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

Here we can type long passages or description of our data without the need of “hashing” out our comments with our # symbol. In our first example, we will be using the tooth growth dataset. In this experiment, guinea pigs (literal) were given different amounts of vitamin C to observe the effects on the animals’ tooth growth.

To run an R code in a markdown, we need to denote the section that is consdidered a code. We call these secitons “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

#The tilde sign can demarcate code chunks from prose or narration.

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$coefficients

plot(len ~ dose, data = Toothdata)

abline(lm(fit <- 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 9.7635714

Section Headers:

We can also input sections and subsections into our R Markdown file, similar to number or words on our Word documents. This is done with hashtags, “#,” which we previously used to denote text within an R script. The number of hashtags denotes the level of the header.

First level header

Second level header

Third level header

Make sure to add a space after each hashtag, else it will not work.

We can also add bullet point-type marks in our R markdown file. The space after notation also applies here (see below). Indentation will add subpoints, and pressing enter after every tab will preserve the position.

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

It’s important to note here 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 add 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 insert nice formatted formulas into Markdown using two dollar signs.

Hardy-Weinberg Formula:

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

And it can be really complex, as seen below:

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

Code chunks

Code chunk options

There are also options for your R Markdown file on how knitr, which interprets 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 the results will still print.

These two options can be used to hide analyses that are not yet sound or confirmed.

Cache: If enabled, the same code chunk will not be evaluated the next time that knitr is run. This is great for code that has very 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 documents IN THE R DOCUMENT.

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 our YAML code (which is the weird code at the very top of the document). WE can add this:

title: “HTML Tutorial” author: “Me” date: “2024-06-24” output: html_document: toc: true toc_float: true

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

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 become a new tab.

Themes

You can also add themes to your HTML document that change the highlighting color and hyperlink color of your 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 or option or ways for you to customize your R code using 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.