Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands

Jeremy Irvin; Sharon Zhou; Gavin McNicol; Fred Lu; Vincent Liu; Etienne Fluet-Chouinard; Zutao Ouyang; Sara Helen Knox; Antje Lucas-Moffat; Carlo Trotta; Dario Papale; Domenico Vitale; Ivan Mammarella; Pavel Alekseychik; Mika Aurela; Anand Avati; Dennis Baldocchi; Sheel Bansal; Gil Bohrer; David I Campbell; Jiquan Chen; Housen Chu; Higo J Dalmagro; Kyle B Delwiche; Ankur R Desai; Eugenie Euskirchen; Sarah Feron; Mathias Goeckede; Martin Heimann; Manuel Helbig; Carole Helfter; Kyle S Hemes; Takashi Hirano; Hiroki Iwata; Gerald Jurasinski; Aram Kalhori; Andrew Kondrich; Derrick YF Lai; Annalea Lohila; Avni Malhotra; Lutz Merbold; Bhaskar Mitra; Andrew Ng; Mats B Nilsson; Asko Noormets; Matthias Peichl; A. Camilo Rey-Sanchez; Andrew D Richardson; Benjamin RK Runkle; Karina VR Schäfer; Oliver Sonnentag; Ellen Stuart-Haëntjens; Cove Sturtevant; Masahito Ueyama; Alex C Valach; Rodrigo Vargas; George L Vourlitis; Eric J Ward; Guan Xhuan Wong; Donatella Zona; Ma. Carmelita R Alberto; David P Billesbach; Gerardo Celis; Han Dolman; Thomas Friborg; Kathrin Fuchs; Sébastien Gogo; Mangaliso J Gondwe; Jordan P Goodrich; Pia Gottschalk; Lukas Hörtnagl; Adrien Jacotot; Franziska Koebsch; Kuno Kasak; Regine Maier; Timothy H Morin; Eiko Nemitz; Walter C Oechel; Patricia Y Oikawa; Keisuke Ono; Torsten Sachs; Ayaka Sakabe; Edward A Schuur; Robert Shortt; Ryan C Sullivan; Daphne J Szutu; Eeva-Stiina Tuittila; Andrej Varlagin; Joeseph G Verfaillie; Christian Wille; Lisamarie Windham-Myers; Benjamin Poulter; Robert B Jackson; Sveriges lantbruksuniversitet

doi:10.1016/j.agrformet.2021.108528

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Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands

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Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands

Jeremy Irvin, Sharon Zhou, Gavin McNicol, Fred Lu, Vincent Liu, Etienne Fluet-Chouinard, Zutao Ouyang, Sara Helen Knox, Antje Lucas-Moffat, Carlo Trotta, …

Agricultural and forest meteorology, Vol.308-309, p.108528

10/15/2021

DOI: https://doi.org/10.1016/j.agrformet.2021.108528

Abstract

flux

gap-filling

imputation

Machine learning

methane

time series

wetlands

•We evaluate methane flux gap-filling methods across 17 boreal-to-tropical wetlands•New methods for generating realistic artificial gaps and uncertainties are proposed•Decision tree algorithms perform slightly better than neural networks on average•Soil temperature and generic seasonality are the most important predictors•Open-source code is released for gap-filling steps and uncertainty evaluation Time series of wetland methane fluxes measured by eddy covariance require gap-filling to estimate daily, seasonal, and annual emissions. Gap-filling methane fluxes is challenging because of high variability and complex responses to multiple drivers. To date, there is no widely established gap-filling standard for wetland methane fluxes, with regards both to the best model algorithms and predictors. This study synthesizes results of different gap-filling methods systematically applied at 17 wetland sites spanning boreal to tropical regions and including all major wetland classes and two rice paddies. Procedures are proposed for: 1) creating realistic artificial gap scenarios, 2) training and evaluating gap-filling models without overstating performance, and 3) predicting half-hourly methane fluxes and annual emissions with realistic uncertainty estimates. Performance is compared between a conventional method (marginal distribution sampling) and four machine learning algorithms. The conventional method achieved similar median performance as the machine learning models but was worse than the best machine learning models and relatively insensitive to predictor choices. Of the machine learning models, decision tree algorithms performed the best in cross-validation experiments, even with a baseline predictor set, and artificial neural networks showed comparable performance when using all predictors. Soil temperature was frequently the most important predictor whilst water table depth was important at sites with substantial water table fluctuations, highlighting the value of data on wetland soil conditions. Raw gap-filling uncertainties from the machine learning models were underestimated and we propose a method to calibrate uncertainties to observations. The python code for model development, evaluation, and uncertainty estimation is publicly available. This study outlines a modular and robust machine learning workflow and makes recommendations for, and evaluates an improved baseline of, methane gap-filling models that can be implemented in multi-site syntheses or standardized products from regional and global flux networks (e.g., FLUXNET). [Display omitted]

