DOI: 10.5281/zenodo.7307446
title: Eddy covariance SAFE Flux Tower

description: <strong>Description: </strong> The eddy covariance technique was used to record continuous, non-invasive measurements of CO2, H2O and energy exchange between the ecosystem and the atmosphere. The measuring system consists of a semi-open path infrared gas analyser LI-7200 (LI-COR, USA), and a CSAT3 Sonic Anemometer (Campbell Scientific, USA) at a measuring height of 52 m over a canopy height of ~25 m. Data were recorded at a frequency of 20 Hz that was treated using the post-processing software EddyPro® (v.7.0.6; www.licor.com/eddypro) to compute fluxes for each 30-minute averaging period. To treat the raw fluxes, primary data processing steps were applied, including spike removal (Vickers, 1997 J Atmos Ocean Technol), coordinate rotation, block averaging detrending of CO2, H2O and sonic temperature, time lag compensation using covariance maximisation detection method, random uncertainty estimation (Finkelstein et al. 2001 Journal of Geophysical Research Atmospheres), computation of turbulent fluxes and mean fluxes, spectral corrections (Moncrieff et al. 1997 J Hydrol Amst) using correction of low-pass filtering effects, planar fit rotation (Wilczak et al. 2001 Boundary Layer Meteorol) and quality flagging policy (Göckede et al. 2006 Boundary Layer Meteorol). Eddy covariance meteorological data from above and below canopy is available at DOI 10.5281/zenodo.3888374. Cells with -9999 represent not enough data collected, which can be regarded as NA.<br> <br> This data has been collected over a heavily logged landscape between 2012 - 2018, please note 2016 was removed from this dataset. Before 2015, the landscape was ~10 years recovering from it's previous round of logging (four times logged). During 2015 the landscape was salvaged logged, removing 75% of tree stand basal area.<br> <br> The first data sheet, named "Raw_data" contains all raw fluxes that have been treated by EddyPro, which have not been filtered or quality controlled.<br> <br> The second sheet, named "Daily_fluxes" contains daily mean fluxes of net ecosystem CO2 exchange (NEE), ecosystem respirationn (Reco) and gross primary productivity and their associated standard errors. Net ecosystem CO2 exchange (NEE) was calculated by adding the estimated CO2 storage flux to the observed CO2 flux. Data was subjecto quality control including the removal of quality flags 4 and 5 (Göckede et al. 2006 Boundary Layer Meteorol) and the application of a mean u* threshold of &gt;0.29 m s-1 to the dataset, as established using the package "REddyProc" (v.1.2; (Wultzer et al. 2019 Biogeosciences)) in based on the Moving Point Method (Reichstein et al. 2005, GCB). Data was subsequently gap filled and partitioned, as descripted within the variable methods of this sheet. This data was part of an analysis of carbon fluxes within three periods of data collection: in 2012 – 2013, which captured the four-times logged ecosystem ~10 years after its previous round of logging, in 2015 during a new round of active salvage logging, and in 2017 – 2018 when the ecosystem was recovery 2-3 years after the salvage logging. Days with large standard errors for Reco (&gt; ± 5 µmol m−2 s−1) were deemed as bad quality and removed from the dataset and we used only days that had four or more observed half-hourly values of NEE. Of the final dataset , 29.5% of the half-hourly values are original observed fluxes, and 70.5% gap-filled. Of the 455 days remaining after all filtering processes were applied, 65 days were during the 10-years recovery phase (2012-2013), 100 during the active salvage logging (2015) and 290 during the 2-3 years recovery from active salvage logging phase (2017-2018). <strong>Project: </strong>This dataset was collected as part of the following SAFE research project: <strong>Changing carbon dioxide and water budgets from deforestation and habitat modification</strong> <strong>XML metadata: </strong>GEMINI compliant metadata for this dataset is available here <strong>Files: </strong>This consists of 1 file: SAFE_EC_byYear.xlsx <strong>SAFE_EC_byYear.xlsx</strong> This file contains dataset metadata and 6 data tables: <strong>Raw_data_2012_2013</strong> (described in worksheet Raw_data_2012_2013) Description: EddyPro output of eddy covariance data collected at 52m at