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

Here we can type long passages or describtions of our data without the need of “hashing” out our comments with teh # 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 a markdown file, we need to denote the section that is considered R code. We call these suctions “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 chunks, the results are printed inline of 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 amounts of vitamin C

Figure 1: The tooth growth of Guinea Pigs when given variable amounts of vitamin C

The slope of 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 the # that we previously used to denote text in R script.

First level Headers

Second level headers

Third level headers

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

We can also add bullet point-type marks in our r markdown file.

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

Its important to note here that in R markdown identation 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 markdown document. We do this by using “>” symbol.

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

— sam kean

Formulas

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

Hard-Weinberg formulla

\[p^2 + 2pq + q^2 =1\]

And you get really complex as well!

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

print("Hello World")
## [1] "Hello World"

code chunks

Code chunk options

There are also options for your R markdown file on how knitr interprits the code chunk. There are the following options.

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

Echo(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 knitr is run. Great for code has LONG runtimes

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

out.width or out.height: The output size of R plots IN THE R DOCUMENT.

fig.cap: the words for 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: “Ms. Kowsar” date: “2026-03-26” 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 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 of your html output. This can be nice asthetically. 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 simplx yeti null

You can also change the color by specifying highlight:

default tango payments kate monochorome espresso zenburn haddock textmate

Code folding

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

code_folding hide: 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 “portoflio” of you rwork if you are trying to market yourself to interested parties.