Package: fluxible 0.0.4

Joseph Gaudard

fluxible: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup

Processes the raw data from closed loop flux chamber (or tent) setups into ecosystem gas fluxes usable for analysis. It goes from a data frame of gas concentration over time (which can contain several measurements) and a meta data file indicating which measurement was done when, to a data frame of ecosystem gas fluxes including quality diagnostics. Functions provided include different models (exponential as described in Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, quadratic and linear) to estimate the fluxes from the raw data, quality assessment, plotting for visual check and calculation of fluxes based on the setup specific parameters (chamber size, plot area, ...).

Authors:Joseph Gaudard [aut, cre], Jonas Trepel [aut], Michael Mustri [aut], Pekka O Niittynen [aut], Paul Efren Santos-Andrade [aut], Richard James Telford [aut]

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fluxible.pdf |fluxible.html
fluxible/json (API)
NEWS

# Install 'fluxible' in R:
install.packages('fluxible', repos = c('https://plant-functional-trait-course.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/plant-functional-trait-course/fluxible/issues

Datasets:

On CRAN:

4.98 score 9 scripts 481 downloads 7 exports 60 dependencies

Last updated 4 days agofrom:338be8ce00. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winNOTENov 19 2024
R-4.5-linuxNOTENov 19 2024
R-4.4-winNOTENov 19 2024
R-4.4-macNOTENov 19 2024
R-4.3-winNOTENov 19 2024
R-4.3-macNOTENov 19 2024

Exports:flux_calcflux_fittingflux_flag_countflux_gepflux_matchflux_plotflux_quality

Dependencies:backportsbitbit64broomclicliprcolorspacecpp11crayondplyrfansifarverforcatsgenericsggforceggplot2gluegtablehavenhmsisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpolyclipprettyunitsprogresspurrrpurrrlyrR6RColorBrewerRcppRcppEigenreadrrlangscalesstringistringrsystemfontstibbletidyrtidyselecttimechangetweenrtzdbutf8vctrsviridisLitevroomwithrzoo

Practical example: from raw gas concentration data to clean ecosystem gas fluxes.

Rendered fromfluxible_practical_example.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-11-19
Started: 2024-08-14

Readme and manuals

Help Manual

Help pageTopics
CO2 concentrationco2_conc
CO2 concentrationco2_conc_missing
CO2 concentration with missing dataco2_df_missing
CO2 concentrationco2_df_short
CO2 fluxesco2_fluxes
CO2 concentration at Liahovdenco2_liahovden
calculates ecosystem gas fluxesflux_calc
check the items inside 'flux_fun_check'flux_check_item
filter cut data before calculating fluxesflux_cut
to check the type of fitflux_fit_type
Fitting a model to concentration data and estimating the slopeflux_fitting
Fitting a model to the gas concentration curve and estimating the slope over time, using the exponential model from Zhao et al (2018)flux_fitting_exp
linear fit to gas concentration over timeflux_fitting_lin
quadratic fit to gas concentration over timeflux_fitting_quadratic
counts quality flagsflux_flag_count
checking that arguments and columns are in the correct classflux_fun_check
Calculates GEPflux_gep
Matching continuously measured fluxes with measurement IDs and meta dataflux_match
prepares text to print for flux_plot functionflux_param_exp
prepares text to print in flux_plotflux_param_lm
plotting fluxes for visual evaluationflux_plot
plotting fluxes with exponential fitflux_plot_exp
creates the flag column to be used by flux_plotflux_plot_flag
plotting fluxes with linear fitflux_plot_lin
plotting fluxes with a quadratic fitflux_plot_quadratic
assessing quality of slopes calculated with flux_fittingflux_quality
quality assessment for the slopes estimated by flux_fittingflux_quality_exp
quality assessment for the slopes estimated by flux_fittingflux_quality_lm
Measurements meta data at Liahovdenrecord_liahovden
Measurements meta datarecord_short
Slopes for each fluxslopes0
Slopes for each fluxslopes0_flag
Slopes for each fluxslopes0_temp
Slopes for each fluxslopes0_vol
Slopes for each fluxslopes0_vol_tube
Slopes for each fluxslopes0lin
Slopes for each fluxslopes0lin_flag
Slopes for each fluxslopes30
Slopes for each fluxslopes30_flag
Slopes for each fluxslopes30lin
Slopes for each fluxslopes30lin_flag
Slopes for each fluxslopes30qua
Slopes for each fluxslopes30qua_flag
Slopes for each fluxslopes60
Slopes for each fluxslopes60lin