I updated the RMark Workshop notes and included the example data files and R code. The notes contain about 8 pages discussing formulas and design matrices. In addition I included a file LinearModels.pdf which may be useful if you are unfamiliar with design matrices and formulas. Download the zip file at http://www.phidot.org/software/mark/rmark/RMarkDocumentation.zip. Please read the README.txt file in the zip. Also section C21 in Appendix C was updated.
regards --jeff