Question: Does COMET Farm take into account the removal of diseased or dead trees within an orchard. 


Yes, this is taken into account when Orchard/Vineyard crop is selected. Then the user has the option to select "Did you renew?" If this is selected, the model assumes this event occurred in January and that every plant within the marked field was included. So, if this event did not occur on the whole field, it would be recommended to subdivide the field into their own sections.