Create a new Raster* object that has the same values as x, except for the cells that are NA (or other maskvalue) in a 'mask'. These cells become NA (or other updatevalue). The mask can be either another Raster* object of the same extent and resolution, or a Spatial* object (e.g. SpatialPolygons) in which case all cells that are not covered by the Spatial object are set to updatevalue. You can use inverse=TRUE to set the cells that are not NA (or other maskvalue) in the mask, or not covered by the Spatial* object, to NA (or other updatvalue).