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Thefluxible R package is made to transform any dataset of gasconcentration over time measured with closed loop chamber systems into agas flux dataset.

Thanks to its flexibility, it works for all kinds of field setup (manualor automated chambers, tents, soil respiration chambers, …) and datacollection strategies (separated files for each measurement vscontinuous logging, variable vs constant chamber volume, variable vsconstant measurement length, …). It is organized as a toolbox with onefunction per steps, which offers a lot of freedom and backwardscompatibility for ongoing projects. If environmental data were recordedsimultaneously (photosynthetically active radiation, soil temperature,…), they can also be processed (mean, sum or median), with the samefocus window as the flux estimate.

The goal offluxible is to provide a workflow that removes individualevaluation of each flux, reduces risk of bias, and makes itreproducible. Users set specific data quality standards and selectionparameters as function arguments that are applied to the entire dataset.fluxible offers different methods to estimate fluxes: linear,quadratic, exponential (Zhaoet al., 2018), and the original HM model(Hutchinson and Mosier, 1981; Pedersenet al., 2010). The kappamaxmethod (Hüppiet al., 2018) is also included, at the quality controlstep. The package runs the calculations automatically, without promptingthe user to take decisions mid-way, and provides quality flags and plotsat the end of the process for a visual check.

This makes it easy to use with large flux datasets and to integrate intoa reproducible and automated data processing pipeline such as thetargets R package (Landau,2021). Using thefluxible Rpackage makes the workflow reproducible, increases compatibility acrossstudies, and is more time efficient.

For a visual overview of the package, seetheposter.

fluxible can be installed from CRAN.

install.packages("fluxible")

You can install the development version offluxible from theGitHubrepo with:

# install.packages("devtools")devtools::install_github("plant-functional-trait-course/fluxible")

library(fluxible)conc_df<- flux_match(co2_df_short,record_short,datetime,start,measurement_length=220)slopes_df<- flux_fitting(conc_df,conc,datetime,fit_type="exp_zhao18",end_cut=60)#> Cutting measurements...#> Estimating starting parameters for optimization...#> Optimizing fitting parameters...#> Calculating fits and slopes...#> Done.slopes_flag_df<- flux_quality(slopes_df,conc)#>#>  Total number of measurements: 6#>#>  ok   6   100 %#>  discard      0   0 %#>  zero     0   0 %#>  force_discard    0   0 %#>  start_error      0   0 %#>  no_data      0   0 %#>  force_ok     0   0 %#>  force_zero   0   0 %#>  force_lm     0   0 %#>  no_slope     0   0 %flux_plot(slopes_flag_df,conc,datetime,f_ylim_lower=390,f_ylim_upper=650,facet_wrap_args=list(ncol=3,nrow=2,scales="free"  ))#> Plotting in progress

Output of flux_plot, showing fluxes plotted individually withdiagnostics and quality flags.

fluxes_df<- flux_calc(slopes_flag_df,f_slope_corr,datetime,temp_air,conc_unit="ppm",flux_unit="mmol/m2/h",cols_keep= c("turfID","type"),cols_ave= c("temp_soil","PAR"),setup_volume=24.575,atm_pressure=1,plot_area=0.0625)#> Cutting data according to 'keep_arg'...#> Averaging air temperature for each flux...#> Creating a df with the columns from 'cols_keep' argument...#> Creating a df with the columns from 'cols_ave' argument...#> Calculating fluxes...#> R constant set to 0.082057 L * atm * K^-1 * mol^-1#> Concentration was measured in ppm#> Fluxes are in mmol/m2/hfluxes_gpp<- flux_gpp(fluxes_df,type,datetime,id_cols="turfID",cols_keep= c("temp_soil_ave"))#> Warning in flux_gpp(fluxes_df, type, datetime, id_cols = "turfID", cols_keep = c("temp_soil_ave")):#>  NEE missing for measurement turfID: 156 AN2C 156fluxes_gpp#> # A tibble: 9 × 5#>   datetime            type  f_flux temp_soil_ave turfID#>   <dttm>              <chr>  <dbl>         <dbl> <chr>#> 1 2022-07-28 23:43:25 ER     51.9           10.9 156 AN2C 156#> 2 2022-07-28 23:47:12 GPP     9.72          10.7 74 WN2C 155#> 3 2022-07-28 23:47:12 NEE    32.0           10.7 74 WN2C 155#> 4 2022-07-28 23:52:00 ER     22.3           10.7 74 WN2C 155#> 5 2022-07-28 23:59:22 GPP    -6.63          10.8 109 AN3C 109#> 6 2022-07-28 23:59:22 NEE    44.3           10.8 109 AN3C 109#> 7 2022-07-29 00:03:00 ER     50.9           10.5 109 AN3C 109#> 8 2022-07-29 00:06:25 GPP    NA             12.2 29 WN3C 106#> 9 2022-07-29 00:06:25 NEE    32.7           12.2 29 WN3C 106

