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Example of R Markdown on Github

GitHub Documents

This is an example of using R Markdown format for publishing markdown documents to GitHub. When you click the Knit button all R code chunks are run and a markdown file (.md) suitable for publishing to GitHub is generated. Commiting everything to a repository results in this page.

I have adapted the below from Jeromy Anglim who created an earlier example of R Markdown (from before it could be knit into Github markdown).

This post examines the features of R Markdown using knitr in Rstudio. This combination of tools provides an exciting improvement in usability for reproducible analysis. Specifically, this post (1) discusses getting started with R Markdown and knitr in Rstudio; (2) provides a basic example of producing console output and plots using R Markdown; (3) highlights several code chunk options such as caching and controlling how input and output is displayed; (4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and (5) discusses the implications of R Markdown. This post was produced with R Markdown. The original post on which it was based can be found here as a gist. The post may be most useful if the source code and displayed Github page are viewed side by side.

Getting started

To work with R Markdown, if necessary:

  • Install R
  • Install the lastest version of RStudio
  • Install the latest version of the knitr package: install.packages("knitr")

To run the basic working example that produced this blog post:

  • Open R Studio, and go to File - New - R Markdown
  • If necessary install ggplot2 and lattice packages: install.packages("ggplot2"); install.packages("lattice")
  • Paste in the contents of the raw .Rmd file
  • Click Knit

Prepare for analyses

set.seed(1234)
library(ggplot2)
library(lattice)

Basic console output

To insert an R code chunk, you can type it manually or just press Chunks - Insert chunks or use the shortcut key. Pressing tab when inside the braces will bring up code chunk options.

The following R code chunk labelled basicconsole is as follows:

```r
x <- 1:10
y <- round(rnorm(10, x, 1), 2)
df <- data.frame(x, y)
df
```

```
##     x     y
## 1   1 -0.21
## 2   2  2.28
## 3   3  4.08
## 4   4  1.65
## 5   5  5.43
## 6   6  6.51
## 7   7  6.43
## 8   8  7.45
## 9   9  8.44
## 10 10  9.11
```

The code chunk input and output is then displayed as follows:

x <- 1:10
y <- round(rnorm(10, x, 1), 2)
df <- data.frame(x, y)
df
##     x     y
## 1   1  0.52
## 2   2  1.00
## 3   3  2.22
## 4   4  4.06
## 5   5  5.96
## 6   6  5.89
## 7   7  6.49
## 8   8  7.09
## 9   9  8.16
## 10 10 12.42

Plots

Images generated by knitr are saved in a files folder in the associated Github repo. Pushing them creates a .md file with all of the correct file paths.

Simple plot

Here is a basic plot using base graphics:

plot(x)

Note that unlike traditional Sweave, there is no need to write fig=TRUE.

Multiple plots

Also, unlike traditional Sweave, you can include multiple plots in one code chunk:

boxplot(1:10~rep(1:2,5))

plot(x, y)

ggplot2 plot

Ggplot2 plots work well:

qplot(x, y, data=df)

lattice plot

As do lattice plots:

xyplot(y~x)

Note that unlike traditional Sweave, there is no need to print lattice plots directly.

R Code chunk features

Create Markdown code from R

The following code hides the command input (i.e., echo=FALSE), and outputs the content directly as code (i.e., results=asis, which is similar to results=tex in Sweave).

Here are some dot points

* The value of y[1] is 0.52
* The value of y[2] is 1
* The value of y[3] is 2.22

Here are some dot points

  • The value of y[1] is 0.52
  • The value of y[2] is 1
  • The value of y[3] is 2.22

Create Markdown table code from R

x y
1 0.52
2 1
3 2.22
4 4.06
5 5.96
6 5.89
7 6.49
8 7.09
9 8.16
10 12.42

Control output display

The folllowing code supresses display of R input commands (i.e., echo=FALSE) and removes any preceding text from console output (comment=""; the default is comment="##").

  x    y
1 1 0.52
2 2 1.00
3 3 2.22
4 4 4.06
5 5 5.96
6 6 5.89

I also highly reccomend reviewing the kable function in the printr package here for pretty printing.

Control figure size

The following is an example of a smaller figure using fig.width and fig.height options.

plot(x)

Cache analysis

Caching analyses is straightforward. Here's example code. On the first run on my computer, this took about 10 seconds. On subsequent runs, this code was not run.

If you want to rerun cached code chunks, just delete the contents of the cache folder

for (i in 1:5000) {
  lm((i+1)~i)
  }

Basic markdown functionality

For those not familiar with standard Markdown, the following may be useful. See the source code for how to produce such points. However, RStudio does include a Markdown quick reference button that adequatly covers this material.

Dot Points

Simple dot points:

  • Point 1
  • Point 2
  • Point 3

and numeric dot points:

  1. Number 1
  2. Number 2
  3. Number 3

and nested dot points:

  • A
    • A.1
    • A.2
  • B
    • B.1
    • B.2

Equations

Equations are included by using LaTeX notation and including them either between single dollar signs (inline equations) or double dollar signs (displayed equations). If you hang around the Q&A site CrossValidated you'll be familiar with this idea.

I added JavaScript from this gist to get the follwoing inline equation to work: (y_i = \alpha + \beta x_i + e_i).

Tables

Tables can be included using the following notation

A B C
1 Male Blue
2 Female Pink

Hyperlinks

Images

Here's an example image:

image from redmond barry building unimelb

Code

Here is Markdown R code chunk displayed as code:

```r
x <- 1:10
x
```

```
##  [1]  1  2  3  4  5  6  7  8  9 10
```

And then there's inline code such as x <- 1:10.

Quote

Let's quote some stuff:

To be, or not to be, that is the question: Whether 'tis nobler in the mind to suffer The slings and arrows of outrageous fortune,

Conclusion

  • R Markdown is awesome.
    • The ratio of markup to content is excellent.
    • For exploratory analyses, blog posts, and the like R Markdown will be a powerful productivity booster.
    • For journal articles, LaTeX will presumably still be required.
  • The RStudio team have made the whole process very user friendly.
    • RStudio provides useful shortcut keys for compiling to HTML, and running code chunks. These shortcut keys are presented in a clear way.
    • The incorporated extensions to Markdown, particularly formula and table support, are particularly useful.
    • Jump-to-chunk feature facilitates navigation. It helps if your code chunks have informative names.
    • Code completion on R code chunk options is really helpful. See also chunk options documentation on the knitr website.
  • Other recent posts on R markdown include those by :