 R for Data Science : Hadley Wickham and Garrett Grolemund have written this amazing resources on using R. Most of the chapters are based on packages developed by Hadley.
 R Graphic Cookbook : The book is very useful for learning the ggplot2 package in R. The book is freely available online and has many useful tips and recipes for creating visualizations in R.
 Tidy Text Mining in R : A free book on text mining in R.
 Elements of Statistical Learning : A great way to get acquainted to Machine Learning.
 Interactive Data Visualization (D3) : A great way to get started on learning D3. The book is free to read online.
 Networks : A free online book for learning Network Science.
 Journal of Economic Perspective : All the articles on this website are freely downloadable. Almost all articles have data sets and code for replication.
 100 free data science books : Has a very good collection of data science books , not just limited to R.
Open books and journals

Pingback: Atmajit GohilSome Free resources to learn data visualization in R