fluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way

Joseph Gaudard; Richard J. Telford; Julia Chacon-Labella; Hilary Rose Dawson; Brian J. Enquist; Joachim P. Töpper; Jonas Trepel; Vigdis Vandvik; Marta Baumane; Kristine Birkeli; Mukhlish Jamal Musa Holle; Jason R. Hupp; Paul Efren Santos-Andrade; Tin Widyani Satriawan; Aud H. Halbritter

doi:10.1111/2041-210X.70161

fluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way

Joseph Gaudard^*, Richard J. Telford, Julia Chacon-Labella, Hilary Rose Dawson, Brian J. Enquist, Joachim P. Töpper, Jonas Trepel, Vigdis Vandvik, Marta Baumane, Kristine Birkeli, Mukhlish Jamal Musa Holle, Jason R. Hupp, Paul Efren Santos-Andrade, Tin Widyani Satriawan, Aud H. Halbritter

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

Abstract

Measuring ecosystem gas fluxes is crucial to understanding the dynamics of ecosystem water and energy cycling. A common method to measure ecosystem gas fluxes (CO₂, CH₄, N₂O) and to compare experimental treatments is the use of closed-loop chambers. However, the output data require extensive processing before analysis, making the workflow prone to bias and limiting comparability between studies. While there are various methods to process flux data, they lack reproducibility and automation. The fluxible R package provides a reproducible way to process raw gas concentration data from closed-loop chambers into an analysis-ready dataset of ecosystem gas fluxes. The processing steps include (1) separating the measurements, (2) fitting a linear, quadratic, or exponential model, (3) assessing the quality of the fit, (4) plotting the fluxes for visual inspection and (5) calculating the fluxes. In addition to reproducibility, fluxible focuses on homogeneity and automation in data processing, thus reducing the time investment for users while improving comparability across studies.

Originalsprog	Engelsk
Tidsskrift	Methods in Ecology and Evolution
Vol/bind	16
Nummer	11
Sider (fra-til)	2560-2568
Antal sider	9
ISSN	2041-210X
DOI	https://doi.org/10.1111/2041-210X.70161
Status	Udgivet - nov. 2025

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10.1111/2041-210X.70161Licens: CC BY

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Gaudard, J., Telford, R. J., Chacon-Labella, J., Dawson, H. R., Enquist, B. J., Töpper, J. P., Trepel, J., Vandvik, V., Baumane, M., Birkeli, K., Holle, M. J. M., Hupp, J. R., Santos-Andrade, P. E., Satriawan, T. W., & Halbritter, A. H. (2025). fluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way. Methods in Ecology and Evolution, 16(11), 2560-2568. https://doi.org/10.1111/2041-210X.70161

@article{13bc2199c9de41de8248a59efc087053,

title = "fluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way",

abstract = "Measuring ecosystem gas fluxes is crucial to understanding the dynamics of ecosystem water and energy cycling. A common method to measure ecosystem gas fluxes (CO2, CH4, N2O) and to compare experimental treatments is the use of closed-loop chambers. However, the output data require extensive processing before analysis, making the workflow prone to bias and limiting comparability between studies. While there are various methods to process flux data, they lack reproducibility and automation. The fluxible R package provides a reproducible way to process raw gas concentration data from closed-loop chambers into an analysis-ready dataset of ecosystem gas fluxes. The processing steps include (1) separating the measurements, (2) fitting a linear, quadratic, or exponential model, (3) assessing the quality of the fit, (4) plotting the fluxes for visual inspection and (5) calculating the fluxes. In addition to reproducibility, fluxible focuses on homogeneity and automation in data processing, thus reducing the time investment for users while improving comparability across studies.",

keywords = "ecosystem gas fluxes, flux chambers, greenhouse gas emissions, R package, reproducible workflow",

author = "Joseph Gaudard and Telford, \{Richard J.\} and Julia Chacon-Labella and Dawson, \{Hilary Rose\} and Enquist, \{Brian J.\} and T{\"o}pper, \{Joachim P.\} and Jonas Trepel and Vigdis Vandvik and Marta Baumane and Kristine Birkeli and Holle, \{Mukhlish Jamal Musa\} and Hupp, \{Jason R.\} and Santos-Andrade, \{Paul Efren\} and Satriawan, \{Tin Widyani\} and Halbritter, \{Aud H.\}",

