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Planar index #76
No we don't, this is "future-proofing". The GEOS STRTree is used a little in rgeos (could be more, but prepared geometries aren't predicate-ready), but only easily searches for intersecting envelopes, which don't work for points. We know too little yet about vector tiling, but indexing seems to be needed for that. GPKG has RTree Spatial Indexes extensions, I guess others will be close soon. I can't predict where this is going, but if spatial is big, then indices will be part of the solution.
added a commit
Jun 22, 2017
The current implementation computes indexes on the fly for most binary operations, and discards them afterwards; see http://r-spatial.org/r/2017/06/22/spatial-index.html