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Hi Argiro,
LEAP is set up to allow a variety of economic and costing modeling approaches, so there is no "right" assumption to use for indigenous cost.
The simplest way to model resource costs would be to use the same value for imports, exports and indigenous production. LEAP has different variables to allow users to model higher levels of complexity where each value would be different.
Resource depletion cost is one method of including indigenous resource costs. If you would like to learn more about this costing methodology, feel free to read the Wikipedia article (linked below) or to search for more detailed resources on your own.
http://en.wikipedia.org/wiki/Depletion_(accounting)
Best,
Tory