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

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dc.contributor.authorGaudard, Josephen
dc.contributor.authorTelford, Richard J.en
dc.contributor.authorChacon-Labella, Juliaen
dc.contributor.authorDawson, Hilary Roseen
dc.contributor.authorEnquist, Brian J.en
dc.contributor.authorTöpper, Joachim P.en
dc.contributor.authorTrepel, Jonasen
dc.contributor.authorVandvik, Vigdisen
dc.contributor.authorBaumane, Martaen
dc.contributor.authorBirkeli, Kristineen
dc.contributor.authorHolle, Mukhlish Jamal Musaen
dc.contributor.authorHupp, Jason R.en
dc.contributor.authorSantos-Andrade, Paul Efrenen
dc.contributor.authorSatriawan, Tin Widyanien
dc.contributor.authorHalbritter, Aud H.en
dc.date.accessioned2026-01-02T09:42:45Z
dc.date.available2026-01-02T09:42:45Z
dc.date.issued2025-09-25en
dc.description.abstract1. 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.  2. 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.  3. 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.  4. 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.en
dc.description.sponsorshipThe fluxible R package is the result of discussions and methodology conceptualization about ecosystem gas fluxes data processing during the Plant Functional Traits Courses (PFTC) 6 and 7, and the ThreeD and INCLINE projects. The ThreeD project was funded by the Research Council of Norway KLIMAFORSK project 287801 (2019–2023). The INCLINE project was funded by FRIMEDBIO project 274712 (2018–2022). The PFTC6 course was funded under the Research Council of Norway projects RECITE INTPART project 274831 (2018–2021), ExperTS INTPART project 287784 (2019–2022) and the Norwegian Centre for International Cooperation in Education (SIU) project TraitTrain HNP-2015/10037 (2016–2018). We also would like to thank Vincent Belde who, as an early user of fluxible during his master thesis, came up with valuable improvement suggestions, and Adam Klimes for his help in analytics and R coding.en
dc.description.statusPeer-revieweden
dc.format.extent9en
dc.identifier.issn2041-210Xen
dc.identifier.otherORCID:/0000-0003-4613-762X/work/195678583en
dc.identifier.scopus105017843627en
dc.identifier.urihttps://hdl.handle.net/1885/733802660
dc.language.isoenen
dc.provenanceThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.en
dc.rights© 2025 The Author(s). en
dc.sourceMethods in Ecology and Evolutionen
dc.subjectecosystem gas fluxesen
dc.subjectflux chambersen
dc.subjectgreenhouse gas emissionsen
dc.subjectR packageen
dc.subjectreproducible workflowen
dc.titlefluxible: An R package to process ecosystem gas fluxes from closed-loop chambers in an automated and reproducible wayen
dc.typeJournal articleen
dspace.entity.typePublicationen
local.contributor.affiliationGaudard, Joseph; University of Bergenen
local.contributor.affiliationTelford, Richard J.; University of Bergenen
local.contributor.affiliationChacon-Labella, Julia; Universidad Autónoma de Madriden
local.contributor.affiliationDawson, Hilary Rose; Division of Ecology and Evolution, Research School of Biology, ANU College of Science and Medicine, The Australian National Universityen
local.contributor.affiliationEnquist, Brian J.; University of Arizonaen
local.contributor.affiliationTöpper, Joachim P.; Norwegian Institute for Nature Researchen
local.contributor.affiliationTrepel, Jonas; Aarhus Universityen
local.contributor.affiliationVandvik, Vigdis; University of Bergenen
local.contributor.affiliationBaumane, Marta; University of Copenhagenen
local.contributor.affiliationBirkeli, Kristine; University of Bergenen
local.contributor.affiliationHolle, Mukhlish Jamal Musa; Gadjah Mada Universityen
local.contributor.affiliationHupp, Jason R.; LI-CORen
local.contributor.affiliationSantos-Andrade, Paul Efren; Universidad Nacional San Antonio Abad del Cuscoen
local.contributor.affiliationSatriawan, Tin Widyani; National University of Singaporeen
local.contributor.affiliationHalbritter, Aud H.; University of Bergenen
local.identifier.citationvolume16en
local.identifier.doi10.1111/2041-210X.70161en
local.identifier.pure95dd4b32-a25a-452f-8194-cac137395a94en
local.identifier.urlhttps://www.scopus.com/pages/publications/105017843627en
local.type.statusE-pub ahead of printen

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