This is the flowchart describing how the calculation is done on the Endomondo website. Note: This is not how the calories are calculated on the app. Calories on the app use a simpler formula.
Aha! I noticed this too- my app result shows yesterday's cycling workout burned 598 cal, and the website shows 597 cal. For Thursday's run, the app shows 743 cal, but the website shows 810 cal. Very strange. So why such the huge difference between running with the app and the website, but basically no difference at at for the cycling workout? Very strange. This looks like it needs more digging. More info to come...
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