R Under development (unstable) (2024-01-28 r85838 ucrt) -- "Unsuffered Consequences"
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> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
> x = c(0.5, 1.5, 0.5, 1.5, 1.6)
> y = c(1.5, 1.5, 0.5, 0.5, 0.5)
> xy = cbind(x,y)
> dimnames(xy)[[1]] = c("a", "b", "c", "d", "e")
> pts = SpatialPoints(xy)
> z = data.frame(z1 = 1:5, z2=5:1, f = c("a", "a", "b", "b", "b"))
> row.names(z) = c("a", "b", "c", "d", "e")
> ptsdf = SpatialPointsDataFrame(pts, z)
> 
> xpol = c(0,1,1,0,0)
> ypol = c(0,0,1,1,0)
> pol = SpatialPolygons(list(
+ 	Polygons(list(Polygon(cbind(xpol-1,ypol))), ID="x9"),
+ 	Polygons(list(Polygon(cbind(xpol,ypol))), ID="x2"),
+ 	Polygons(list(Polygon(cbind(xpol,ypol-1))), ID="x3"),
+ 	Polygons(list(Polygon(cbind(xpol+1,ypol))), ID="x4")
+ 	))
> z = data.frame(z = c(10, 15, 25, 3), zz = 1:4, f = c("z", "q", "r", "z"), 
+ 	row.names = c("x9", "x2", "x3", "x4"))
> poldf = SpatialPolygonsDataFrame(pol, z)
> plot(pol, xlim = c(-1.5, 2))
> points(pts, col='red')
> 
> over(pts, pol)
 a  b  c  d  e 
NA NA  2  4  4 
> over(pts, poldf)
   z zz    f
a NA NA <NA>
b NA NA <NA>
c 15  2    q
d  3  4    z
e  3  4    z
> over(pts, poldf[1:2], fn = mean)
   z zz
a NA NA
b NA NA
c 15  2
d  3  4
e  3  4
> 
> #rbind(poldf, over(pts, poldf[1:2], fn = mean))
> 
> over(pol, pts)
x9 x2 x3 x4 
NA  3 NA  4 
> over(pol, ptsdf)
   z1 z2    f
x9 NA NA <NA>
x2  3  3    b
x3 NA NA <NA>
x4  4  2    b
> over(pol, ptsdf[1:2], fn = mean)
    z1  z2
x9  NA  NA
x2 3.0 3.0
x3  NA  NA
x4 4.5 1.5
> 
> pts[pol]
SpatialPoints:
    x   y
c 0.5 0.5
d 1.5 0.5
e 1.6 0.5
Coordinate Reference System (CRS) arguments: NA 
> 
> points(pts[pol], col='green', pch=16, cex=.8)
> summary(pol[pts])
Object of class SpatialPolygons
Coordinates:
  min max
x   0   2
y   0   1
Is projected: NA 
proj4string : [NA]
> plot(pol[pts], border='blue', add=TRUE)
> 
> gt = GridTopology(c(.5,.5), c(1,1), c(3,2))
> sg = SpatialGrid(gt)
> df6 = data.frame(z = 6:1, f = c("a", "a", "b", "b", "c", "c"))
> sgdf = SpatialGridDataFrame(gt, df6)
> over(sg, pol)
 1  2  3  4  5  6 
NA NA NA  2  4 NA 
> over(sg, poldf)
   z zz    f
1 NA NA <NA>
2 NA NA <NA>
3 NA NA <NA>
4 15  2    q
5  3  4    z
6 NA NA <NA>
> over(sg, poldf[1:2])
   z zz
1 NA NA
2 NA NA
3 NA NA
4 15  2
5  3  4
6 NA NA
> 
> spix = as(sg, "SpatialPixels")
> spixdf = as(sgdf, "SpatialPixelsDataFrame")
> over(spix, pol)
 1  2  3  4  5  6 
NA NA NA  2  4 NA 
> over(spix, poldf)
   z zz    f
1 NA NA <NA>
2 NA NA <NA>
3 NA NA <NA>
4 15  2    q
5  3  4    z
6 NA NA <NA>
> over(spix, poldf[1:2])
   z zz
1 NA NA
2 NA NA
3 NA NA
4 15  2
5  3  4
6 NA NA
> 
> over(pol, sg)
x9 x2 x3 x4 
NA  4 NA  5 
> over(pol, sgdf)
    z    f
x9 NA <NA>
x2  3    b
x3 NA <NA>
x4  2    c
> over(pol, sgdf[1], fn = mean)
    z
x9 NA
x2  3
x3 NA
x4  2
> 
> over(pol, spix)
x9 x2 x3 x4 
NA  4 NA  5 
> over(pol, spixdf)
    z    f
x9 NA <NA>
x2  3    b
x3 NA <NA>
x4  2    c
> over(pol, spixdf[1], fn = mean)
    z
x9 NA
x2  3
x3 NA
x4  2
> 
> over(pts, sg)
a b c d e 
1 2 4 5 5 
> over(pts, spix)
a b c d e 
1 2 4 5 5 
> over(pts, sgdf)
  z f
a 6 a
b 5 a
c 3 b
d 2 c
e 2 c
> over(pts, spixdf)
  z f
a 6 a
b 5 a
c 3 b
d 2 c
e 2 c
> 
> #over(pts, sg, returnList=TRUE)
> #over(pts, spix, returnList=TRUE)
> #over(pts, sgdf, returnList=TRUE)
> #over(pts, spixdf, returnList=TRUE)
> 
> proc.time()
   user  system elapsed 
   0.82    0.07    0.89