Statistical uncertainty of eddy covariance CO2 fluxes inferred using a residual bootstrap approach

High-frequency eddy-covariance measurements of net ecosystem CO2 exchange (NEE) with the atmosphere are valuable resources for model parameterization, calibration, and validation. However, uncertainties in measured data, i.e., data gaps and inherent random errors, create problems for researchers attempting to quantify uncertainties in model projections of terrestrial ecosystem carbon cycling. Here, we demonstrate that a model-data fusion method (residual bootstrap) produces defensible annual NEE sums, through mimicking the behavior of random errors, filling missing values, and simulating gap-filling biases. This study estimated annual NEE sums for 53 site-years based on nine eddy-covariance tower sites in the USA, and found that our annual estimates were, in most cases, comparable in magnitude with those obtained from AmeriFlux gap-filled data. Additionally, compared to the AmeriFlux standardized gap-filling, our approach provides better NEE estimates for moderate to longer, and more frequent, data gaps. Annual accumulated uncertainties in NEE at the 95% confidence level were ±30 gC m−2 year−1 for evergreen needleleaf forests; ±60 gC m−2 year−1 for deciduous broadleaf forests; and ±80 gC m−2 year−1 for croplands. The residual bootstrap performed worst when gap length was greater than one month or data exclusion greater than 90% during the growing season, common to other gap-filling techniques. However, this study produced robust results for most site years when monthly data coverage during the growing season is not extremely low. We therefore suggest that the inclusion of NEE uncertainty estimates and better estimation for moderate to longer, and more frequent, data gaps as provided by the residual bootstrap approach can be beneficial for ecosystem model evaluation.