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Disclaimer: I park links here that come up repeatedly in my own work and in my teaching. I freshen/organize very sporadically.
My links to certain eBooks and repositories are tuned to UBC users.
Books (updated January 2014; older list below)
ggplot2: Elegant Graphics for Data Analysis available via SpringerLink by Hadley Wickham, Springer (2009) | online docs (nice!) | author's website for the book, including all the code | author's landing page for the package
Dynamic documents with R and knitr by Yihui Xie, part of the CRC Press / Chapman & Hall R Series (2013). ISBN: 9781482203530. No online access (yet?).
Reproducible Research with R & RStudio by Christopher Gandrud, part of the CRC Press / Chapman & Hall R Series (2013). ISBN: 978-1466572843. Book website | Examples and code | Book source. Very new, no online access (yet?).
plyr package for data aggregation
Smart editor/IDE set-ups for R programming (M = Mac OS or other *nix, W = Windows, A = both)
Potentially helpful links related to the editor/IDE issue (no guarantees these are good, current, etc.)
R style, coding conventions, and philosophy
eBooks (your mileage may vary depending on your personal or institutional subscription coverage)
R Programming for Bioinformatics by R Gentleman, CRC Press
The Elements of Statistical Learning: Data Mining, Inference, and Prediction by Hastie, Tibshirani, & Friedman, Springer (2009)
Statistical DNA Forensics by Wing Kam Fung and Yue-Qing Hu, Wiley (2008)
Statistics and Data with R by Yosef Cohen and Jeremiah Y. Cohen, Wiley (2008)
Statistics for Microarrays by Ernst Wit and John McClure, Wiley (2004)
Nonparametric Regression Methods for Longitudinal Data Analysis by Wu Hulin, Zhang Jin-Ting, Wiley (2006)