The manuals I have seen are a bit frustrating. They are either too simple, or too complex. Is there a manual that has a strong intro to R, good explanation of multivariate stats, and good intro to graphics? Should I look for separate manuals then?
Brian Everitt has authored some books on the topic. I can vouch for "Handbook of Statistical Analyses Using R" in particular. It contains chapters on multivariable regression models, clustering, multidimensional scaling, and principal component analysis to give a brief overview.
Data analysis and Visualization with R by Duursma, Powell and Stone is a good introductory book to R, with plant ecophysiology examples and online data. This is the link: http://www.remkoduursma.com/hier
I can second the Hothorn and Everett "Handbook of Statistical Analyses Using R" I was a little disappointed in the Bayesian section in the third edition but still a good book, I also liked Everitt's "Analyzing Medical Data using S-Plus"