We use the first handout as an example. The others are similar. Our explanation will run backwards from output to input (from final result produced by the computer to the file the author provides).
The output is a PDF file
(Adobe Palatable Dog Food format). Adobe would have you call it
Portable Document Format
, but it's portable only in their dreams.
As far as the world wide web (WWW) goes, PDF is the most evil and rude format imaginable, rude because it's gratuitously incompatible with the WWW and evil and rude because the incompatibilities are apparently there to lock hapless customers and developers into the Adobe way.
Nevertheless, PDF has been somewhat freed
by the open source community.
There commands (in unix) to convert various other file formats to PDF.
And R can produce PDF output for graphics.
The middle level is a LaTeX file. We won't say much about this. It's produced by the computer and used by the computer. The author doesn't touch it (though sometimes it's interesting and informative to look at it to see how certain things are being done).
The input, the file written by the author,
is an R noweb file having
the extension Rnw on its file name.
This is the R literate programming
format.
The Rnw file is turned into LaTeX by the R command
Sweave("mle.Rnw")
This conversion can also be done outside R (in unix) by the unix command
echo "library(tools); Sweave(\"mle.Rnw\")" | R --vanilla --quiet
This LaTeX file can then be converted to the standard TeX output format DVI by the unix command
latex mle
Or the LaTeX file can be converted to PDF by the unix command
pdflatex mle
If you don't have pdflatex, then the following two unix
commands will also do the job
dvips -o mle.ps -P pdf mle ps2pdf mle.ps