For running, you should go by weight and distance, not time or heart rate.
http://www.runnersworld.com/article/...0-1069,00.html
In fact, you can reverse the calculations on fitday to see that they are about the same as the ones on this calculator.
To do what you propose, you would need a heart rate monitor that had calorie count built in, since the rate is constantly changing.
That being said, this method would not be accurate for many activities that are not purely aerobic activities. Weight training comes to mind. The calories burned by muscle repair in the days after lifting are far more than those burned during the lifting itself.
There's really no way to get to a truly accurate number. You can get close enough to your maintance level, then add or subtract a decent amount to lose or gain weight. After that, you just have to track your progress and adjust accordingly.
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