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

Here we can type long passages or descriptions of our data without the need of “hashing” out our comments with the # symbol. In our first example, we be using the Tooth Growth data set. In this experiment, Guinea Pigs(literally) were given different amount of vitamins 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 “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 p[rinted 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 Pig when given variable amounts of vatmins C

The slope of the regression line is 9.7635714.

Section Header

We can also put sections and subsections in our r markdown file, similar to numbers or bullet points in a work 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 hashtag, otherwise it will not work!

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

one item
one item
one item
- one item
- one item
- one item
  - one item

Its important to note here that in r markdown indentation matters!

First Item
Second Item
Third Item

sub item 1
sub item 2
sub item 3

Block Quotes

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

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

— Sam Kean

Hyperlinks

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

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 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 file on how to knitr interprets the code chunk. Here are the following options.

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

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

Cache: If you enable, the same code chunk will not be evaluated the next time the knitr is run. Great for codes that have 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 Content

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: “Ulanda Lewis” date: “2024-10-10” 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 ass 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. 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 TON of options and ways for you to customize to your R code using the HTML format. This is also a great way to display a “portfolio” of your work if you are trying to market yourself to interest particles.