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Problem 1: The eddy covariance method delivers continuous data sets of mass and energy exchange between ecosystem and atmosphere. However, gaps due to unfavorable micro-meteorological conditions and due to instrument failure are inherent in the data stream. Thus a standardized filling of those gaps is necessary (gap-filling), e.g. to obtain daily, monthly or annually integrated balances.
Problem 2: The eddy covariance method measures the net ecosystem exchange. However, particularly for CO2 exchange a lot more understanding of the ecosystem is gained, when the net flux is partitioned into the main components, gross carbon uptake (GPP) and ecosystem respiration (Reco) (flux-partitioning).
Problem 3: During stable stratification and low turbulent mixing the eddy covariance method faces several problems that introduce bias and uncertainties. These problems primarily happen during night and lead to an underestimation of the night-time flux, i.e. the ecosystem respiration. These problems can be detected via a micro-meteorological quality control that tests if the assumptions of the eddy covariance method are not too strongly violated for a particular half hour (e.g. Foken and Wichura, 1996; http://www.bayceer.uni-bayreuth.de/qaqc/en/forschung/21826/Task122.php). Under circumstances where the necessary information for those tests is not available, a heuristic class of methods is widely accepted that assumes that a treshhold of friction velocity (u*) can be site and season specifically established above that night-time fluxes are considered valid. This threshold is usually established by relating the night-time flux to friction velocity while accounting for temperature as a covariate (u*-filtering).