R Help

R is a free software very similar to S-PLUS and it can be downloaded from http://www.r-project.org where you also find the wonderful quickly responding mailingslist r-help.

At the Centre for Mathematical Sciences, R is available on all Sun Solaris and Suse Linux machines by typing

 % R

at the prompt. Old (and new versions) of R can explicitly be accessed by Rnnn where nnn is the version number without dots, e.g. R181 for R v1.8.1 and so on.

R Coding and Documentation Conventions

• RCC - R Coding Conventions (a first draft), Henrik Bengtsson, 2002-2003.
• Writing .Rd Files For S4 Classes, Generic Functions and Methods, Gordon Smyth, 2003.

Object-oriented programming in R

• Safely creating S3 generic functions using setGenericS3()
• Going from S3 to S4 object oriented programming in R definitely not complete!

Programming with references

• The R.oo package - Object-oriented programming with references using S3/UseMethod
• Programming with References - a case study using the R.oo package
• Implementing support for references in R

Local packages & bundles

• Henrik Bengtsson, The R.classes bundle (R.oo and friends), 2001-2004. Installation instructions included (takes 30 seconds)
• Henrik Bengtsson, aroma - An R Object-oriented Microarray Analysis environment written in 100% R, 2001-2004. With installation instructions too (takes 30 seconds). This package was formerly known as com.braju.sma (see below).
• Henrik Bengtsson, The com.braju.sma package - A microarray analysis packages based on an object-oriented design and reference variables, extended abstract, Mathematical Statistics, Lund University, November 2002. (pdf, ps)
• Henrik Bengtsson, R.matlab - Local and remote Matlab connectivity in R, 2002-2004. Communicate with Matlab from within R.

Introduction to R

• Emmanuel Paradis, R for Beginners, Université Montpellier II, France, Aug 2002. (pdf)
• Jonathan Baron, Notes on the use of R for psychology experiments and questionnaires, University of Pennsylvania, Aug 2001. (HTML, pdf)
• Ko-Kang Wang, R for Windows Users, Department of Statistics, New Zealand, October 2002. (HTML, pdf, ps, tex)
• Ross Ihaka, Statistics 120 - Information Visualisation (HTML) - A great set of lecture notes and R packages for graphical presentation of data etc. Look at it!

Quick references to R

• Jonathan Baron, R reference card, University of Pennsylvania, Aug 2001. ( pdf)
• Robin Hankin, R For Octave [& Matlab] Users, 2001. (txt)

How to's and Code examples

• Paul Johnson, Rtips ("StatsRus"), University of Kansas. (HTML)
• R TclTk Examples, James Wettenhall (some really nice code examples)
• Code example explaining image()

R on Windows

• H. Bengtsson, Windows bat file to get a Command prompt ready for R. See instructions in header comments. RCMDprompt.bat.

Other R help pages

• R Help Center at the Institute de Statistique, Universite catholique de Louvain, Belgium

Miscellaneous

• D. Murdoch, Debugging in R, 2004.
• H. Bengtsson, Exception handling in R, 2004.
• D. Adler and O. Nenadic, RGL - 3D visualization for R.
• Barry Rowlingson, R Imagemap Creator - "This library helps you create clickable imagemaps from your R graphics to put on the web."

How do I print from R?

After you have created a plot you have to save it to file and from there print it. Example

  plot(sin(1:10))
  dev.print(postscript, file="/tmp/out.ps")
  system("lpr -Pps3 /tmp/out.ps")           # Call lpr from within R

How to autosave the command history

To save the command-line history automatically when exiting R just add the following in your ~/.Rprofile file:

.Last <- function() {
  savehistory();
}

Sweave

Sweave is a really great tool, which allows you to incorporate executable R code within for instance LaTeX documents. First Sweave() is called on your R-LaTeX hybrid document, the R code is extracted and evaluated. Figures that are generated are saved as EPS and PDF files, necessary LaTeX code to incorporate the figures in the LaTeX document is inserted in place. The final result is a LaTeX document (together with figure files), which can be compiled as usual. How does it work? See help(Sweave) in the tools package.

One common problem is that people encounter is that the Sweave.sty file is missing. It is located at ${RHOME}/share/texmf/Sweave.sty; just save it in the same directory as your LaTeX document.