I think they could try to estimate digital sales as they receive announcements for various games, like Pay Day 2 selling 80% digital. They will eventually be able to work out a typical % of digital sales for a particular genre, or even franchise. It will add to the inherent inaccuracy of the SW numbers but they are very inaccurate already. So all SW sales should be seen a ballpark figures rather than reliable approximations of reality.
It also makes a mockery of NPD software sales too given they only count disc sales, and I bet the USA is a huge downloading market.
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