I have a raster file with 5 classifications developed from habitat modelling algorithms. I'd like to know how much of 2 classes of the raster is covered by the network of protected areas (Shapefile).
Could any one advise me how to do so?
I would recommend clipping the raster to the shapefile, then in the resulting raster you can look at the number of cells present for each of your classes. The area can be calculated by multiplying the number of cells by the area covered each pixel (cell size squared).
It's a different approach than the equally valid solution offered above but from a slightly different angle. A little variation never hurts!
This can be accomplished using three main steps:
Convert your raster to polygons using the Raster To Polygon tool