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Why does that cartograph of yours blow up states entirely blue that were in fact very closely divided and in many cases only tipped to the blue side because of one or several large cities?
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I don't know, probably for the same reason your map colors states with very close counts entirely red. Why would whether or not the votes came from "one or several large cities" matter? (Not trying to be confrontational, but I'm not sure what you're getting at here.)
I included the source of the map, read it for yourself if you have any questions as to its methodology. (I did.)
FWIW the 2004 presidential election had the smallest percentage margin of victory--2.5%--of any sitting president ever. (
Wikipedia page on the 2004 presidential election)