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Title: Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands
Creators - without role: Jeremy Irvin - Department of Computer Science, Stanford University, Stanford, California, USA| Stanford University Department of Computer Science
Sharon Zhou - Department of Computer Science, Stanford University, Stanford, California, USA| Stanford University Department of Computer Science
Gavin McNicol - Department of Earth and Environmental Sciences, University of Illinois at Chicago, Chicago, IL, USA
Fred Lu - Department of Statistics, Stanford University, Stanford, California, USA| Stanford University Department of Statistics
Vincent Liu - Department of Computer Science, Stanford University, Stanford, California, USA| Stanford University Department of Computer Science
Etienne Fluet-Chouinard - Department of Earth System Science, Stanford University, Stanford, California| Stanford University
Zutao Ouyang - Department of Earth System Science, Stanford University, Stanford, California| Stanford University
Sara Helen Knox - Department of Geography, The University of British Columbia, Vancouver, British Columbia, Canada| The University of British Columbia
Antje Lucas-Moffat - German Meteorological Service (DWD), Centre for Agrometeorological Research, 38116 Braunschweig, Germany| German Meteorological Service (DWD), Centre for Agrometeorological Research, 38116 Braunschweig, Germany
Carlo Trotta - euroMediterranean Center on Climate Change CMCC, Lecce, Italy| Euro-Mediterranean Center for Climate Change, Centro Euro-Mediterraneo sui Cambiamenti Climatici
Dario Papale - Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università degli Studi della Tuscia, Largo dell'Universita, Viterbo, Italy; euroMediterranean Center on Climate Change CMCC, Lecce, Italy| Universita degli Studi della Tuscia Dipartimento per la Innovazione nei sistemi Biologici Agroalimentari e Forestali
Domenico Vitale - euroMediterranean Center on Climate Change, Lecce, 73100, Italy| Euro-Mediterranean Center for Climate Change: Centro Euro-Mediterraneo sui Cambiamenti Climatici
Ivan Mammarella - Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki, Finland| University of Helsinki Faculty of Science: Helsingin yliopisto Matemaattis-luonnontieteellinen tiedekunta
Pavel Alekseychik - Natural Resources Institute Finland (LUKE), Helsinki, Finland| Natural Resources Institute Finland: Luonnonvarakeskus
Mika Aurela - Finnish Meteorological Institute, PO Box 501, 00101 Helsinki, Finland| Finnish Meteorological Institute: Ilmatieteen Laitos
Anand Avati - Department of Computer Science, Stanford University, Stanford, California, USA| Stanford University Department of Computer Science
Dennis Baldocchi - Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA| ESPM: University of California Berkeley Department of Environmental Science Policy and Management
Sheel Bansal - U.S. Geological Survey, Northern Prairie Wildlife Research Center, 8711 37th St Southeast, Jamestown, ND 58401 USA| US Geological Survey Northern Prairie Wildlife Research Center
Gil Bohrer - Department of Civil, Environmental & Geodetic Engineering, Ohio State University| The Ohio State University College of Engineering
David I Campbell - School of Science, University of Waikato, Hamilton, New Zealand| University of Waikato School of Science
Jiquan Chen - Department of Geography, Environment, and Spatial Sciences, Michigan State University, East Lansing, MI 48823, USA| Michigan State University Department of Geography: Michigan State University Department of Geography Environment and Spatial Sciences
Housen Chu - Climate and Ecosystem Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94702, USA| Lawrence Berkeley National Laboratory: E O Lawrence Berkeley National Laboratory A
Higo J Dalmagro - Universidade de Cuiaba, Cuiaba, Mato Grosso, Brazil| Universidade de Cuiabá: Universidade de Cuiaba
Kyle B Delwiche - Department of Earth System Science, Stanford University, Stanford, California| Stanford University
Ankur R Desai - Dept of Atmospheric and Oceanic Sciences, University of Wisconsin-Madison, Madison, WI 53706 USA| University of Wisconsin-Madison
Eugenie Euskirchen - University of Alaska Fairbanks, Institute of Arctic Biology, Fairbanks, AK, USA 99775| University of Alaska Fairbanks
Sarah Feron - Department of Earth System Science, Stanford University, Stanford, California; Department of Physics, University of Santiago de Chile, Santiago, Chile; Campus Fryslan,University of Groningen,Leeuwarden, Netherlands| Stanford University
Mathias Goeckede - Max Planck Institute for Biogeochemistry, Jena, Germany| Max Planck Institute for Biogeochemistry: Max-Planck-Institut fur Biogeochemie
