I finished reading this document just now. In fact, it seems to be the first R document I have ever finished reading:
“Using R for Data Analysis and Graphics - Introduction, Examples and Commentary” by John Maindonald (PDF, data sets and scripts are available at JM’s homepage).
I think there were some places which need slight modifications, for instance, the code “> x_c(1,5,NA,8)” on Page 17: the assignment operator “_” is not for R now (only for S-Plus), etc.
In all, this document is good for R novices especially in R basics such as data structures and functions (to obtain an overview of R language), and other parts are quite rough, among which the part for linear models and ANOVA is relatively comprehensive, and other parts such as GLM, tree-based models, time series, linear mixed effect models and multi-level models are not discussed in details.
Besides, the title for this document contains “Graphics”, but I think those blurry bitmaps in the text are not satisfactory at all…