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

To process the file sec1-1.Rnw, ensure that it is in your working
directory, start up R, and type

 Sweave("sec1-1.Rnw")
or
 Sweave("sec1-1")

If all goes well (it should, providing you do not tinker too
inexpertly with the file contents!), this will generate the latex file
sec1-1.tex, and graphs that will be included when sec1-1.tex is
processed through latex or pdflatex.  For this purpose the contents of
sec1-1.tex need to be enclosed between LaTeX preamble commands and
\end{document}.  The wrapper file wrapper.tex that is generated when
wrapper.Rnw is processed through LaTeX is designed for this
purpose. Both pdf and postscript versions of the graphics file are
generated in the working directory, and the necessary \includegraphics
statement is placed in sec1-1.tex.

The R code from sec1-1.Rnw (much of it also in sec1-1.tex) is
in the file sec1-1.R.  You can extract this code by typing,
from within R

 Stangle("sec1-1.Rnw")
or
 Stangle("sec1-1")

The wrapper file
~~~~~~~~~~~~~~~~
By processing the file wrapper.Rnw (which is pure latex) through
Sweave() the wrapper file wrapper.tex is generated.  The effect is to
insert a \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.  Thus, do not use the existing file wrapper.tex on
your machine.  Process wrapper.Rnw through Sweave() to generate a file
wrapper.tex that is right for your setup.

Once you have processed both sec1-1.Rnw and wrapper.Rnw through
Sweave, you can then process wrapper.tex through pdflatex to
generate (if all goes well) the pdf file wrapper.pdf.  Or, you
can use latex and dvipdf.


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
March 7, 2013.