Cropping in a shape of catchment area (not rectangular) in R

Question

I have daily rainfall values in a NetCDF (.nc) file which is of larger extent covering a catchment area of a river basin. I want to crop it and extract the rainfall values that are within the catchment area. I have a shapefile of the catchment area. I am working in R and did like this:

crop(raster,e,filename="cropped_pr.nc",snap='near') 

raster=source file

e<-extent(reference_raster) #extent of catchment area (rectangular boundary)

It crops the source file in a rectangular shape, as expected in the script, and includes values that are outside the catchment area too. However, the catchment area is not rectangular (polygon).

I want to make the values outside the catchment area as 0. It means I want the values which are within the catchment area only.

Answer 1

You can use your polygon as mask.

# r = your_raster
# p = SpatialPolygons(your_polygon)

r_masked <- raster::mask(r, p)

Outside of your polygon will be filled by NA

Then you will probably want to trim unnecessary margins, while replacing NA by 0.

r_trimmed <- trim(r_masked, values = NA)
r_trimmed[is.na(r_trimmed)] <- 0

Answer 2

The crop function subsets to a new rectangular extent and mask turns all values outside the mask area to NA but, does not subset the extent. As such, you want to use the two functions in conjunction eg, mask(extent(x, e), m)