Warning: this post has been substantially updated to use the knitr package instead of Sweave or pgfSweave, and the old version is deprecated now! See this post for most information.
0. Summary
Take a look at the above video if you don’t understand the title. To put it short, you install LyX (>= 2.0.3) and R (>= 2.14.1) with the knitr package as well as a working LaTeX toolkit such as MikTeX or TeXLive or MacTeX, then you are ready to go.
Gregor Gorjanc published an interesting article “Using Sweave with LyX” in R News in 2008, which (I believe) makes it much easier to use Sweave. I use command-line tools a lot every day, but I am still “GUI-addicted”. (I don’t want to comment more about Microsoft Word here.) LyX looks like a WYSIWYG tool based on LaTeX, and on the first time I saw it I decided that Word was completely useless to me from then on. In the past, I did not like writing LaTeX documents just because I hate wasting my time on typing the raw commands. For example, I hate typing \item in an itemize environment each time I need a new item. There might be some text editors which can automatically do this tedious task, but the more serious problem is I cannot see the whole picture – in my eyes there are only commands; my imagination is limited – it is difficult for me to imagine \section{} to be a section title. However, LyX has provided a perfect solution to lazy people like me. We don’t have to write LaTeX documents from scratch, and everything is intuitive in LyX. You can clearly see the structure of your document, as well as figures (instead of \includegraphics{}), tables (instead of the gory \begin{table} numbers 1.4 & 2.2 & 3.8), headings (instead of \title{} \section{}) and math formulae (instead of $\frac{\gamma}{\alpha_{ij}}$)… In all, it is a whole lot easier and faster to write LaTeX documents in LyX. This is the main reason for an easier life of Sweave, because a Sweave document is nothing but a mixture of LaTeX and R code.
1. Introduction
Although Sweave in LyX is convenient to use, it was not a trivial task for beginners to configure and understand how it works, but things have become much better now since LyX 2.0.
As we can see in the above video, R code can be easily embedded into LyX. If you are familiar with Sweave, you don’t even need time to learn anything. For those who do not know Sweave well, a good place to look at is the help page ?Sweave. A Sweave document is dynamic in the sense that everything in the document can be changed by the R code (nothing is hard-coded), so we don’t need to worry too much about the specific numbers and plots in the output. Instead, we focus on the code which produces these output. In the above video, I used a LaTeX macro \Sexpr{} to output the value of pi and I don’t need to write the specific number 3.1415926 there.
2. pgfSweave
Update: I have switched from pgfSweave to the knitr package now, but what was described below is still true.
While Sweave is a great invention for reproducible research, there are other packages which can improve R’s default Sweave functionality. A brilliant one is the pgfSweave package. It was built upon the cacheSweave package to support caching R objects (to avoid unnecessary repeated computations and save time), and it also provided a mechanism to cache graphics! Beside the speed issues, a remarkable feature is the quality of graphics – it is unbeatable. I’m not exaggerating. This packages uses the tikzDevice package to produce pgf/tikz graphics which are essentially LaTeX code, in other words, the R graphics are represented in the LaTeX language so that they are treated (compiled) in the same way as the body of a LaTeX document. This will make the style of graphics completely consistent with the body of a document, e.g. the fonts.
By the way, I also like the nogin option for Sweave.sty to be the default in pgfSweave, because I really don’t like the idea of setting the size of graphics by a LaTeX macro \setkeys{Gin}{width=0.8\textwidth}. In pgfSweave, we just set the width and height naturally in the code chunk options like <<width = 5, height =4>>=.
pgfSweave comes with a command line usage like Sweave: R CMD pgfSweave your-file.Rnw. I’m not using this approach in LyX, because this requires system admin privilege to install pgfSweave. Instead, I use this way:
R -q -e "library(pgfSweave);pgfSweave('yourfile.Rnw')"
R can accept a string in its -e argument, e.g.
yihui@xie:~$ R -q -e "rnorm(5)"
> rnorm(5)
[1] -0.2970093 -0.2171444 1.5645127 0.5422097 0.7359204
Later I’ll explain how to connect LyX and R/pgfSweave in this way.
3. Configuration
Update: the several steps of configuration become one step since LyX 2.0.
To make LyX work with Sweave, we basically only need one step: configure the PATH variable; see the manual for details.
4. Demo
See my lyx and knitr repositories to see many examples.
5. Bad News
Update: all previous bad news has gone.