R problem: Crop Spatialpolygon with another Spatial object returns a square. Why?

Question

I am using the raster::crop function to cut a Shape of multiple polygons (Agricultural Plots Information System) with another polygon (Formal Class spatialPolygonDataframe) and instead of cutting the shape of the MCP (single polygon) return a the first shape in a Square.

Any idea?

The code is:

maps <- c(map21, map22) #multipoligons I want to cut
mcpid2 <- crop(maps[[1]], mcpid)

I get this:

and I want this:

Answer 1

This is what raster::crop does:

Description:

     crop returns a geographic subset of an object as specified by an
     Extent object (or object from which an extent object can be
     extracted/created).  If ‘x’ is a Raster* object, the Extent is
     aligned to ‘x’. Areas included in ‘y’ but outside the extent of
     ‘x’ are ignored (see ‘extend’ if you want a larger area).

Hard to be definitive with what you really need without fuller details, but it sounds like you have sp polygons which means you need functions from the rgeos package to do geometric operations like intersections. Alternatively use the sf package and its functions (eg st_intersection) to chop polygons with polygons.

Answer 2

I solved the problem with

raster::intersect(maps[[1]], mcpid)

Thank you.

This helped: How to perform a true GIS clip of polygons layer using a polygon layer in R?