Toy example of a one to many intersection between points and polygons

intersect_many_polygons.r

library(sp)

# create polygons
p1 <- matrix(c(1,1,
               2,1,
               4,2,
               3,2), ncol = 2, byrow = TRUE)
p2 <- matrix(c(2.2,1,
               3,1,
               3,2,
               3,3,
               2.8,3), ncol = 2, byrow = TRUE)
p1s <- Polygons(list(Polygon(p1)), 3)
p2s <- Polygons(list(Polygon(p2)), 4)
sps <- SpatialPolygons(list(p1s, p2s))

#create points
point <- matrix(c(2.5, 1.5,
                  3.2, 1.75,
                  2,3,
                  1.5, 1.25, 
                  2.75, 2.5), ncol = 2, byrow = TRUE)
points <- SpatialPoints(point)
plot(sps, border = c("black", "blue"))
plot(points, add = TRUE)

#returns only a single hit per point
over(points, sps)

#create list of SpatialPolygons from original SpatialPolygons
sps2 <- lapply(sps@polygons, function(x) SpatialPolygons(list(x)))

#returns a list for each polygon, saying which points are enclosed
lapply(sps2, function(x) over(points, x))