The Johns Hopkins University R courses on Coursera by Roger Peng, Jeff Leek, and Brian Caffo are fantastic and mostly in base R
- R Programming https://www.coursera.org/learn/r-programming
- Advanced R Programming https://www.coursera.org/learn/advanced-r
- Getting & Cleaning Data https://www.coursera.org/learn/data-cleaning
- Exploratory Data Analysis https://www.coursera.org/learn/exploratory-data-analysis
Winston Chang's Cookbook for R: http://www.cookbook-r.com/
An Introduction to Data Cleaning with R free ebook by Edwin de Jonge & Mark van der Loo https://cran.r-project.org/doc/contrib/de_Jonge+van_der_Loo-Introduction_to_data_cleaning_with_R.pdf