Extracting points with polygon in R

Question

I'm trying to extract points by a polygon using the 'sp' package function 'over'

library(sp)
library(rgeos)
#my polygon plgn (many polygon features in one)
plot(plgn)
proj4string(plgn) = CRS("+proj=utm +zone=46 +datum=WGS84 +units=m +no_defs")
#giving spatial reference to point data d
coordinates(d) <- ~X+Y
proj4string(d) = CRS("+proj=utm +zone=46 +datum=WGS84 +units=m +no_defs")
#USE overlay (there are many NAs)
overlay=d[!is.na(over(d, plgn)),]

Unfortunately, I'm getting an ERROR

Error in d[!is.na(over(d, plgn)), ] : 
matrix argument not supported in SpatialPointsDataFrame selection

Any idea?? Is it because my polygon contains 100s of features?

Answer 1

Your plgn is a SpatialPolygonsDataFrame, and as such, is.na(over(d, plgn)) returns a logical matrix. This cannot be used to subset your SpatialPoints*. You can do the following to convert the logical matrix to a vector that the subsetting operation can accommodate:

d[complete.cases(over(d, plgn)), ]