README.md

In grahamstewart12/tidyflux:

tidyflux

This package is an experiment in streamlining and simplifying post-processing of eddy covariance data, while retaining the sophistication necessary for site-specific considerations. Additionally, it aims to conform with tidyverse norms and seamlessly integrate with many popular tidyverse functions/workflows. Many tidyflux functions are adapted from the variety of existing open-source eddy covariance processing programs and R packages; thus, tidyflux attempts to aggregate disparate and potentially non-compatable tools into one framework.

Quality control strategy: 1. Flags are created using package functions and entered as columns in a dedicated qc data frame. 2. Parameters (e.g. thresholds) used in defining flags are saved as attributes of the corresponding flag. 3. Composite flags for each flux variable are created by combining flags for both the variable and its dependents. 4. Composite flags are applied to create a new column for each "cleaned" flux variable in the original data frame. 5. Plots and summaries are generated to document implementation and effect of the custom qc procedure on the data.

Variable names are automatically converted in tidyflux to simplified character strings in order to streamline data processing scripts. The original column names found in the imported data file are saved as varnames attributes and can be easily accessed for reference using str(). The following variable naming conventions are used: All names are in lowercase (e.g. nee, rh) Qualifiers and suffixes are separated by underscores (e.g. t_air, co2_sd) Suffixes are used only in cases when there are multiple versions of a variable or when distinctions must be made between multiple similar variables (e.g. fco2_st, fco2_ad) Mixing ratios are indicated by the name of the gas (e.g. co2, ch4) All quality control flags begin with "qc" (e.g. qc_le) Quality control flags are formatted as "qc_x_y", where x is the flagged variable and y is the indicator of the quality control test Quality control flags that apply to multiple fluxes are indicated by the sensor (e.g. "irga") or by "all" if the flag applies to all fluxes (e.g. qc_irga75_ss, qc_all_pr) Note: "all" does not include momentum flux (tau) All uncertainty estimates begin with "unc" (e.g. unc_h) Uncertainty estimates are formatted as "unc_x_y", where x is the associated variable and y is the source of the uncertainty

Sensor abbreviations: irga75 = LI-7500 infrared gas analyzer (vars: co2, h2o, le, fco2, nee, fh2o) irga77 = LI-7700 infrared gas analyzer (vars: ch4, fch4) * sa = sonic anemometer (vars: u, v, w, ts, h, tau)

Standard suffixes: vadv = vertical advective flux calc = user-calculated ec = derived from fast eddy covariance measurements (used to differentiate the same variable measured by both eddy covariance and biomet system) note: "slow" biomet data are considered to be more accurate than fast data f = final (i.e. all processing finished) gf = gap-filled merged = merged with auxilliary data qccor = quality control-corrected (i.e. cleaned) scf = spectral correction factor sphf = high-frequency spikes stcor = storage-corrected sd = standard deviation st = storage flux tlag = time lag un = uncorrected * var = variance

Quality control (qc) flag suffixes: (no suffix) = integrated turbulence & stationarity test (i.e. Foken flag) abslimhf = high-frequency absolute plausability limits abslimlf = low-frequency absolute plausability limits agg = aggregate of some flags comp = composite of all flags cond = probable condensation on sensor fetch = fetch length filter gf = gap-filling inter = flux interdependence mf = missing fraction p = precipitation pot = potential radiation (for rg only) runs = runs of equal value scf = excessive spectral corection sk = skewness/kurtosis sphf = high-frequency spikes splf = low-frequency spikes ss = signal strength ust = ustar threshold resid = residual (for vertical wind speed only)

Uncertainty (unc) suffixes: (no suffix) = random uncertainty agg = aggregate of all uncertainty gf = gap-filling ust = ustar threshold

Comprehensive list of essential variable names: bowen = bowen ratio of heat fluxes ch4 = methane mixing ratio co2 = carbon dioxide mixing ratio er = ecosystem respiration et = evapotranspiration fch4 = methane flux fco2 = carbon dioxide flux (= nee) fh2o = water vapor flux gpp = gross primary production h = sensible heat flux h2o = water vapor mixing ratio l = monin-obhukov length le = latent heat flux nee = net ecosystem exchange (= fco2) pair = air pressure q = specific humidity rssi75 = LI-7500 relative signal strength rssi77 = LI-7700 relative signal strength tdew = dewpoint temperature tau = momentum flux tke = turbulent kenetic energy ts = sonic temperature urot = rotated horizontal wind speed uunrot = unrotated horizontal wind speed ustar = friction velocity vrot = rotated cross wind speed vunrot = unrotated cross wind speed vpd = vapor pressure deficit wrot = rotated vertical wind speed wunrot = unrotated vertical wind speed wd = wind direction ws = wind speed wsmax = maximum wind speed xpeak = peak fetch length x90p = 90% fetch length zeta = monin-obhukov stability parameter

Biomet g = soil heat flux lwin = incoming longwave radiation lwout = outgoing longwave radiation p = precipitation ppfd = photosynthetic photon flux density rg = global radiation rh = relative humidity rn = net radiation swin = incoming shortwave radiation swout = outgoing shortwave radiation swc = soil water content tair = air temperature tsoil = soil temperature twater = water column temperature * wtd = water table depth

Date/time date = Date-formatted date daytime = day/night indicator (0 = night, 1 = day) doy = numeric timestamp as decimal day of the year hour = decimal hour of the day time = hours and minutes from timestamp timestamp = POSIX-formatted timestamp (end of averaging period)

grahamstewart12/tidyflux documentation built on June 4, 2019, 7:44 a.m.