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 the ToothGrowth datset. In this experiment, Guinea 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 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 in line of r markdown file.

fit<-lm(len ~ dose,data= Toothdata)

b<- fit$coefficients

plot(len~dose, data=Toothdata)
abline(lm(len ~ dose,data= Toothdata))

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 r markdown file.

  • one item
  • one item
  • one item
    • one more item
    • one more item
    • one more item
      • one last item

Make sure that you put a space after the dash otherwise it will not work.

It is important to note here that in R. Markdown indentation matters!

  1. First Item
  2. Second Item
  3. Third Item
    • subitem 1
    • subitem 2
    • subitem 3

In this case we have to use 4 spaces to indent the subitems.

Block Quotes

We can putt really nice quotes into the markdown document. We do this by usgin the “>” symbol.

“Genes are the like 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.

Hard-Weinberg Formula

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

And you can get really complex as well!!

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

All of this is done using LaTex so look up a latex cheat sheet to be ready to write

Code Chunks

Code chunk opitions

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

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

fit<-lm(len ~ dose,data= Toothdata)

b<- fit$coefficients

plot(len~dose, data=Toothdata)
abline(lm(len ~ dose,data= Toothdata))

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

fit<-lm(len ~ dose,data= Toothdata)

b<- fit$coefficients

plot(len~dose, data=Toothdata)
abline(lm(len ~ dose,data= Toothdata))

Does not show code or output^

Cache: If enable, 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: Create words for the figure caption

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 ammounts of vitamin C

Figure 1: The tooth growth of Guinea pigs when given variable ammounts of vitamin C

Table of Contents

We can also add a table of contentws 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: "Sam"
date: "`r Sys.Date()`"
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. (refer to line 103)

Themes

You can also add themes to your HTML document that changes 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 one of the following:

cerulean journal flatly readable spacelab united cosmo lumen paper sandstone simplex yeti null

title: "HTML_Tutorial"
author: "Sam"
date: "`r Sys.Date()`"
output: 
    html_document:
      toc: true
      toc_float: true
      theme: sandstone

You can also change the color by specifying hihglightL

default tango payments kate monochrome espresso zenburn haddock textmate

title: "HTML_Tutorial"
author: "Sam"
date: "`r Sys.Date()`"
output: 
    html_document:
      toc: true
      toc_float: true
      theme: united
      hightlights: espresso

Themes might overired highlights and vice versa

Code folding

you can also use the colding_folding option to allow the reader to toggle between displaying the code and hiding the code. This is done with:

code_folding: hide

title: "HTML_Tutorial"
author: "Sam"
date: "`r Sys.Date()`"
output: 
    html_document:
      toc: true
      toc_float: true
      theme: united
      hightlights: espresso
      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 “Portofolio” of your work if you are trying to market yourself to interest parties.