Can you query points with a polygon?

Hello Kenneth

In the sp package you find the function "point.in.polygon".
  

Yes, and a convenient wrapper method, called "overlay" which basically 
overlays a polygon coverage (SpatialPolygonsDataFrame) with a point 
coverage (SpatialPointsDataFrame). Try

 > library(sp)
 > ?overlay
 > methods?overlay

--
Edzer