R, knitr & markdown = HTML

July 7, 2012

(This article was first published on FishyOperationsCategory Archives: r, and kindly contributed to R-bloggers)

Welcome to this demo of how R code and results can be combined into an HTML report. This entire blogpost was generated by using a combination of R, knitr and markdown.

Beforehand, make sure you have the following libraries installed (latest version);

  • knitr
  • markdown
  • ggplot2 (to run the example script)

Syntax references for markdown can be found here.

Let's make two separate files, a .R file and an .Rmd file.

The .R file

The .R file should be used to load necessary libraries, define and transform data and, possibly, to define the plots beforehand. After a useful comment from Yihui I recommend including the code to define the dataset and create the plot within the .Rmd file. This in order to create a self-contained document that can be reproduced without special instructions. As, and I quote from the comment below: 'a reproducible report should be self-contained and not rely on external objects'.

My .R file looks as follows:


#transform the .Rmd to a markdown (.md) file.

#transform the .md to HTML format
markdownToHTML("r-knitr-markdown.md", "r-knitr-markdown.html",fragment.only = TRUE)

When using the output in a blogpost it is important to set the 'fragment.only' option to TRUE, otherwise it will generate a full-fledged HTML page (HTML tags / CSS / etc.).

In the .Rmd file, the following code is used to start a so called R 'chunk'. A 'chunk' is a place in the .Rmd file where R code will be run and evaluated. An R chunk is defined as follows;

R chunk

Let's try this and check out the result.

# your R code goes here, e.g.
1 + 1
## [1] 2

Let's create a dataset and define a plot for testing purposes.

# define the dataset
dataset <- data.frame(x = seq(1, 100), y = runif(100))

# let's load the ggplot2 library

# define the plot to be used in the final HTML report
graph <- ggplot(dataset, aes(x = x, y = y)) + geom_line(colour = "red")

What if we print the plot thas was defined in the 'graph' variable? This would be the result;

# show the graph

plot of chunk unnamed-chunk-3

There are a bunch of options available to e.g. hide the printout of the R script (echo) or to hide warning messages. Also the size of the graph output can be adjusted. All these option are explained on Yihui's knitr website.

I hope this gives an idea of how R can be used to generate reproducible data analysis reports, easy-to-update business intelligence reports and of course blog posts.

The files used to produce this output can be found here;

The post R, knitr & markdown = HTML appeared first on FishyOperations.

To leave a comment for the author, please follow the link and comment on their blog: FishyOperationsCategory Archives: r.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...

If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Tags: , ,

Comments are closed.


Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)