Thursday, 15 August 2013

Creating a Quick Report with knitr, xtable, R Markdown, Pandoc (and some OpenBLAS Benchmark Results)

To cut a long story short, I always wanted to write professional-looking documents (technical reports and potentially my thesis) with R codes. No more copy and paste. No more Microsoft Word. At the same time, I don't feel comfortable with LaTeX. Somehow I found a workaround with knitr, xtable, R Markdown and Pandoc.

I must say that my solution is far from perfect as I haven't mastered the document layout configuration yet. But I did manage to get some satisfactory results (well, from a seasoned MS Word user's point of view) with minimal R Markdown, xtable and knitr codes.

Instead of showing some dummy results, I created a simple report on R-25 benchmark results with two versions of OpenBLAS (ver. 0.2.6-1: the default, 2-threaded version on my Linux and ver. 0.2.8-1: the latest, multi-threaded version which had been made available recently). In short, the latest OpenBLAS performed slightly better in most of the R-25 tests but two. For more details, download the full pdf here.

The code-generated report looks like this ...

... which I think is pretty enough for a quick report. When I look at the source R Markdown file which is nothing but geeky plain text (see below), I just can't find words to describe the awesomeness of knitr + xtable + pandoc. Thank you very much Yihui, RStudio team, David, Charles and John.

The codes are available on Github. This was my first attempt to code a report, the code structure isn't pretty enough for showcase but I had commented as much as possible. I hope you enjoy this blog post and give this code-generated report routine a try!

Updated (21 Aug 2012): A basic 4-step example can be found here.
Updated (01 Feb 2014): The basic 4-step example is now here.

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