Thelicoread Rpackage, developed incollaboration withLI-COR, provides an easyway to import raw files from LI-COR gas analyzers as R objects that canbe used directly with thefluxible R package.

We are working on a tool to automatically select the window of themeasurement on which to fit a model. This selection will be based onenvironmental variable, such as photosynthetically active radiation(PAR), or residuals.

So farfluxible works in fractional concentration (e. g. ppm) andtransforms it in mol when calculating the fluxes, using the averagetemperature of the measurement. This has the advantage to work even ifthe setup does not provide temperature for each gas concentration datapoint. Recent setups provide temperature at the same frequency as gasconcentration, and this allows to transform the concentration inmol/volume earlier in the process, accounting better for temperaturechanges during the measurement. This will be implemented in a futureversion offluxible.

Joseph Gaudard, Universityof Bergen, Norway

joseph.gaudard@pm.me

GitHub page

Gaudard J, Telford RJ, Chacon-Labella J, Dawson HR, Enquist BJ, TöpperJP, Trepel J, Vandvik V, Baumane M, Birkeli K, Holle MJM, Hupp JR,Santos-Andrade PE, Satriawan TW, Halbritter AH. “fluxible: An Rpackage to process ecosystem gas fluxes from closed-loop chambers in anautomated and reproducible way” (2025).Methods in Ecology andEvolution,doi:10.1111/2041-210X.70161.

Gaudard J, Telford RJ, Chacon-Labella J, Dawson HR,Enquist BJ,Töpper JP, Trepel J, Vandvik V, Baumane M, Birkeli K, Holle MJM, HuppJR, Santos-Andrade PE, Satriawan TW, Halbritter AH. “fluxible: An Rpackage to process ecosystem gas fluxes from closed-loop chambers in anautomated and reproducible way”, Poster, 2025 AmeriFlux Annual Meeting,Tucson AZ, USA.

Gaudard J, Telford RJ, Chacon-Labella J, Dawson HR, Enquist BJ, TöpperJP, Trepel J,Vandvik V, Baumane M, Birkeli K, Holle MJM, Hupp JR,Santos-Andrade PE, Satriawan TW, Halbritter AH. “fluxible: An Rpackage to process ecosystem gas fluxes from closed-loop chambers in anautomated and reproducible way”, Poster, ITEX Meeting 2025, Göteborg,Sweden.

Gaudard J, Trepel J, Dawson HR, Enquist B, Halbritter AH, Mustri M,Niittynen P, Santos-Andrade PE, Töpper JP, Vandvik V, and Telford RJ.“fluxible: an R package to calculate ecosystem gas fluxes from closedloop chamber systems in a reproducible and automated workflow”, Oralpresentation, EGU General Assembly 2025, Vienna, Austria, 27 Apr-2 May2025, EGU25-12409,doi:10.5194/egusphere-egu25-12409.

Gaudard J, Dawson HR, Enquist B, Halbritter AH, Mustri M, NiittynenP, Santos-Andrade PE, Töpper JP, Trepel J, Vandvik V, and Telford RJ.“fluxible: an R package to calculate ecosystem gas fluxes from closedloop chamber systems in a reproducible and automated workflow”, Poster,LI-COR Connect 2025, Tucson AZ, USA, 24-27 Feb 2025.

Gaudard J, Telford R, Vandvik V, and Halbritter AH: “fluxible: anR package to calculate ecosystem gas fluxes in a reproducible andautomated workflow”, Poster, EGU General Assembly 2024, Vienna, Austria,14-19 Apr 2024, EGU24-956,doi:10.5194/egusphere-egu24-956.

fluxible builds on the earlier effort from the Plant Functional TraitsCourse Communityco2fluxtent (Brummeret al.,2023).