# make 2 rasters of the same extent, different resolutions
ext <- extent(0,1000,0,1000)
r1 <- raster(nrows=1000, ncols=1000,ext)
r1[] <- sample(seq(from = 1, to = 6, by = 1), size = 1000000, replace = TRUE)
r2 <- raster(nrows=10, ncols=10,ext)
r2[] <- sample(seq(from = 0, to = 1, by = 0.05), size = 100, replace = TRUE)
# create areas of interest in coarser raster
r2[r2 < 0.9] <- NA

# disaggregate the coarser raster to the same res as the finer raster
r2 <- disaggregate(r2,fact=c(100,100))
# mask the fine by the coarse
r3 <- mask(r1,r2)
# and return a frequency table of the finer resolution
freq(r3,useNA="no")