R_Markdown

Reproducible research using R Markdown tutorial.

We can type long passages or descriptions of data that we record without having to use the using the symbol # to type our comments like in normal r. ToothGrowth dataset is going to be used in the first example we are given. In this experiment we use, real Guinea Pigs were given different amounts of VItamin C to see if the animal’s teeth were affected.

When running the r code you have to denote what is going to be considered the R code. These sections are called “code chunks”.

Below is a code chunk:

Toothdata <- ToothGrowth 

head(ToothGrowth)

##    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

The R Markdown file printed the code chunck after pressing the print button.

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 into our markdown file in a similar way to numbers and bullet points in a word document. We do this with the “#” that we used previously to denote and detect R script.

First level header

Second level header

Third level header

Always make sure to put a space after the hashtag or it will not work!!

We can also add bullet point-tyoe marks in our r markdown file.

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

It’s important to note that indentation matters in r markdown.

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 document. We can do this by 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 you are interested in showing them. Here we will use the link to R Markdown’s homepage for this example. Markdown

Formulas

We can also put nice formatted formulas into R Markdown using two dollar signs.

Hard-Weinberg Formula

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

You can get very complex!

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

Code Chunks

Code chunk options

There are options with R markdown files that can interprit the code chunk. These are the following options:

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

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 kniter is run. Great for a 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 documents.

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: “R_Markdown” author: “MLD” date: “2024-11-12” 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 the report. To do this you need to specify each section that you want to become a tab by placing {.tabset} after the line.

Themes

You can add themes to the HTML document that change the highlighting color and hyperlink color of your HTML output. This can be nice aesthetically. To do this, 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 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 many options for you to customize your R code using the HTML format. This is also a great way to display any “portfolio” of your work if you are trying to market yourself to interested parties.