lines.

\begin{aligned} line 1 &= \alpha + \beta \\ \text{plain text} &= \gamma + \delta \\ line 3 &= \lambda + \sigma \\ \textbf{bold plain text} &= \Lambda + \Sigma \end{aligned}

Caligraphic, blackboard bold and bold. $\mathcal{F}, \mathbb{F}, \mathbf{F}.$

If you need a math symbol but you don’t know what to type, go to http://detexify.kirelabs.org/classify.html and draw the symbol using your mouse! For example, you can draw $$\pm$$ there and see that the command is “pm”.

# Embedding R

• The main advantage of using R markdown is that we can run R within the document.

• In other words, we can alternate between plain text and R code.

• In terms of homework submission, this is handy because you don’t need to separately submit the code or copy the R output into the document.

Below is an example of the R code (which we shall call “chunk”) run within the document.

Sys.setenv(lang="EN") ### this command sets the R locale to English ###
courseNo = "ECON 21130"
print(courseNo)
##  "ECON 21130"
• Note that it displays not only the code but also the result.

• Also, the R chunks are cumulative; that is, the variable courseNo defined in the above can be used in the later chunks.

Below is an example.

courseTitle = "Topics in Microeconometrics"
print(paste(courseNo, courseTitle, sep = " - "))
##  "ECON 21130 - Topics in Microeconometrics"
• R markdown offers options to configure how the R chunks are displayed. For example, you can decide whether to hide the code, whether to hide the result, whether to display the error message, etc.

• For a list of such options, check 5. Embed code of the R markdown cheatsheet.

• For example, eval=FALSE option tells R to not execute the code.

Below is an example.

ROOT2 = 1.414

In the above chunk, I specified eval=FALSE option. So the above chunk is not executed, which means ROOT2 is not defined.

In the below chunk, we can confirm that ROOT2 is not defined.

print(ROOT2)
## Error in print(ROOT2): object 'ROOT2' not found

If you check the source code of this document, you will notice that I specified error=TRUE in the above chunk.

You must specify this option if you want R to print the error message. Otherwise the source code will not be compiled into the HTML document due to the error.