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Load your shapefiles into R as SpatialPolygonsDataFrame objects - lets call them p1 for the year 2000 and p2 for the year 2010. Drop any rows in p1 with fips codes that aren't in p2 - these would be county fips codes that don't exist any more, so their geometry has changed. Also, drop any rows in p2 that don't have a fips code in p1. These are new fips ...

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