This is a tutorial on how to use R markdown for repoducible research.

Here we can type a long passage or a description of our data iwhtout the need of “hashing” out our comments with the symbol “#”. In our first example, we will be using the ToothGrow data set. In this experiment we will see how Guinea Pigs were given different amounts of vitamin C to see the different effects of the animals tooth growth.

To run this in a mardown file, we need to denote the section that is considered R code, we call this section “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 chunk code, the results are printed inline of the r markdown file.

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

b <- fit$coefficents

plot(len ~ dose, data = ToothData)

abline(lm(len ~ dose, data = ToothData))
Figure 1: The tooth growth of Guinea Pigs when given variable amounts of vitaminC

Figure 1: The tooth growth of Guinea Pigs when given variable amounts of vitaminC

the slope of the regression line is ‘r b[2]’.

Section Headers

We can also put sections and subsections in our r markdown file, similar to numbers or bullet points in a word doc. This is done with hashing.

First level header

Second level header

Third level header

Make sure you put a space after the hashtag, ptherwise 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 more item

It is important to note 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 nice quotes into the markdown document. we do this by using the “>”

“Genes are like the story, and DNA is the language that the story is written in.”

– Sam Kean

Formulas

We can also put formulas into the markdown usig 2 dollar signs.

Hardy-Weinberg Formula \[p^2 + 2pq +q^2 = 1\]

and you can make it complex as well

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

Code Chunks

Code chunk options

There are also options for R Markown file on hoe to knitr interprints the code chunk. there are the following examples

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, bu the results will still print.

Cache: If enable, the same chunk will not ne evaluated the next time that the knitr is ran.

fig.width or fig.height: the (graphical device) size of the r plots in inches. the figures are first written to the knit r document then to files that are saved sepeartely.

out.width or out.height: the output size of the R plot in the r document

fig.cap the words o=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: “HTML TUTURIAL” author: “Carson Henry” date: “2024-11-11” output: html_document: toc: true toc_float: true

This will give us a nice floating table of contents on the right hand side of the document.

Tabs

You can also addd tabs to our report. You need to specify each section that you want to become a tab by placing {.tabset} after the line. Each subsequent header will be a new tab.

Themes

You can also add themes to you HTML document with highlighting color and hyperlink color of your HTML output. Do 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 monochromes espresso zenburn haddock textmate

code folding

you can also use the code_folding option to allow the reader to toggel between displaying the code and hiding the color by doing this:

code_folding: hide

Summary

There are a ton of options and ways you can customize your code usinf HTML format. This is grreat to display a “portfolio” of your rwork to show off to interest parties.