flux_quality {fluxible} | R Documentation |
assessing quality of slopes calculated with flux_fitting
Description
indicates if slopes should be discarded or replaced by 0 according to quality thresholds set by user
Usage
flux_quality(
slopes_df,
fit_type = c(),
ambient_conc = 421,
error = 100,
fluxid_col = "f_fluxID",
slope_col = "f_slope",
weird_fluxes_id = c(),
force_ok_id = c(),
ratio_threshold = 0,
pvalue_col = "f_pvalue",
rsquared_col = "f_rsquared",
pvalue_threshold = 0.3,
rsquared_threshold = 0.7,
conc_col = "f_conc",
b_col = "f_b",
time_col = "f_time",
fit_col = "f_fit",
cut_col = "f_cut",
rmse_threshold = 25,
cor_threshold = 0.5,
b_threshold = 1,
cut_arg = "cut"
)
Arguments
slopes_df |
dataset containing slopes |
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 |
fluxid_col |
column containing unique IDs for each flux |
slope_col |
column containing the slope of each flux (as calculated by the flux_fitting function) |
weird_fluxes_id |
vector of fluxIDs that should be discarded by the user's decision |
force_ok_id |
vector of fluxIDs for which the user wants to keep the calculated slope despite a bad quality flag |
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 |
pvalue_col |
column containing the p-value of each flux (linear and quadratic fit) |
rsquared_col |
column containing the r squared of each flux (linear and quadratic fit) |
pvalue_threshold |
threshold of p-value below which the change of gas concentration over time is considered not significant (linear and quadratic fit) |
rsquared_threshold |
threshold of r squared value below which the linear model is considered an unsatisfactory fit (linear and quadratic fit) |
conc_col |
column containing the measured gas concentration (exponential fit) |
b_col |
column containing the b parameter of the exponential expression (exponential fit) |
time_col |
column containing the time of each measurement in seconds (exponential fit) |
fit_col |
column containing the modeled data (exponential fit) |
cut_col |
column containing the cutting information |
rmse_threshold |
threshold for the RMSE of each flux above which the fit is considered unsatisfactory (exponential fit) |
cor_threshold |
threshold for the correlation coefficient of gas concentration with time below which the correlation is considered not significant (exponential fit) |
b_threshold |
threshold for the b parameter. Defines a window with its opposite inside which the fit is considered good enough (exponential fit) |
cut_arg |
argument defining that the data point should be cut out |
Value
same dataframe with added quality flags and corrected slope column
Examples
data(slopes0lin)
flux_quality(slopes0lin, fit_type = "li")
data(slopes30)
flux_quality(slopes30, fit_type = "expo", slope_col = "f_slope")