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Is it possible to perform a cookie cut in R?

Firstly, I have a polygon shapefile of many polygon some of which overlap. I then have a second polygon shapefile with contiguous non-overlapping polygons. I want to establish the parts of the first (potentially overlapping) polygons that fall within each of the second (non-overlapping) polygons. The first shapefile is a number of layers of cookie dough to cut and the second is the cutter to apply. Alternatively I can use QGIS if people think that's the best way to go.

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    Have you looked at the operations on polygons provided by the sf package? In particular st_difference might be the one. – Spacedman Jul 29 '18 at 17:00
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The solution in R:

library(rgeos)
library(rgdal)
dough <- readOGR("poly1.shp")
cutter <- readOGR("poly2.shp")
cookies <- gIntersection(dough, cutter, byid=TRUE)
  • Thanks Micha, looks so elegant that it must be true. I'll try this later in the week and hopefully come back with a tick. – Stephen Clark Jul 30 '18 at 8:00
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    Note this uses sp classes for spatial data - a solution with sf classes should always be preferred, which would use st_intersection – Spacedman Jul 30 '18 at 13:30
  • I have the following class for my spatial data, so I think I'm good to go. > class(iso) [1] "SpatialPolygonsDataFrame" attr(,"package") [1] "sp" – Stephen Clark Jul 31 '18 at 14:59

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