This is just a quick reference to someone else's work. First of all the basics:
1. lme
http://stat.ethz.ch/R-manual/R-patched/library/nlme/html/lme.html
2. lmer
http://cran.r-project.org/web/packages/lme4/index.html
Professor Vardeman (Iowa State) has posted a very nice summary for the basic functionality of these functions. It is important to heed is warning that these functions are constantly under development (which is generally applicable to R).
http://www.public.iastate.edu/~vardeman/stat511/stat511.html
search for: lme() and lmer() Functionality (4/17/09)
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