html_tutorial

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 “hashtaging” our comments with the # symbol. In our first example we will be using the ToothGrowth dataset. In this experiemnt Guinea pigs were given different amounts of vitaimin C to see the affects on the animals teeth 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 results in the code chunk 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))

Guinea Pig Tooth Growth

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 you put a space after the hashtag, otherwise it will not work!

we can also add bullet points-type marks in our r markdown file.

• one item
• one item
• one item
  • oone more item
  • one more item
  • one more item
    • one last indentation

its important to note here that 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 quootes into the markdown document. We do this by using the “>” symbool.

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

— Sam Kean

“If you ain’t first you’re last”

— Ricky Bobby

hyperlinks

Hyperlinks can also be incorperated into these files. This is especially useful in HTML files, since they are in a web browser anf will redirect the reader to the material that you are interested in showing the. Here we will use the link to R markdown’s homepage for this example. RMarkdown

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 Chunk Options

There are alsso options for your R markdown file on how Knitr interprits the code chunk. There are the following options.

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

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

cache: if you 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 DOCUMENT.

fig.cap: the words for the figure caption