Resources for R:

R Project Site: The R Project's homepage with Documentation, Downloading R, FAQs, more (subset given below)

An Introduction to R (updated version of the Intro notes)

R introductions identified by Duke StatSci grad students (scroll to bottom of linked page)

• R CRAN SITE (downloads, documentation, packages and more)
  
• FAQs (please read before posting a question!)
  
• R Reference Card (J Baron)
  
• Writing R Extensions (Explanations of writing packages and calling C from R)

Books

• WN Venables, DM Smith and the R Development Core Team (2004) An introduction to R. [Amazon ]
• P Dalgaard (2002) Introductory statistics with R, Springer-Verlag, New York
• WN Venables and BD Ripley (2002) Modern applied statistics with S, 4th edition. Springer-Verlag, New York. [Online complements]
• JM Chambers (1998) Programming with data : A guide to the S Language. Springer-Verlag, New York.
• JM Chambers and TJ Hastie (eds) (1991) Statistical models in S. Chapman & Hall, New York.

Resources for BUGS:

• BUGS Homepage
  
• WinBugs (Windows) Downloads, FAQS, Examples
  
• Running WinBUGS on a MAC
• Running WinBUGS under Linux (For DSS computers)
  
• WinBugs: The Movie Demonstrates where to point and click using the GUI version of Winbugs.
  
• Running WinBugs from R
  
• coda

Resources for Emacs:

ESS (Emacs Speaks Statistics) provides a common, generic and useful interface to many statistical packages through Emacs. It currently has interfaces to S, R, XLisp-Stat, and SAS, with other statistical languages such as Stata, SPSS, and Fiasco slated for implementations in the future.

ESS Reference Card (pdf)

Running R/S-Plus with ESS locally

Emacs Quick Reference Card

Emacs Quick Tutorial

Gnu Emacs Site and XEmacs Site

Getting Started with LaTeX and Sweave

Simple LaTeX Introduction ( pdf , LaTeX source),

Including Graphs in LaTeX (adding-graphics.tex, geyser-plot.ps, geyser-plot.pdf)

Charlie Geyer's website for using Sweave

AucTeX (emacs mode for editing LaTeX) refcard (pdf)

Other Useful Software (Ghostview, Acroread, Emacs, etc)