Hands-On Geospatial Analysis with R and QGIS
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Further reading

To get a good idea about the various aspects of data management and writing functions in R, please refer to R Cookbook by Paul Teetor and Advanced R by Hadley Wickham. If you are looking for a thorough introduction to QGIS, please refer to the books QGIS2 Cookbook by A Mandel et al and Mastering QGIS by K Menke et al.