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

Here we can type long passages or decriptions 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 were giving different amounts of vitamin c to see the effects on the animals’ tooth growth.

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

Below in 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$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 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 the “#” 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 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 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 is written in.”

— Sam Kean

Formulas

We can also put nice formated 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 your R Markdown on how knitr 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

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 files that are saved separately.

out.width or out.height: the output size of the R plots 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 the YAML code (the weird chunk at the very top of the document.)

title: “HTML_Tutorial” author: “Paris Endris” date: “2024-11-04” output: html_document: toc: true toc_float: true

This will give us a nice floating toc on the left hand side of the document

Tabs

We 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 your html output. This can be nice aesthetically. To do this, you can change your theme in the YAML to one of the following:

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

You can aLso change the color by specifying highlight:

default tango payments kate monochrome expresso 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 it. 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 a great way to display a “portfolio” of your work if you are trying to market yourself to interested parties.