Changelog • fluxible

fluxible 1.2.2

flux_calc:
- chamber_volume and tube_volume are deprecated, use setup_volume instead
- cols_nest = "all" allows to nest all the columns, to keep raw data
flux_match:
- ratio_threshold is deprecated, use ratio_threshold in flux_quality() instead
- f_conc is no longer needed, deprecated
flux_quality: ratio_threshold default value is now 0.5, was 0 previously, which does not make sense

flux_quality: new no_slope quality flag for when the model could not be fitted to the data.
flux_match: startcrop argument is deprecated as flux_fitting(start_cut) has a similar function.

flux_calc
- variables in cols_ave, cols_med and and cols_cum gets suffix added so it is possible to provide a variable to several of those arguments.
- cols_nest: new argument for variable to keep in a nested tibble after flux calculation.

CRAN release: 2025-05-22

flux_flag_count: does not need the cut argument anymore, so it can also be used after calculating fluxes to provide a table with the number of measurements for each quality flag.

CRAN release: 2025-05-13

CRAN release: 2025-04-22

flux_quality: fluxes with bad fit are now flagged as zero if their linear slope is below the minimal detectable slope (calculated as $2 \times \text{instrument error} / \text{length of flux}$ ) instead of discard.

flux_fitting:
- exp_hm to use the HM model (Pedersen et al., 2010; Hutchinson and Mosier, 1981).
- returns the linear slope besides the chosen method.
flux_quality:
- kappamax = TRUE to apply the kappamax method (Hüppi et al., 2018) on any of the exponential fits.
- g-factor in the output shows the ratio of slope over the linear slope.
- force_linear and force_exp to force the use of the linear or exponential slope (kappamax method).
flux_match: option to feed a column with the end time instead of a fixed measurement length, in case fluxes do not all have the same length
flux_calc:
- cols_sum columns for which the values will be summed for each flux.
- cols_med columns for which the median will be provided for each flux.

stupeflux: a wrap function to directly process raw gas concentration data into ecosystem gas fluxes.
flux_fitting: if optim returns non-finite values, the slope is NA and the function does not crash anymore.
flux_fitting: new model exp_tz. Same as exp_zhao18 except the user defines t_zero.

flux_gep: fluxes presents in the dataset that are neither NEE nor ER (soilR, LRC or other) are not lost anymore.

flux_quality: added force_zero argument to force a flux to be replaced by zero.

Error corrected in flux_gep: the columns in the cols_keep argument are filled for GEP flux with values from NEE flux, and NA if missing, but not values from ER fluxes.

flux_gep allows to keep all columns without naming them.
Order of columns in the output of flux_match is more logical (f_start before f_end…).

Vignettes temporarily back in Rmd until quarto_render bug is fixed (https://github.com/r-lib/pkgdown/issues/2830)

Added a vignette describing how to prepare the data for fluxible.
flux_plot now adds a vertical line showing where t_zero is.
‘flux_plot’: scale_x_datetime arguments are now past as a list.
Functions now recycle user’s column names instead of renaming them. Columns created by fluxible functions have the suffix ‘f_’.

Correction in flux_quality: ‘zero’ and ‘discard’ flags were inverted when using the linear fit.

All plots are colored the same (colors code for raw concentration data points and fit and slope in black).
Legend for line types in plots.
Plot subtitles indicating the fit type.

flux_calc allows to choose units.
flux_calc alows plot area as a variable.
flux_fitting with exponential model works when concentration data are missing in the middle of the measurement.