the top of the flux tower. Number of fields: 105 Number of data rows: 24213 Fields: <strong>Location</strong>: SAFE flux tower location name, as in the SAFE Gazetteer (Field type: location) <strong>date</strong>: Date of the end of the averaging period (Field type: date) <strong>time</strong>: Time of the end of the averaging period (Field type: time) <strong>DOY</strong>: decimal day of year (Field type: numeric) <strong>daytime</strong>: Daytime or nightime, 1 = daytime, 0 = nighttime (Field type: numeric) <strong>file_records</strong>: Number of valid records found in the raw file (or set of raw files) (Field type: numeric) <strong>used_records</strong>: Number of valid records used for current the averaging period (Field type: numeric) <strong>Tau</strong>: Corrected momentum flux (Field type: numeric) <strong>qc_Tau</strong>: Quality flag for momentum flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_Tau</strong>: Random error for momentum flux, if selected (Field type: numeric) <strong>H</strong>: Corrected sensible heat flux (Field type: numeric) <strong>qc_H</strong>: Quality flag for sensible heat flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_H</strong>: Random error for momentum flux, if selected (Field type: numeric) <strong>LE</strong>: Corrected latent heat flux (Field type: numeric) <strong>qc_LE</strong>: Quality flag of latent heat flux based on Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_LE</strong>: Random error for latent heat flux, if selected (Field type: numeric) <strong>co2_flux</strong>: CO2 flux (Field type: numeric) <strong>qc_co2_flux</strong>: Quality flag for CO2 flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_co2_flux</strong>: Random error of CO2 flux (Field type: numeric) <strong>h2o_flux</strong>: H2O flux (Field type: numeric) <strong>qc_h2o_flux</strong>: Quality flag of H20 flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_h2o_flux</strong>: Random error of CO2 flux (Field type: numeric) <strong>H_strg</strong>: Estimate of storage sensible heat flux (Field type: numeric) <strong>LE_strg</strong>: Estimate of storage latent heat flux (Field type: numeric) <strong>co2_strg</strong>: Estimate of storage CO2 flux (Field type: numeric) <strong>h2o_strg</strong>: Estimate of storage H20 flux (Field type: numeric) <strong>co2_v.adv</strong>: Estimate of vertical advection flux of CO2 (Field type: numeric) <strong>h2o_v.adv</strong>: Estimate of vertical advection flux of H20 (Field type: numeric) <strong>co2_molar_density</strong>: Measured or estimated molar density of gas (Field type: numeric) <strong>co2_mole_fraction</strong>: Measured or estimated mole fraction of gas (Field type: numeric) <strong>co2_mixing_ratio</strong>: Measured or estimated mixing ratio of gas (Field type: numeric) <strong>co2_time_lag</strong>: Time lag used to synchronize gas time series (Field type: numeric) <strong>co2_def_timelag</strong>: Flag: whether the reported time lag is the default (1) or calculated (0) (Field type: numeric) <strong>h2o_molar_density</strong>: Measured or estimated molar density of gas (Field type: numeric) <strong>h2o_mole_fraction</strong>: Measured or estimated mole fraction of gas (Field type: numeric) <strong>h2o_mixing_ratio</strong>: Measured or estimated mixing ratio of gas (Field type: numeric) <strong>h2o_time_lag</strong>: Time lag used to synchronize gas time series (Field type: numeric) <strong>h2o_def_timelag</strong>: Flag: whether the reported time lag is the default (1) or calculated (0) (Field type: numeric) <strong>sonic_temperature</strong>: Mean temperature of ambient air as measured by the anemometer (Field type: numeric) <strong>air_temperature</strong>: Mean temperature of ambient air, either calculated from high frequency air temperature readings, or estimated from sonic temperature (Field type: numeric) <strong>air_pressure</strong>: Mean pressure of ambient air, either calculated from high frequency air pressure readings, or estimated based on site altitude (barometric pressure) (Field type: numeric) <strong>air_density</strong>: Density of ambient air (Field type: numeric) <strong>air_heat_capacity</strong>: Specific heat at constant pressure of ambient air (Field type: numeric) <strong>air_molar_volume</strong>: Molar volume of ambient air (Field type: numeric) <strong>ET</strong>: