Short answer: you are doing it wrong. The names you are viewing are not in the same order as the polygons in the county database. To do what you want, you should use the following:
map("county") map("county", "arizona,maricopa", col="#ABCABC", fill=T, add=T)

Alternatively, if you really need to map auxiliary values ββusing state,county name, you can do something like the following:
## Get state,county names in the order they will be plotted: c <- map("county", namesonly=T) c1 <- rep("#FFFFFF", length(c)) c1[which(c=="arizona,maricopa")] <- "#FF0000" map("county", col=c1, fill=T)

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