Martin Heimann - Max Planck Institute for Biogeochemistry, Jena, Germany| Max Planck Institute for Biogeochemistry: Max-Planck-Institut fur Biogeochemie
Manuel Helbig - Université de Montréal, Département de géographie, Université de Montréal, Montréal, QC H2V 0B3, Canada; Dalhousie University, Department of Physics and Atmospheric Science, Halifax, NS B2Y 1P3, Canada| Université de Montréal: Universite de Montreal
Carole Helfter - UK Centre for Ecology and Hydrology, Edinburgh, UK| UK Centre for Ecology & Hydrology
Kyle S Hemes - Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; Woods Institute for the Environment, Stanford University, Stanford, California| ESPM: University of California Berkeley Department of Environmental Science Policy and Management
Takashi Hirano - Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan| Hokkaido University School of Agriculture Graduate School of Agriculture Research Faculty of Agriculture: Hokkaido Daigaku Nogakubu Daigakuin Nogaku Kenkyuin Nogakuin
Hiroki Iwata - Department of Environmental Science, Faculty of Science, Shinshu University| Shinshu University Faculty of Science: Shinshu Daigaku Rigakubu
Gerald Jurasinski - University of Rostock, Rostock, Germany| University of Rostock: Universitat Rostock
Aram Kalhori - GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany| GFZ: Deutsches Geoforschungszentrum Potsdam
Andrew Kondrich - Department of Computer Science, Stanford University, Stanford, California, USA| Stanford University Department of Computer Science
Derrick YF Lai - Department of Geography and Resource Management, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China| The Chinese University of Hong Kong
Annalea Lohila - Finnish Meteorological Institute, PO Box 501, 00101 Helsinki, Finland; Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki, Finland;| Finnish Meteorological Institute: Ilmatieteen Laitos
Avni Malhotra - Department of Earth System Science, Stanford University, Stanford, California| Stanford University
Lutz Merbold - Mazingira Centre, International Livestock Research Institute, PO Box 30709, 00100 Nairobi, Kenya; Agroscope, Research Division Agroecology and Environment, Reckenholzstrasse 191, 8046 Zurich, Switzerland| International Livestock Research Institute
Bhaskar Mitra - Northern Arizona University, School of Informatics, Computing and Cyber Systems| Northern Arizona University
Andrew Ng - Department of Computer Science, Stanford University, Stanford, California, USA| Stanford University Department of Computer Science
Mats B Nilsson - Dept. of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden| Swedish University of Agricultural Sciences: Sveriges lantbruksuniversitet
Asko Noormets - Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas, USA| Texas A&M University College Station
Matthias Peichl - Dept. of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden| Swedish University of Agricultural Sciences: Sveriges lantbruksuniversitet
A. Camilo Rey-Sanchez - Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA| University of California Berkeley Department of Environmental Science Policy and Management
Andrew D Richardson - School of Informatics, Computing & Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA| Northern Arizona University
Benjamin RK Runkle - Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States| University of Arkansas
Karina VR Schäfer - Dept of Earth and Environmental Science, Rutgers University Newark, NJ| Rutgers University Newark
Oliver Sonnentag - Université de Montréal, Département de géographie, Université de Montréal, Montréal, QC H2V 0B3, Canada| Université de Montréal: Universite de Montreal
Ellen Stuart-Haëntjens - U.S. Geological Survey, California Water Science Center, 6000 J Street, Placer Hall, Sacramento, CA, 95819, USGS: US Geological Survey
Cove Sturtevant - National Ecological Observatory Network, Battelle, 1685 38th St Ste 100, Boulder, Colorado, 80301, USA| National Ecological Observatory Network
Masahito Ueyama - Graduate School of Life and Environmental Sciences, Osaka Prefecture University| Osaka Prefecture University
Alex C Valach - Agriculture and Climate Group, Agroscope, Switzerland| Agroscope
Rodrigo Vargas - Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA| University of Delaware Department of Plant and Soil Sciences A
George L Vourlitis - California State University San Marcos, San Marcos, CA, USA| California State University San Marcos
Eric J Ward - U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette LA| USGS: US Geological Survey
Guan Xhuan Wong - Sarawak Tropical Peat Research Institute, Sarawak, Malaysia| Sarawak Tropical Peat Research Institute
Donatella Zona - Dept. Biology, San Diego State University, San Diego, CA 92182, USA; Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom| San Diego State University
