library(raster)
library(rgdal)

# Load footprint from file into rasterBrick object
path_to_footprint_nc <- './footprint.nc'
footprint <- brick(path_to_footprint_nc)

# Sum values per-cell into raster object
r_all <- sum(footprint)

# Read in counties shapefile
shape <- readOGR(dsn = 'Counties', layer = 'Counties')

# Grab the SLCo polygon from the counties shapefile
slco <- spTransform(subset(shape, NAME == 'SALT LAKE'), CRS('+proj=longlat'))

# Replace values outside of SLCo with NA
r_slco <- mask(r, slco)

# Plot pre-crop and post-crop for validation
op <- par(mfrow = c(1, 2))
plot(r_all, main = 'Full Domain')
plot(r_slco, main = 'SLCo')
par(op)