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

Here we can type long passages or descriptions of our data with the need of “hashing” our comments with the # symbol. In our first example, we will be using the ToothGrowth dataset. In this experiment, Guinea Pigs were given different amounts of vitamin C to see the effects on the animal’s tooth growth.

To run our code in a markdown file, we need to denote the section that is considered R code. We call these sections 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 in line of the r markdown file.

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

b <- fit$coefficients

plot(len ~ dose, data = Toothdata)

abline(lm(len ~ dose, data = Toothdata))
Figure 1: The tooth growth of Guinea Pigs when given variable amount of Vitamin C.

Figure 1: The tooth growth of Guinea Pigs when given variable amount of Vitamin C.

The slope of the regression line is 9.7635714.

Section Headers

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

First level Header

Second level Header

Third level Header

Make sure you put a space after the hashtag, otherwise it will not work.

We can also add bullet point type marks in ur r markdown file

  • one item
  • one item
  • one item
    • one item
    • one item
    • one item
      • on last item

It’s important to note here that indentation matters in R markdown!

  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 can do this by using the “>” symbol.

“Genes are like the story and DNA is like 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 R Markdown file on knitr interprets the code chunk. There are the following options.

Eval (T or F): whether or not to evaluate a code chunk

Echo (T or F): whether or not to show the code for the chunk, but results will print,

Cache: If you enable, the same code chunk will not be evaluated the next time that 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 files that are saved separately.

out.width or out.height: the output size of the R plots IN THE R DOCUMENTS

fig.cap: the word 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 chunk at the VERy top of the document). We can add this:

title: “HTML_Tutorial” author: “LindaM” date: “2026-09-21” output: html_document: toc: true toc_float: true

This will give us 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 placing “{.tabset}” after the line.Every subsequent header will be a new tab.

Themes

You can also add themes to your HTML Document that change the highlighting color and hyperlink color of you html output. This can be nice aesthetically. To do this, you change your theme in the YAML to one of the following:

cerulean journal flatly readable spacelab united cosmo lumen paper sandstone simplex yeti null

You can also change the color by specifying highlight:

default tango payments kate monochrome espresso zenburn haddock textmate

Code Folding

you can also use the code_folding option 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 play a “portfolio” of your work if you are trying to market yourself to interested parties.