Intersecting Points and Polygons in R

You do this in one line with point.in.poly fom spatialEco package.

library(spatialEco)

new_shape <- point.in.poly(pts, polys)

from the documentation: point.in.poly "intersects point and polygon feature classes and adds polygon attributes to points".

With the new sf package this is now fast and easy:

library(sf)
out <- st_intersection(points, poly)

Additional options

If you do not want all fields from the polygon added to the point feature, just call dplyr::select() on the polygon feature before:

library(magrittr)
library(dplyr)
library(sf)

poly %>% 
  select(column-name1, column-name2, etc.) -> poly

out <- st_intersection(points, poly)

If you encounter issues, make sure that your polygon is valid:

st_is_valid(poly)

If you see some FALSE outputs here, try to make it valid:

poly <- st_make_valid(poly) 

Note that these 'valid' functions depend on a sf installation compiled with liblwgeom.

If you do overlay(pts, polys) where pts is a SpatialPointsDataFrame object and polys is a SpatialPolygonsDataFrame object then you get back a vector the same length as the points giving the row of the polygons data frame. So all you then need to do to combine the polygon data onto the points data frame is:

 o = overlay(pts, polys)
 pts@data = cbind(pts@data, polys[o,])

HOWEVER! If any of your points fall outside all your polygons, then overlay returns an NA, which will cause polys[o,] to fail, so either make sure all your points are inside polygons or you'll have to think of another way to assign values for points outside the polygon...