Links
The following are resources that we have found useful in teaching spatial analysis and methods using R. You may find these helpful as a reference. Free resources are denoted with an asterisk.
Spatial Data Analysis in R

Spatial R Task View*: Provides an overview of the R ecosystem for spatial data analysis

Applied Spatial Data Analysis with R (2nd Edition), Roger Bivand, Edzer Pebesma and Virgilio GomezRubio (2013): More advanced, indepth coverage of spatial statistical packages in R (assumes quite a bit of R expertise)

Geocomputation in R*: Recent online textbook about manipulating, mapping, and modeling geographic data

Introduction to visualizing spatial data in R*, Robin Lovelace, James Cheshire, Rachel Oldroyd and others (2015) : A good introductory overview of GIS operations in R

An Introduction to Spatial Data Analysis and Visualization in R*, Guy Lansley and James Cheshire (2016): A more extensive introduction to mapping, spatial data manipulation and visualization in R

An Introduction to R for Spatial Analysis and Mapping, Chris Brunsdon and Lex Comber (2015): a more indepth intermediate overview of GIS operations and some spatial analysis in R with lots of illustrations
General R Learning
 R for Data Science*, Garrett Grolemund and Hadley Wickham (2017): A collection of data science “skills” using R, with an emphasis on “data munging” using specialized R packages called the “tidyverse” – highly recommended if you are serious about data science using R