About AGL:
With Football Outsiders' Adjusted Games Lost (AGL) metric, we are able to quantify how much teams were affected by injuries based on two principles: (1) Injuries to starters, injury replacements and important situational reserves matter more than injuries to bench warmers; and (2) Injured players who do take the field are usually playing with reduced ability, which is why Adjusted Games Lost is based not strictly on whether the player is active for the game or not, but instead is based on the player's listed status that week (IR/PUP, out, doubtful, questionable or probable).
As long as NFL teams are solely responsible for producing weekly injury reports, we cannot say that every single injury has been accounted for, but secrecy is an unavoidable aspect of this side of the game.
FO's 2013 AGL report: http://www.footballoutsiders.com/stat-analysis/2014/2013-adjusted-games-lost
2014: http://www.footballoutsiders.com/stat-analysis/2015/2014-adjusted-games-lost