This code takes three polygonspatial dataframes, samples, poly1 and Poly 2 it selects the polygons of poly1 and poly2 inside each of the sampling windows, rasterizes them as "change, no-change" binary masks, compares them and calculates the contingency matrices for each window using the function CompareRaster form the greenbrown package (http://greenbrown.r-forge.r-project.org) It offers the option to plot the agreement maps and export them as Geotiffs. The script returns a list with all the contingency tables I need to update thies readme to actually tell waht the different functions do and why i propse to achieve with this.