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Abstract

With the eddy-covariance (EC) technique, net fluxes of carbon dioxide (CO2) and other greenhouse gases as well as water and energy fluxes can be measured at the ecosystem level. These flux measurements are a main source for understanding biosphere-atmosphere interactions and feedbacks by cross-site analysis, model-data integration, and up-scaling. The raw fluxes measured with the EC technique require an extensive and laborious data processing. While there are standard tools available in open source environment for processing high-frequency (10 or 20 Hz) data into half-hourly quality checked fluxes, there is a need for more usable and extensible tools for the subsequent post-processing steps. We tackled this need by developing the REddyProc package in the cross-platform language R that provides standard CO2-focused post-processing routines for reading (half-)hourly data from different formats, estimating the uStar threshold, gap-filling, flux-partitioning, and visualizing the results. In addition to basic processing, the functions are extensible and allow easier integration in extended analysis than current tools. New features include cross year processing and a better treatment of uncertainties. A comparison of REddyProc routines with other state-of the art tools resulted in no significant differences in monthly and annual fluxes across sites. Lower uncertainty estimates of both uStar and resulting gap-filled fluxes with the presented tool was achieved by an improved treatment of seasons during the bootstrap analysis. Higher estimates of uncertainty in day-time partitioning resulted from a better accounting of the uncertainty in estimates of temperature sensitivity of respiration. The provided routines can be easily installed, configured, used, and integrated with further analysis. Hence the eddy covariance community will benefit from using the provided package, allowing easier integration of standard post-processing with extended analysis.