I have two raster objects r1 (in grey and green) and r2 (in pink) that I want to intersect with R. I tried with the R function intersect from the raster package but it only intersect the extent of the two objects :

enter image description here

I would like to get a raster object r3 that have the shape of r2 (pink), but the values of r1.

Do you know how I can do this ?


I have a find a solution by firstly insersecting r1 and r2 into r3 then converting r3 and r2 to SpatialPolygonsDataFrame using the rasterToPolygonsfonction. The intersection of r3 and r2 converted into SpatialPolygonsDataFrame is close to what I wanted to get :

enter image description here

  • you can build a mask with r2 where pink =1, no-pink=0 (or reclassify); then r3=new-r2*r1.
    – Pau
    Commented Feb 19, 2015 at 15:02

1 Answer 1


This is exactly what the function raster::mask(x, mask) is for. It sets cells in x to NA when the corresponding cell in mask is NA.


# Create some sample data
r1 <- raster(nrows=40, ncols=40, xmn=0, xmx=2, ymn=0, ymx=2)
r1[] <- seq(1, 100, length.out=ncell(r1))
r2 <- raster(outer(1:20,20:1), xmn=0, xmx=1, ymn=0, ymx=1)
r2 <- reclassify(r2, c(0,100,NA))


The rasters must be of the same resolution and, if they're not the same extent, as is the case in the example I constructed, you should apply crop first.

# Bring to the same extent with crop then
# Use mask to set cells in r1 to NA when corresponding r2 cell is NA
r3 <- mask(crop(r1, r2), r2)


This assumes that the part of r2 that you want to remove from r1 is coded as NA/NoData. If not, use raster::subs() to make this the case.

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