Book recommendations: biological data analysis/error
There are many books that teach statistics and R together. I would personally not recommend these books. Learn the fundamentals and just google what command already exist in R to perform the analysis you need to do.

I would recommend Experimental Design and Data Analysis for Biologists by Quinn and Keough. It is general, applied and pleasant to read.

As you already have good basis in statistics, you won't need an intro textbook but for other users (and because I personally work with one of the authors) I would like to mention The Analysis of Biological Data by Schluter and Whitlock.