This is a tutorial on how to use R markdown for reproducable 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 the ToothGrowth dataset. In this experiment, Guinea Pigs (literal) were given different ammounts of vitamin C to see the effects on the animal’s tooth growth.

To run R code in 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 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, similae 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 hashtage 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 one
  2. subitem two
  3. subitem three

Block Quotes

We can put really nice quotes into the markdwon 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 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 chuck options

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

Eval (T ot F): Whether or not to evaluate the code chuck

Echo (T or F): Whether or not to show the code for the chuck, but results will still print

Cache: If you enable, the same code chuck will not be evaluated the next time that knitr is run. This is great for code that has LONG run times.

fignwidth or fig.height: the (graphical device) size of the R plot 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 Documents. We do this by altering the YAML code (The weird code chunk at the top of the document.) We can add this:

title: “HTML_Tutorial” author: “Ilea Watson” date: “2024-06-29” 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 a 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 in a new tab.

Themes

You can also add themes to you HTML document that change the highlighting color and hyperlink color of your HTML output. This can be nice asthetically. To do this, change your theme in the YAML to one of the following:

cerulean journal flatly readable spacelab united cosmo lumen paper sanstone 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 HTML formating. This is also a great way to display your work if you’re trying to market yourself to interested parties.