This is a tutorial on how to use R markdown for reproducible research.

Here we can type long passages or descriptions of our data without the need of hashing out our comments with the # symbol. In our first example, we will be using the ToothGrowth dataset. In this experiment, Guinea Pigs (literal) were given different amounts of vitamin C to see the effects on the animal’s tooth growth.

To run R code in markdown file, we need to denote the section that is considered R code. We call these “code chunks”

Below is a code chunk:

Toothdata <- ToothGrowth

head(Toothdata)
##    len supp dose
## 1  4.2   VC  0.5
## 2 11.5   VC  0.5
## 3  7.3   VC  0.5
## 4  5.8   VC  0.5
## 5  6.4   VC  0.5
## 6 10.0   VC  0.5

As you can see, from running the “play” button on the code chunk, the results are printed inline of the r markdown file.

fit <- lm(len ~ dose, data = Toothdata)

b <- fit$coeffients

plot(len ~ dose, data = Toothdata)

abline(lm(len ~ dose, data = Toothdata))
Figure 1: The Tooth Growth of Guinea Pigs when given variable amounts of Vitamin C

Figure 1: The Tooth Growth of Guinea Pigs when given variable amounts of Vitamin C

The slope of the regression line is .

Section Headers

We can also put sections and subsections in our markdown file, similar to our numbers or bullet points in a work document. This is done with a # that we previously used to denote text in an R script

First level header

Second level header

Third level header

Make sure that you put a space after the # otherwise it will not work

we can also add bullet point-type in our markdown file.

  • one item
  • one item
  • one item
    • one more item
    • one more item
    • one more item
      • one last time

Its important to note that in R markdown indentation matters!

  1. First Item
  2. Second Item
  3. Third Item
  1. subitem 1
  2. subitem 2
  3. subitem 3

Block Quotes

We can put really nice quotes into the markdown document. We do this by using the “>” symbol.

“Genes are like the story, and DNA is the language that the story is written in.”

— Sam Kean

Formulas

We can also put nice formatted formulas into Markdown using two dollar signs.

Hard-weinberg formula

\[p^2 + 2pq + q^2 = 1\] and you can get really complex as well

\[\Theta = \begin{pmatrix}\alpha & \beta\\ \gamma & \delta \end{pmatrix}\]

Code Chunks

Code chunk options

There are also options for you R Markdown file on how knitr interprints the code chunk. There are the following options

Eval (T or F): Whether or not to evaluate the code chunk

Eval (T or F): Whether or not to show the code for the chunk, but results will still print

Cache: If enable, the same code chunk will not be evaluated the next time that the knitr is run. Great for code that has LONG run times.

fig.width or fig.height: the (graphical device) size of the R plots in inches. The figures are first written to the knitr document then to the files that are saved separately.

fig.cap: the words for the figure caption

Table of Contents

We can also add a table of contents to our HTML Document. We do this by altering the YAML code (The weird code at the VERY top of the document).We can add this:

title: “HTML Tutorial” author: “Jordan Lawrence” date: “2026-08-04” output: html_document: toc: true toc_float: true

This will give us a very nice floating table of contents on the right hand side of the document.

Tabs

You can also add TABS in our report. To do this you need to specify each section that you want to become a tab by place “{.tabset}” after the line. Every subsequent header will be a new tab.

Code Folding

You can also use the code_folding options to allow the reader to toggle between displaying the code and hiding the code. This is done with:

code_folding: hide

Summary

There are a TON of options and ways for you to customize your R code using the HTML format. This is also a great way to display a “portfolio” of your work if you are trying to market yourself to interested parties.