Looking back on the work I’ve done so far (finding a thesis topic, finding data, finding tools) I can definitely recommend the two books below. They’re R-related and they contain a lot of examples which still help in implementing the ideas I have. The first is Modern Applied Statistics with S (Venables/Ripley) and the other one is Applied Spatial Data Analysis with R (Bivand/Pebesma/Gómez-Rubio) from the „Use R!“ series. It’s just perfect to look up things in those books which you might need in your current implementation. Besides, there’s still the R mailing lists to ask your questions and the authors of the above books are typically present at those lists.

If you prefer a bookstore, look out for these on the shelves: