Basic and extensible post-processing of eddy covariance flux data with REddyProc

With the eddy covariance (EC) technique, net fluxes of carbon dioxide (CO2) and other trace 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 through cross-site analysis, model-data integration, and upscaling. The raw fluxes measured with the EC technique require extensive and laborious data processing. While there are standard tools1 available in an 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 span styleCombining double low line classCombining double low linetext typewriter 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 threshold, as well as 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 span styleCombining double low line classCombining double low linetext typewriter 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 and resulting gap-filled fluxes by 50"‰% with the presented tool were achieved by an improved treatment of seasons during the bootstrap analysis. Higher estimates of uncertainty in daytime partitioning (about twice as high) resulted from a better accounting for the uncertainty in estimates of temperature sensitivity of respiration. The provided routines can be easily installed, configured, and used. Hence, the eddy covariance community will benefit from the span styleCombining double low line classCombining double low linetext typewriterREddyProc/span package, allowing easier integration of standard post-processing with extended analysis.