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I am using the method outlined in a previous question - Extracting land cover type in Google Earth Engine? - to identify habitat type and area with a defined polygon. I would now like to take this information from different years to calculate forest cover loss over time. How is this best achieved? I am using google earth engine for this process.

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You can find global forest loss/gain from 2000-2015 in the following raster:

var hansen = ee.Image("UMD/hansen/global_forest_change_2015_v1_3");

How you can use it is explained in this Google Earth Engine tutorial.

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