Ma. Carmelita R Alberto - International Rice Research Institute, Philippines| International Rice Research Institute
David P Billesbach - University of Nebraska-Lincoln, Department of Biological Systems Engineering, Lincoln, NE 68583, USA| University of Nebraska-Lincoln
Gerardo Celis - Agronomy Department, University of Florida, Gainesville FL, 32601| UF: University of Florida
Han Dolman - Department of Earth Sciences, Vrije Universiteit, Amsterdam, Netherlands| Vrije Universiteit Amsterdam
Thomas Friborg - University of Copenhagen, Department of Geosciences and Natural Resource Management| University of Copenhagen: Kobenhavns Universitet
Kathrin Fuchs - Institute of Meteorology and Climate Research - Atmospheric Environmental Research, Karlsruhe Institute of Technology (KIT Campus Alpin), 82467 Garmisch-Partenkirchen, Germany| Karlsruhe Institute of Technology: Karlsruher Institut fur Technologie
Sébastien Gogo - ISTO, Université d'Orléans, CNRS, BRGM, UMR 7327, 45071, Orléans, France| ISTO: Institut des Sciences de la Terre d'Orleans
Mangaliso J Gondwe - Okavango Research Institute, University of Botswana, Maun, Botswana.| University of Botswana Okavango Research Institute
Jordan P Goodrich - School of Science, University of Waikato, Hamilton, New Zealand| University of Waikato School of Science A
Pia Gottschalk - GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany| GFZ: Deutsches Geoforschungszentrum Potsdam
Lukas Hörtnagl - Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland| ETH Zurich
Adrien Jacotot - ISTO, Université d'Orléans, CNRS, BRGM, UMR 7327, 45071, Orléans, France| Universite d'Orleans
Franziska Koebsch - University of Rostock, Rostock, Germany| University of Rostock: Universitat Rostock
Kuno Kasak - Department of Geography, University of Tartu, Vanemuise st 46, Tartu, 51410, Estonia| University of Tartu
Regine Maier - Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland| ETH Zurich
Timothy H Morin - Environmental Resources Engineering, SUNY College of Environmental Science and Forestry| SUNY College of Environmental Science and Forestry
Eiko Nemitz - UK Centre for Ecology and Hydrology, Edinburgh, UK| UK Centre for Ecology & Hydrology
Walter C Oechel - Dept. Biology, San Diego State University, San Diego, CA 92182, USA| San Diego State University
Patricia Y Oikawa - Department of Earth and Environmental Sciences, Cal State East Bay, Hayward CA 94542 USA| California State University East Bay
Keisuke Ono - National Agriculture and Food Research Organization, Tsukuba, Japan| National Agricultural and Food Research Organization Tsukuba
Torsten Sachs - GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany| GFZ: Deutsches Geoforschungszentrum Potsdam
Ayaka Sakabe - Hakubi center, Kyoto University, Kyoto, Japan| Kyoto University: Kyoto Daigaku
Edward A Schuur - Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA| Northern Arizona University
Robert Shortt - Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA| ESPM: University of California Berkeley Department of Environmental Science Policy and Management
Ryan C Sullivan - Environmental Science Division, Argonne National Laboratory, Lemont, IL, USA| Argonne National Laboratory
Daphne J Szutu - Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA| ESPM: University of California Berkeley Department of Environmental Science Policy and Management
Eeva-Stiina Tuittila - School of Forest Sciences, University of Eastern Finland, Joesnuu, Finland| University of Eastern Finland Faculty of Science and Forestry: Ita-Suomen yliopisto Luonnontieteiden ja metsatieteiden tiedekunta
Andrej Varlagin - A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences| Russian Academy of Sciences: Rossijskaa akademia nauk
Joeseph G Verfaillie - Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA| ESPM: University of California Berkeley Department of Environmental Science Policy and Management
Christian Wille - GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany| GFZ: Deutsches Geoforschungszentrum Potsdam
Lisamarie Windham-Myers - U.S. Geological Survey, Water Mission Area, 345 Middlefield Road, Menlo Park, CA, 94025| USGS: US Geological Survey
Benjamin Poulter - Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, NASA Goddard Space Flight Center
Robert B Jackson - Department of Earth System Science, Stanford University, Stanford, California; Woods Institute for the Environment, Stanford University, Stanford, California; Precourt Institute for Energy, Stanford University, Stanford, California| Stanford University
Sveriges lantbruksuniversitet
Publication Details: Agricultural and forest meteorology, Vol.308-309, p.108528
Publisher: Elsevier B.V
Identifiers: 99877303304826
Academic Unit: Department of Environmental Resources Engineering
Language: English
Resource Type: Journal article