Introduction

R Markdown lets you combine code, output, and text in the same document. You can write your analysis, include plots, and explain your results — all in one file — and render it into an HTML, PDF, or Word report.

This guide will help you:

  1. Understand the basic structure of an .Rmd file
  2. Write text using Markdown formatting
  3. Add and run R code chunks
  4. Render the document to HTML

R Markdown Structure

An R Markdown file has three parts:

  1. YAML header – appears at the top between --- lines (title, author, etc.)
  2. Markdown text – regular writing with formatting
  3. Code chunks – blocks of R code surrounded by three backticks

Writing Text with Markdown

You can write italic, bold, and even lists:

  • Item 1
  • Item 2
  • Item 3
You can also add links: 
 [Visit RStudio's R Markdown site](https://rmarkdown.rstudio.com)

Visit RStudio’s R Markdown site

And equations:

 `$E = mc^2$` → \(E = mc^2\)

$E = mc^2$ → \(E = mc^2\)

Code Chunks

To include R code, use a code chunk using this syntax: 
 ```{r}  x <- 5 x + 10 ```

Ends up looking like this:

# A simple calculation
x <- 5
y <- 10
x + y
## [1] 15

Adding Plots

Plots can be added using the same ‘chunk’ syntax:

# Make a simple scatterplot

plot(mtcars$mpg, mtcars$wt,
     xlab = "Miles per Gallon",
     ylab = "Weight",
     main = "Car Weight vs MPG")

Chunk Options

You can control what appears in your report with chunk options in with the {r} curly braces: e.g., 
 ```{r, echo=FALSE, eval=FALSE}  x <- 5 x + 10 ```

:

  • echo=FALSE → hide code, show results
  • eval=FALSE → show code, but don’t run it
  • message=FALSE, warning=FALSE → hide messages/warnings

Rendering Your Document

Click Knit in RStudio and choose Knit to HTML.

R will:

  • Run all the code chunks
  • Combine them with your text
  • Produce a clean, shareable report

Tips for Success:

  • Save your .Rmd file often.
  • Knit regularly to catch errors early.
  • Use clear headings (#, ##, ###) to organize your report.
  • Keep code readable: use comments (#) to explain what it does.
  • Load the libraries you need at the beginning of the document. Don’t try to use an object you haven’t defined earlier in the document. Rmd runs the R code from the beginning of the file to the end, so if the library or object haven’t been defined, the Rmd file won’t run.
  • Don’t install.packages or use View(data) in Rmd files.

Practice

Try using the mtcars dataset and adding:

  1. A summary statistic, mean of disp
  2. A histogram of disp
  3. A short paragraph explaining what you found
  4. Then knit again and see how your document updates!