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

Here we can type long passages or descriptoins 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 differnt amounts of vitamin C to see the effects on the animal’s tooth growth

To run R cod ein 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 chynk, the resulsts are printed in line 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 Guniea Pigs when given variable amounts of vitamins c

Figure 1: The tooth growth of Guniea Pigs when given variable amounts of vitamins 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 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 rmarkdown file.

  • one item
  • one item
  • one item

    • one more item

    • one more item

    • one more item

      • one last item

      It’s 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 into 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 reallyi complex as well!

\[\Theta = \begin{pmatrix}\alpha & \beta\\\gamma & \delta\end{pmatrix}\] LaTex cheat sheet// already provided in the course homepage

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 chunk

Echo (T or F): whether or not to ecaluate the code chunk

Echo (T or F): whether ro 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 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 the files saved seperatly.

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 at the VERY top of the document.)

We can add this: title: “HTML_Tutorial” author: “Eli Watkins” date: “6/28/2022” output: html_document: toc: true toc_float: true

This will give us a very nice floating table of contents on the rights 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 a new tab.

Themes

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

cerulean journal flatly readable paper cosmo sandstone simplex yeti null united

You cna also chagen the color by specifiying the highlinght:

Default tango payments kate espresso zenburn 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 by:

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.