year = "2025",

month = nov,

doi = "10.1111/2041-210X.70161",

language = "English",

volume = "16",

pages = "2560--2568",

journal = "Methods in Ecology and Evolution",

issn = "2041-210X",

publisher = "John Wiley \& Sons Inc.",

number = "11",

}

Gaudard, J, Telford, RJ, Chacon-Labella, J, Dawson, HR, Enquist, BJ, Töpper, JP, Trepel, J, Vandvik, V, Baumane, M, Birkeli, K, Holle, MJM, Hupp, JR, Santos-Andrade, PE, Satriawan, TW & Halbritter, AH 2025, 'fluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way', Methods in Ecology and Evolution, bind 16, nr. 11, s. 2560-2568. https://doi.org/10.1111/2041-210X.70161

fluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way. / Gaudard, Joseph; Telford, Richard J.; Chacon-Labella, Julia et al.
I: Methods in Ecology and Evolution, Bind 16, Nr. 11, 11.2025, s. 2560-2568.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

TY - JOUR

T1 - fluxible

T2 - An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way

AU - Gaudard, Joseph

AU - Telford, Richard J.

AU - Chacon-Labella, Julia

AU - Dawson, Hilary Rose

AU - Enquist, Brian J.

AU - Töpper, Joachim P.

AU - Trepel, Jonas

AU - Vandvik, Vigdis

AU - Baumane, Marta

AU - Birkeli, Kristine

AU - Holle, Mukhlish Jamal Musa

AU - Hupp, Jason R.

AU - Santos-Andrade, Paul Efren

AU - Satriawan, Tin Widyani

AU - Halbritter, Aud H.

PY - 2025/11

Y1 - 2025/11

N2 - Measuring ecosystem gas fluxes is crucial to understanding the dynamics of ecosystem water and energy cycling. A common method to measure ecosystem gas fluxes (CO2, CH4, N2O) and to compare experimental treatments is the use of closed-loop chambers. However, the output data require extensive processing before analysis, making the workflow prone to bias and limiting comparability between studies. While there are various methods to process flux data, they lack reproducibility and automation. The fluxible R package provides a reproducible way to process raw gas concentration data from closed-loop chambers into an analysis-ready dataset of ecosystem gas fluxes. The processing steps include (1) separating the measurements, (2) fitting a linear, quadratic, or exponential model, (3) assessing the quality of the fit, (4) plotting the fluxes for visual inspection and (5) calculating the fluxes. In addition to reproducibility, fluxible focuses on homogeneity and automation in data processing, thus reducing the time investment for users while improving comparability across studies.

AB - Measuring ecosystem gas fluxes is crucial to understanding the dynamics of ecosystem water and energy cycling. A common method to measure ecosystem gas fluxes (CO2, CH4, N2O) and to compare experimental treatments is the use of closed-loop chambers. However, the output data require extensive processing before analysis, making the workflow prone to bias and limiting comparability between studies. While there are various methods to process flux data, they lack reproducibility and automation. The fluxible R package provides a reproducible way to process raw gas concentration data from closed-loop chambers into an analysis-ready dataset of ecosystem gas fluxes. The processing steps include (1) separating the measurements, (2) fitting a linear, quadratic, or exponential model, (3) assessing the quality of the fit, (4) plotting the fluxes for visual inspection and (5) calculating the fluxes. In addition to reproducibility, fluxible focuses on homogeneity and automation in data processing, thus reducing the time investment for users while improving comparability across studies.

KW - ecosystem gas fluxes

KW - flux chambers

KW - greenhouse gas emissions

KW - R package

KW - reproducible workflow

UR - https://www.scopus.com/pages/publications/105017843627

U2 - 10.1111/2041-210X.70161

DO - 10.1111/2041-210X.70161

M3 - Journal article

AN - SCOPUS:105017843627

SN - 2041-210X

VL - 16

SP - 2560

EP - 2568

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

IS - 11

ER -

fluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible way

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