Best ways to run an affiliate program for a mobile app?

I have a website design background, and so I understand well how this works on websites. But it seems a bit more convoluted to me when it comes to mobile apps because you have that little intermediary of the app store itself and I have no idea if they have any way to track some kind of affiliate link from an email, through the app store download, and into the app.

Obviously we can simply give out affiliate codes, but they would require the user to actually enter the code in for the affiliate to get credit, whereas with a web app, the tracking ID can be built into the link the affiliates give to their prospects.

Are there any 3rd party tech companies that have solved this problem?

Chris