Evapotranspiration flux (Field type: numeric) <strong>water_vapor_density</strong>: Ambient mass density of water vapor (Field type: numeric) <strong>e</strong>: Ambient water vapor partial pressure (Field type: numeric) <strong>es</strong>: Ambient water vapor partial pressure at saturation (Field type: numeric) <strong>specific_humidity</strong>: Ambient specific humidity on a mass basis (Field type: numeric) <strong>RH</strong>: Ambient relative humidity (Field type: numeric) <strong>VPD</strong>: Ambient water vapor pressure deficit (Field type: numeric) <strong>Tdew</strong>: Ambient dew point temperature (Field type: numeric) <strong>u_unrot</strong>: Wind component along the u anemometer axis (Field type: numeric) <strong>v_unrot</strong>: Wind component along the v anemometer axis (Field type: numeric) <strong>w_unrot</strong>: Wind component along the w anemometer axis (Field type: numeric) <strong>u_rot</strong>: Rotated u wind component (mean wind speed) (Field type: numeric) <strong>v_rot</strong>: Rotated v wind component (should be zero) (Field type: numeric) <strong>w_rot</strong>: Rotated w wind component (should be zero) (Field type: numeric) <strong>wind_speed</strong>: Mean wind speed (Field type: numeric) <strong>max_wind_speed</strong>: Maximum instantaneous wind speed (Field type: numeric) <strong>wind_dir</strong>: Direction from which the wind blows, with respect to Geographic or Magnetic north (Field type: numeric) <strong>yaw</strong>: First rotation angle (Field type: numeric) <strong>pitch</strong>: Second rotation angle (Field type: numeric) <strong>u.</strong>: Friction velocity (Field type: numeric) <strong>TKE</strong>: Turbulent kinetic energy (Field type: numeric) <strong>L</strong>: Monin-Obukhov length (Field type: numeric) <strong>X.z.d..L</strong>: Monin-Obukhov stability parameter - (z-d)/L (Field type: numeric) <strong>bowen_ratio</strong>: Sensible heat flux to latent heat flux ratio (Field type: numeric) <strong>T.</strong>: Scaling temperature (Field type: numeric) <strong>model</strong>: Model for footprint estimation, 1- Kljun et al. (2004): A crosswind integrated parameterization of footprint estimations obtained with a 3D Lagrangian model by means of a scaling procedure.2 - Kormann and Meixner (2001): A crosswind integrated model based on the solution of the two dimensional advection-diffusion equation given by van Ulden (1978) and others for power-law profiles in wind velocity and eddy diffusivity, 3 - Hsieh et al. (2000): A crosswind integrated model based on the former model of Gash (1986) and on simulations with a Lagrangian stochastic model. (Field type: numeric) <strong>x_peak</strong>: Along-wind distance providing &lt;1% contribution to turbulent fluxes (Field type: numeric) <strong>x_offset</strong>: Along-wind distance providing the highest (peak) contribution to turbulent fluxes (Field type: numeric) <strong>x_10.</strong>: Along-wind distance providing 10% (cumulative) contribution to turbulent fluxes (Field type: numeric) <strong>x_30.</strong>: Along-wind distance providing 30% (cumulative) contribution to turbulent fluxes (Field type: numeric) <strong>x_50.</strong>: Along-wind distance providing 50% (cumulative) contribution to turbulent fluxes (Field type: numeric) <strong>x_70.</strong>: Along-wind distance providing 70% (cumulative) contribution to turbulent fluxes (Field type: numeric) <strong>x_90.</strong>: Along-wind distance providing 90% (cumulative) contribution to turbulent fluxes (Field type: numeric) <strong>un_Tau</strong>: Uncorrected momentum flux (Field type: numeric) <strong>Tau_scf</strong>: Spectral correction factor for momentum flux (Field type: numeric) <strong>un_H</strong>: Uncorrected sensible heat flux (Field type: numeric) <strong>H_scf</strong>: Spectral correction factor for sensible heat flux (Field type: numeric) <strong>un_LE</strong>: Uncorrected latent heat flux (Field type: numeric) <strong>LE_scf</strong>: Spectral correction factor for latent heat flux (Field type: numeric) <strong>un_co2_flux</strong>: Uncorrected gas flux (Field type: numeric) <strong>co2_scf</strong>: Spectral correction factor for gas flux (Field type: numeric) <strong>un_h2o_flux</strong>: Uncorrected gas flux (Field type: numeric) <strong>h2o_scf</strong>: Spectral correction factor for gas flux (Field type: numeric) <strong>spikes_hf</strong>: Hard flags for individual variables for spike test (Field type: numeric) <strong>amplitude_resolution_hf</strong>: Hard flags for individual variables for amplitude resolution (Field type: numeric) <strong>drop_out_hf</strong>: Hard flags for individual variables for drop-out test (Field type: numeric) <strong>absolute_limits_hf</strong>: Hard flags for individual variables for absolute limits (Field type: numeric) <strong>skewness_kurtosis_hf</strong>: Hard flags for individual variables for skewness and kurtosis (Field type: numeric) <strong>skewness_kurtosis_sf</strong>: Soft flags for individual variables for skewness and kurtosis test (Field type: numeric) <strong>discontinuities_hf</strong>: Hard flags for individual variables for discontinuities test (Field type: numeric) <strong>discontinuities_sf</strong>: Soft flags for individual variables for discontinuities test (Field type: numeric) <strong>timelag_hf</strong>: Hard flags for gas concentration for time lag test (Field type: numeric) <strong>timelag_sf</strong>: Soft flags for gas concentration for time lag test (Field type: numeric) <strong>attack_angle_hf</strong>: Hard flags for gas concentration for time lag test (Field type: numeric) <strong>non_steady_wind_hf</strong>: Soft flags for gas concentration for time lag test (Field type: numeric) <strong>u_spikes</strong>: Number of spikes detected and eliminated for rotated u wind component (Field type: numeric) <strong>v_spikes</strong>: Number of spikes detected and eliminated forrotated v wind component (Field type: numeric) <strong>w_spikes</strong>: Number of spikes detected and eliminated for rotated w wind component (Field type: numeric) <strong>ts_spikes</strong>: Number of spikes detected and eliminated for ts variable (Field type: numeric) <strong>co2_spikes</strong>: Number of spikes detected and eliminated for co2 variable (Field type: numeric) <strong>h2o_spikes</strong>: Number of spikes detected and eliminated for h2o variable (Field type: numeric) <strong>Raw_data_2014</strong> (described in worksheet Raw_data_2014) Description: EddyPro output of eddy covariance data collected at 52m at the top of the flux tower. There is a significant data gap, with some intermittent records available during the daytime, between 17/2/2014-17/06/2014 due to the problems in the power supply. Number of fields: 105 Number of data rows: 17520 Fields: <strong>Location</strong>: SAFE flux tower location name, as in the SAFE Gazetteer (Field type: location) <strong>date</strong>: Date of the end of the averaging period (Field type: date) <strong>time</strong>: Time of the end of the averaging period (Field type: time) <strong>DOY</strong>: decimal day of year (Field type: numeric) <strong>daytime</strong>: Daytime or nightime, 1 = daytime, 0 = nighttime (Field type: numeric) <strong>file_records</strong>: Number of valid records found in the raw file (or set of raw files) (Field type: numeric) <strong>used_records</strong>: Number of valid records used for current the averaging period (Field type: numeric) <strong>Tau</strong>: Corrected momentum flux (Field type: numeric) <strong>qc_Tau</strong>: Quality flag for momentum flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_Tau</strong>: Random error for momentum flux, if selected (Field type: numeric) <strong>H</strong>: Corrected sensible heat flux (Field type: numeric) <strong>qc_H</strong>: Quality flag for sensible heat flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_H</strong>: Random error for momentum flux, if selected (Field type: numeric) <strong>LE</strong>: Corrected latent heat flux (Field type: numeric) <strong>qc_LE</strong>: Quality flag of latent heat flux based on Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_LE</strong>: Random error for latent heat flux, if selected (Field type: numeric) <strong>co2_flux</strong>: CO2 flux (Field type: numeric) <strong>qc_co2_flux</strong>: Quality flag for CO2 flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best, "5" is worst (Field type: numeric) <strong>rand_err_co2_flux</strong>: Random error of CO2 flux (Field type: numeric) <strong>h2o_flux</strong>: H2O flux (Field type: numeric) <strong>qc_h2o_flux</strong>: Quality flag of H20 flux, Göckede et al., 2006: A system based on 5 quality grades. "0" is best,