Sweave is a tool for making statistical analyses more reproducible by using literate programming in statistics. Sweave embeds R code inside LaTeX and replaces the code with the result of running the code, much like web development languages such as PHP embed code inside HTML.
Sweave is often launched from an interactive R session, but this can defeat the whole purpose of the tool. When you run Sweave this way, the Sweave document inherits the session’s state. Here’s why that’s a bad idea.
Say you’re interactively tinkering with some plots to make them look like you want. As you go, you’re copying R code into an Sweave file. When you’re done, you run Sweave on your file, compile the resulting LaTeX document, and get beautiful output. You congratulate yourself on having gone to the effort to put all your R code in an Sweave file so that it will be self-contained and reproducible. You forget about your project then revisit it six months later. You run Sweave and to your chagrin it doesn’t work. What happened? What might have happened is that your Sweave file depended on a variable that wasn’t defined in the file itself but happened to be defined in your R session. When you open up R months later and run Sweave, that variable may be missing. Or worse, you happen to have a variable in your session with the right name that now has some unrelated value.
I recommend always running Sweave from a batch file. On Windows you can save the following two lines to a file, say
sw.bat, and process a file
foo.Rnw with the command
R.exe -e "Sweave('%1.Rnw')" pdflatex.exe %1.tex
pdflatex.exe are in your path. If they are not, you could either add them to your path or put their full paths in the batch file.
Running Sweave from a clean session does not insure that your file is self-contained. There could still be other implicit dependencies. But running from a clean session improves the chances that someone else will be able to reproduce the results.
See Troubleshooting Sweave for some suggestions for how to prevent or recover from other possible problems with Sweave.
Update: See the links provided by Gregor Gorjanc in the first comment below for related batch files and bash scripts.