[R] Sweave findings

[Frank E Harrell Jr]

Dear Group:

After struggling with escape sequences using the LaTeX listings package 
(used by the R SweaveListingUtils package), I have come to the 
conclusing that listings' interaction with the LaTeX fancyvrb package 
prevents escapes such as

   plot(x)  # See Figure \ref{my.plot}

The only way I could solve the problem in general is to use a Perl 
script to pretty-print the R code, and to let Perl handle escapes.  I 
have posted information about this at
http://biostat.mc.vanderbilt.edu/SweaveTemplate along with an example 
pdf file.  This involves the use of a modification of Sweave.sty which 
I've called Sweavel.sty, which also incorporates colors and boxes the R 
output.  This process involves more user setup but ultimately allows 
much more control.  Luckily latex and pdflatex implement the 
--shell-escape option to allow Perl and other programs to be executed on 
chunks of LaTeX code.

Note that the Perl script s2latx.pl will be improved and replaced in the 
next few days to handle escapes with more generality.

Regarding the issue of preventing Sweave from issuing the Gin option to 
set all graphics output to have a width of 0.8\textwidth, it's as easy 
as using \usepackage[nogin]{Sweave} or \usepackage[nogin]{Sweavel}.

To force black and white output I implemented \usepackage[bw]{Sweavel}.

The motive behind all this is to make Sweave produce output nice enough 
for a book.

Our template page also has a concise way to use \figure environments.

Frank
-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University