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

Here we can type long passages 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 Vitamine C to see the effects on the animals tooth growth.

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

Below is a code chunk:

Toothdata <- ToothGrowth

head(ToothGrowth)

##    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 given variable amounts of Vitamin C.

The slope of the regression line 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 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 item
- one item
- one item
  - one item

It is important to note her that in R Markdown indentation matters!

First Item
Second item
Third Item

subitem 1
subitem 2
subitem 3

Block Quites

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

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

— Sam Kean

Hyperlinks

Hyperlinks can also be incorporated into these files. This is especially useful in HTML files, since they are in a web browser and will redirect the reader to the material you are interested in showing them. Here we will use the ink to R Markdown’s homepage for this example. RMarkdown

Formulas

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

Hardy-Weinberg Formula

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

And you can get really complex as well!

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

LaTex

Code Chunks

Code Chunk Options

There are also options for your R Markdown file on how the 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 results will still print

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

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: words for the figure caption

We can also add a table of contents to out TTML Document. We do this by altering the YAML code (the wierd code chunk at the VERY top of the )

title: “HTML_Tutorial” author: “Jacob Wiebe” date: “2024-06-25” 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 your report. To do this you need to specify each sections 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 the HTML that change the the highliting and hyperlink color of the 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 yeti null

You can also change the highlight by specifying the highlight:

default tango payments kate monochrome espresso zenburn haddock textmate

Code Folding

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

code_folding: hide

Summary

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

HTML_Tutorial

Jacob Wiebe

2024-06-25