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 will be using ToothGrowth dataset. In this experiment, Guinew Pigs (literal) were given differen amounts of vitamin C to see the effects on theanimal’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 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 tootch growth of Guinea Pigs when given variable amouns of Vitamin C

Figure 1: The tootch growth of Guinea Pigs when given variable amouns 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 pionts in a word document. This is donw 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 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 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 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!

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

LaTex is a cheat sheet that you can google.

Code Chunks

Code chunk options

There are also options for your R Markdown file on how knitr interprets the code chunk. There are the following options.

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

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

Cache: If enabled, 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 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: “Katie Pierce” date: “4/27/2022” 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 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 the highlight:

default tango payments kate monochrome espresso zenburn haddock textmate

Code Folding

You can also use the code_folding option to allow the read 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 work if you are trying to market yourself to interested parties.