flux_quality: Assessing the quality of the fits

In fluxible: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup

Assessing the quality of the fits

Description

Indicates if the slopes provided by flux_fitting should be discarded or replaced by 0 according to quality thresholds set by user

Usage

flux_quality(
  slopes_df,
  f_conc = f_conc,
  f_fluxid = f_fluxid,
  f_slope = f_slope,
  f_time = f_time,
  f_start = f_start,
  f_end = f_end,
  f_fit = f_fit,
  f_cut = f_cut,
  f_pvalue = f_pvalue,
  f_rsquared = f_rsquared,
  f_slope_lm = f_slope_lm,
  f_fit_lm = f_fit_lm,
  f_b = f_b,
  force_discard = c(),
  force_ok = c(),
  force_zero = c(),
  force_lm = c(),
  force_exp = c(),
  ratio_threshold = 0.5,
  gfactor_threshold = 10,
  fit_type = c(),
  ambient_conc = 421,
  error = 100,
  pvalue_threshold = 0.3,
  rsquared_threshold = 0.7,
  rmse_threshold = 25,
  cor_threshold = 0.5,
  b_threshold = 1,
  cut_arg = "cut",
  instr_error = 5,
  kappamax = FALSE
)

Arguments

slopes_df	dataset containing slopes
f_conc	column containing the measured gas concentration (exponential fits)
f_fluxid	column containing unique IDs for each flux
f_slope	column containing the slope of each flux (as calculated by the flux_fitting function)
f_time	column containing the time of each measurement in seconds (exponential fits)
f_start	column with datetime of the start of the measurement (after cuts)
f_end	column with datetime of the end of the measurement (after cuts)
f_fit	column containing the modeled data (exponential fits)
f_cut	column containing the cutting information
f_pvalue	column containing the p-value of each flux (linear and quadratic fits)
f_rsquared	column containing the r squared of each flux (linear and quadratic fits)
f_slope_lm	column containing the linear slope of each flux (as calculated by the flux_fitting function)
f_fit_lm	column with the fit of the linear model. (as calculated by the flux_fitting function)
f_b	column containing the b parameter of the exponential expression (exponential fits)
force_discard	vector of fluxIDs that should be discarded by the user's decision
force_ok	vector of fluxIDs for which the user wants to keep the calculated slope despite a bad quality flag
force_zero	vector of fluxIDs that should be replaced by zero by the user's decision
force_lm	vector of fluxIDs for which the linear slope should be used by the user's decision
force_exp	vector of fluxIDs for which the exponential slope should be used by the user's decision (kappamax method)
ratio_threshold	ratio of gas concentration data points over length of measurement (in seconds) below which the measurement will be considered as not having enough data points to be considered for calculations
gfactor_threshold	threshold for the g-factor. Defines a window with its opposite outside which the flux will be flagged discard (exponential quadratic fits).
fit_type	model fitted to the data, linear, quadratic or exponential. Will be automatically filled if slopes_df was produced using flux_fitting
ambient_conc	ambient gas concentration in ppm at the site of measurement (used to detect measurement that started with a polluted setup)
error	error of the setup, defines a window outside of which the starting values indicate a polluted setup
pvalue_threshold	threshold of p-value below which the change of gas concentration over time is considered not significant (linear and quadratic fits)
rsquared_threshold	threshold of r squared value below which the linear model is considered an unsatisfactory fit (linear and quadratic fits)
rmse_threshold	threshold for the RMSE of each flux above which the fit is considered unsatisfactory (exponential fits)
cor_threshold	threshold for the correlation coefficient of gas concentration with time below which the correlation is considered not significant (exponential fits)
b_threshold	threshold for the b parameter. Defines a window with its opposite inside which the fit is considered good enough (exponential fits)
cut_arg	argument defining that the data point should be cut out
instr_error	error of the instrument, in the same unit as the gas concentration
kappamax	logical. If TRUE the kappamax method will be applied.

Details

the kappamax method (Hüppi et al., 2018) selects the linear slope if |b| > kappamax, with kappamax = |f_slope_lm / instr_error|. The original kappamax method was applied to the HMR model (Pedersen et al., 2010; Hutchinson and Mosier, 1981), but here it can be applied to any exponential fit.

Value

a dataframe with added columns of quality flags (f_quality_flag), the slope corrected according to the quality flags (f_slope_corr), and any columns present in the input. It will also print a summary of the quality flags. This summary can also be exported as a dataframe using flux_flag_count

References

Pedersen, A.R., Petersen, S.O., Schelde, K., 2010. A comprehensive approach to soil-atmosphere trace-gas flux estimation with static chambers. European Journal of Soil Science 61, 888–902. https://doi.org/10.1111/j.1365-2389.2010.01291.x

Hüppi, R., Felber, R., Krauss, M., Six, J., Leifeld, J., Fuß, R., 2018. Restricting the nonlinearity parameter in soil greenhouse gas flux calculation for more reliable flux estimates. PLOS ONE 13, e0200876. https://doi.org/10.1371/journal.pone.0200876

Hutchinson, G.L., Mosier, A.R., 1981. Improved Soil Cover Method for Field Measurement of Nitrous Oxide Fluxes. Soil Science Society of America Journal 45, 311–316.

Examples

data(co2_conc)
slopes <- flux_fitting(co2_conc, conc, datetime, fit_type = "exp_zhao18")
flux_quality(slopes, conc)

fluxible documentation built on June 25, 2025, 1:08 a.m.