R is an open source software that is very flexible program that allows to combine statistics and spatial modelling.
I recently took up the challenge to make more and more use of R and slowly replace licensed software. This page presents interesting links to good R documentation with a focus on spatial data processing.

General R

R for dummies by Andrie de Vries and Joris Meys

Spatial R

A book explaining the SP toolbox
Applied Spatial Data Analysis with R by Bivand, Pebsma, Gomez-Rubio

Raster toolbox with very good manual by Hijmans

A quite good lecture on how to krige.

Make your own legends (with RcolorBrewer) 

R Markdown

Markdown is an automatic document generator based on Latex. It can be run as a sort of meta-language in R-studio, and outputs beautiful ready-to-share documentations. This can be very useful to immediately share results from work done in R, but also automatizing the data documentation, i.e. meta data.
Where to find more info about markdown in Rstudio
markdown webpage
and the reference guide 
In order to be able to make pdf in markdown, you will need a Pandoc converster, which itself relies on LaTex. Find more explantition about what you need to install here.

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