country_and_individuals.over <- over(countryPolygons, individuals.df, returnList = TRUE)
country_and_individuals.df <- ldply(country_and_individuals.over, data.frame)

> head(country_and_individuals.df)
    .id  individual_ID
 1   0   5473277
 2   0   3054526
 3   0   3476794
 4   0   4456345
 5   0   1930378
 6   0   1345628