This is a step-by-step guide to ‘Sweave’ a document in R with Lyx on Ubuntu (9.04).
System: Ubuntu 9.04, LyX 1.6.2, R 2.11.0 (Development version, r50178)
- Install LyX with Synaptic if it is not installed yet. (Current version 1.6.2)
- Start LyX, go to menu Help -> About LyX, in the prompting version window note the user directory, by default it is
~/.lyx(following written as $LYXUSRDIR). Note that by using this directory the setting is only applied to the current user. If you want to make the settings applied system-wide, use the LyX system directory, by default /usr/share/lyx, as your $LYXUSRDIR in the following steps.
- Go to LyX on CRAN, download the ‘preferences’ and all files starting with ‘literate’, that is, ‘literate-*.*’.
- Check if a ‘preferences’ file is existing under $LYXUSRDIR (again, by default
~/.lyx). If yes, append the content of downloaded ‘preferences’ to the existing one. Otherwise copy the ‘preferences’ file there.
- Copy ‘literate-*.*’ to
- Close and open LyX, go to menu tools-> reconfigure, to reconfigure LyX and make it recognize our changes.
- Make sure that R is available on your search path (type ‘R’ in the terminal to see whether the familiar command line appears). If you installed R manually (for example by svn-checkout) and have a name other than by default (for example R-devel), maybe you want to set ‘R’ as an alias or by soft linking (
sudo ln -s $MYRHOME/bin/R /usr/bin/R)
- Make sure that the Sweave.sty file is on the searching hash of your latex. The Sweave.sty file can be found in
$RSOURCE/share/texmf/, where the $RSOURCErefers to the path of R source codes (svn checkout). If you are using TexLive distribution of LaTeX, the default path to put style files is /usr/share/texmf-texlive/tex/latex(short as $TEXDIR). To install the style file, you have to create a directory in the $TEXDIR, maybe named ‘RSweave’, and copy the Sweave.sty there under $TEXDIR/RSweave/. Next you have to run the program mktexlsr as root (
sudo mktexlsr), to refresh the hash of TeX. In case of question or another distribution like TeTex, see the reference (3) below.
- Download the Sweave-test-1.lyx file from CRAN to test whether it works.
Sweave supporting in LyX is interesting for R users performing reproducible research and documentation, especially for those using the beamer package to prepare LaTex-style representations. Although it is also possible to use other text editors like Emacs to prepare such presentations, the WYSIWYG principle of LyX makes it a more intuitive way to make professional presentations.