R stat is gaining popularity and is very powerful. While I already have some knowledge on R, I would like to go down to the basic to understand all the basics/fundamentals which will help me as I use it for my research analysis......
I'm not sure whether you are asking for a stats book that happens to use R or a book about R. I am assuming when you say you want to understand the fundamentals of R you mean actually learn more about R; not just how to use it, but why it is like what it is. I think for this Software for Data Analysis ( https://www.springer.com/gp/book/9780387759357 ) is the choice. This will tell you about the fundamentals of R (which is an implementation of S, so this really about S too) especially the philosophy behind it.
in the youtube channel of Mike Marin you find lots of step-by-step explanations and examples of different statistical analyses in R. From the very beginning to the top: https://www.youtube.com/playlist?list=PLqzoL9-eJTNBDdKgJgJzaQcY6OXmsXAHU