indicates if slopes should be discarded or replaced by 0 according to quality thresholds set by user
Usage
flux_quality(
slopes_df,
conc_col,
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,
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
- conc_col
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_dfwas 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
TRUEthe kappamax method will be applied.
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
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.
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")
#> Cutting measurements...
#> Estimating starting parameters for optimization...
#> Optimizing fitting parameters...
#> Calculating fits and slopes...
#> Done.
#> Warning:
#> fluxID 5 : slope was estimated on 205 points out of 210 seconds
#> fluxID 6 : slope was estimated on 206 points out of 210 seconds
flux_quality(slopes, conc)
#>
#> Total number of measurements: 6
#>
#> discard 2 33 %
#> ok 3 50 %
#> zero 1 17 %
#> force_discard 0 0 %
#> start_error 0 0 %
#> no_data 0 0 %
#> force_ok 0 0 %
#> force_zero 0 0 %
#> force_lm 0 0 %
#> # A tibble: 1,251 × 35
#> datetime temp_air temp_soil conc PAR turfID type
#> <dttm> <dbl> <dbl> <dbl> <dbl> <fct> <fct>
#> 1 2022-07-28 23:43:35 NA NA 447. NA 156 AN2C 156 ER
#> 2 2022-07-28 23:43:36 7.22 10.9 447. 1.68 156 AN2C 156 ER
#> 3 2022-07-28 23:43:37 NA NA 448. NA 156 AN2C 156 ER
#> 4 2022-07-28 23:43:38 NA NA 449. NA 156 AN2C 156 ER
#> 5 2022-07-28 23:43:39 NA NA 449. NA 156 AN2C 156 ER
#> 6 2022-07-28 23:43:40 NA NA 450. NA 156 AN2C 156 ER
#> 7 2022-07-28 23:43:41 NA NA 451. NA 156 AN2C 156 ER
#> 8 2022-07-28 23:43:42 NA NA 451. NA 156 AN2C 156 ER
#> 9 2022-07-28 23:43:43 NA NA 453. NA 156 AN2C 156 ER
#> 10 2022-07-28 23:43:44 NA NA 453. NA 156 AN2C 156 ER
#> # ℹ 1,241 more rows
#> # ℹ 28 more variables: f_start <dttm>, f_end <dttm>, f_fluxid <fct>,
#> # f_ratio <dbl>, f_flag_match <chr>, f_time <dbl>, f_cut <fct>,
#> # f_rsquared_lm <dbl>, f_adj_rsquared_lm <dbl>, f_slope_lm <dbl>,
#> # f_intercept_lm <dbl>, f_pvalue_lm <dbl>, f_fit_lm <dbl>, f_Cz <dbl>,
#> # f_Cm <dbl>, f_a <dbl>, f_b <dbl>, f_tz <dbl>, f_slope <dbl>, f_fit <dbl>,
#> # f_fit_slope <dbl>, f_start_z <dttm>, f_min_slope <dbl>, f_cor_coef <dbl>, …