The Handbook of Spatial Analysis, coordinated by Insee with the strong support of Eurostat and the European Forum for Geography and Statistics, draws up the list of analysis that can be carried out with spatial data and the pitfalls to avoid when using them.
The handbook is divided into four parts and fourteen chapters. The first three chapters match the stages one would follow to carry out a study with spatial data: describing the location of the observations, measuring spatial interactions and applying the appropriate model. Each chapter explains the theoretical foundations, gives practical applications based on data coming from public statistical institutes, and displays how to use the R statistical software to carry out the computations.
The handbook is available to download here