HTML_Tutorial

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

Here we can type long passages or distcriptions of our data without the need of “hashing” out our comments with the # symbol. In this experiemnt, Ginea 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 markdownfile, 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 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

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 test 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 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 imorotant 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 put really nice quotes in the markdown document. we do this using the “>” symbol.

“Genes are like the story, and DNA is the 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 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.

Hardy-weinberg Formula

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

And you can get really complex as well!

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

Code Chunks

Code chunk options

print("hello world")

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

Eval (T or F): whether or not to eval 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: 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 code chunk at the VERY top of the document) We can add this:

title: “HTML_Tutorial” author: “Jillian Cochran” date: “5/2/2022” 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 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 documement 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 joural 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 of options and ways for you 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.