Processing .Rnw files through Sweave
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

To process the file rbasics.Rnw, place the file rbasics.Rnw
in your intended working directory, start up R, and type in

 Sweave("rbasics.Rnw")
or
 Sweave("rbasics")

If all goes well (it should, provide you do not tinker too
inexpertly with the file contents!), this will generate the
latex file rbasics.tex, and graphs that will be included when
rbasics.tex is processed through latex or pdflatex.

The R code from rbasics.Rnw (much of it also in rbasics.tex) is 
in the file rbasics.R.  You can obtain this code file by typing,
from within R

 Stangle("rbasics.Rnw")
or
 Stangle("rbasics")

Files for the exercises
~~~~~~~~~~~~~~~~~~~~~~~
The files rbasics.Rnw, rpractice.Rnw, etc, are designed to generate
latex include files.  The file wrapper12.Rnw (which is pure latex) can
be processed through Sweave(), with the argument stylepath=TRUE, to
generate the necessary wrapper file wrapper12.tex.  This has the
effect of inserting the \usepackage{} command that tells latex where
to find the Sweave latex package.  This will certainly, on a PC, be in
a different place from a Mac.

Another possibility, which generates a LaTeX file that is portable
between systems and avoids potential problesm with paths that include
one or more spaces, is to include \usepackage{Sweave.sty} in the
preamble of wrapper12.Rnw.  Then ensure that Sweave.sty is in the
LaTeX path.  To find the path the the file Sweave.sty that is part
of the R installation type, on the R command line: 
paste(R.home(),"share/texmf/", sep="/") 

Once you have processed rbasics.Rnw, rpractice.Rnw and wrapper12.Rnw
through Sweave, you can then process wrapper12.tex through latex to
generate (if all goes well) the pdf file wrapper12.pdf

The file r-exercises.Rnw can be processed through Sweave to generate
one wrapper file, r-exercises.tex, for all the exercises.

What is Sweave?  
~~~~~~~~~~~~~~ 
To quote from the help file for Sweave()

  "'Sweave' provides a flexible framework for mixing text and S
  code for automatic report generation. The basic idea is to
  replace the S code with its output, such that the final
  document only contains the text and the output of the
  statistical anlysis.

  [It allows] automatic generation of reports by mixing word
  processing markup (like latex) and S code. The S code gets
  replaced by its output (text or graphs) in the final markup
  file. This allows to re-generate a report if the input data
  change and documents the code to reproduce the analysis in the
  same file that also produces the report."

The Sweave syntax is based on the Noweb literate syntax.

Reference:
     Friedrich Leisch: Sweave User Manual, 2002
      <URL: http://www.ci.tuwien.ac.at/~leisch/Sweave>

John Maindonald
Dec 27, 2008.