Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands
Abstract
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 whilstmore »
- Authors:
- more »
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); Gordon and Betty Moore Foundation; National Science Foundation (NSF); Natural Sciences and Engineering Research Council of Canada (NSERC); Helmholtz Association of German Research Centres; USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Contributing Org.:
- R Core Team
- OSTI Identifier:
- 1840759
- Alternate Identifier(s):
- OSTI ID: 1902660
- Grant/Contract Number:
- AC02-06CH11357; 1752083; VH-NG-821; N18B 315-11; 146373; 407340_172433; 2011-67003-30371; 7079856; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Agricultural and Forest Meteorology
- Additional Journal Information:
- Journal Volume: 308-309; Journal ID: ISSN 0168-1923
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; 42 ENGINEERING; machine learning; flux; gap-filling; imeseries; imputation; methane; wetlands
Citation Formats
Irvin, Jeremy, Zhou, Sharon, McNicol, Gavin, Lu, Fred, Liu, Vincent, Fluet-Chouinard, Etienne, Ouyang, Zutao, Knox, Sara Helen, Lucas-Moffat, Antje, Trotta, Carlo, Papale, Dario, Vitale, Domenico, Mammarella, Ivan, Alekseychik, Pavel, Aurela, Mika, Avati, Anand, Baldocchi, Dennis, Bansal, Sheel, Bohrer, Gil, Campbell, David I., Chen, Jiquan, Chu, Housen, Dalmagro, Higo J., Delwiche, Kyle B., Desai, Ankur R., Euskirchen, Eugenie, Feron, Sarah, Goeckede, Mathias, Heimann, Martin, Helbig, Manuel, Helfter, Carole, Hemes, Kyle S., Hirano, Takashi, Iwata, Hiroki, Jurasinski, Gerald, Kalhori, Aram, Kondrich, Andrew, Lai, Derrick YF, Lohila, Annalea, Malhotra, Avni, Merbold, Lutz, Mitra, Bhaskar, Ng, Andrew, Nilsson, Mats B., Noormets, Asko, Peichl, Matthias, Rey-Sanchez, A. Camilo, Richardson, Andrew D., Runkle, Benjamin RK, Schäfer, Karina VR, Sonnentag, Oliver, Stuart-Haëntjens, Ellen, Sturtevant, Cove, Ueyama, Masahito, Valach, Alex C., Vargas, Rodrigo, Vourlitis, George L., Ward, Eric J., Wong, Guan Xhuan, Zona, Donatella, Alberto, Ma. R., Billesbach, David P., Celis, Gerardo, Dolman, Han, Friborg, Thomas, Fuchs, Kathrin, Gogo, Sébastien, Gondwe, Mangaliso J., Goodrich, Jordan P., Gottschalk, Pia, Hörtnagl, Lukas, Jacotot, Adrien, Koebsch, Franziska, Kasak, Kuno, Maier, Regine, Morin, Timothy H., Nemitz, Eiko, Oechel, Walter C., Oikawa, Patricia Y., Ono, Keisuke, Sachs, Torsten, Sakabe, Ayaka, Schuur, Edward A., Shortt, Robert, Sullivan, Ryan C., Szutu, Daphne J., Tuittila, Eeva-Stiina, Varlagin, Andrej, Verfaillie, Joeseph G., Wille, Christian, Windham-Myers, Lisamarie, Poulter, Benjamin, and Jackson, Robert B. Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands. United States: N. p., 2021.
Web. doi:10.1016/j.agrformet.2021.108528.
Irvin, Jeremy, Zhou, Sharon, McNicol, Gavin, Lu, Fred, Liu, Vincent, Fluet-Chouinard, Etienne, Ouyang, Zutao, Knox, Sara Helen, Lucas-Moffat, Antje, Trotta, Carlo, Papale, Dario, Vitale, Domenico, Mammarella, Ivan, Alekseychik, Pavel, Aurela, Mika, Avati, Anand, Baldocchi, Dennis, Bansal, Sheel, Bohrer, Gil, Campbell, David I., Chen, Jiquan, Chu, Housen, Dalmagro, Higo J., Delwiche, Kyle B., Desai, Ankur R., Euskirchen, Eugenie, Feron, Sarah, Goeckede, Mathias, Heimann, Martin, Helbig, Manuel, Helfter, Carole, Hemes, Kyle S., Hirano, Takashi, Iwata, Hiroki, Jurasinski, Gerald, Kalhori, Aram, Kondrich, Andrew, Lai, Derrick YF, Lohila, Annalea, Malhotra, Avni, Merbold, Lutz, Mitra, Bhaskar, Ng, Andrew, Nilsson, Mats B., Noormets, Asko, Peichl, Matthias, Rey-Sanchez, A. Camilo, Richardson, Andrew D., Runkle, Benjamin RK, Schäfer, Karina VR, Sonnentag, Oliver, Stuart-Haëntjens, Ellen, Sturtevant, Cove, Ueyama, Masahito, Valach, Alex C., Vargas, Rodrigo, Vourlitis, George L., Ward, Eric J., Wong, Guan Xhuan, Zona, Donatella, Alberto, Ma. R., Billesbach, David P., Celis, Gerardo, Dolman, Han, Friborg, Thomas, Fuchs, Kathrin, Gogo, Sébastien, Gondwe, Mangaliso J., Goodrich, Jordan P., Gottschalk, Pia, Hörtnagl, Lukas, Jacotot, Adrien, Koebsch, Franziska, Kasak, Kuno, Maier, Regine, Morin, Timothy H., Nemitz, Eiko, Oechel, Walter C., Oikawa, Patricia Y., Ono, Keisuke, Sachs, Torsten, Sakabe, Ayaka, Schuur, Edward A., Shortt, Robert, Sullivan, Ryan C., Szutu, Daphne J., Tuittila, Eeva-Stiina, Varlagin, Andrej, Verfaillie, Joeseph G., Wille, Christian, Windham-Myers, Lisamarie, Poulter, Benjamin, & Jackson, Robert B. Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands. United States. https://doi.org/10.1016/j.agrformet.2021.108528
Irvin, Jeremy, Zhou, Sharon, McNicol, Gavin, Lu, Fred, Liu, Vincent, Fluet-Chouinard, Etienne, Ouyang, Zutao, Knox, Sara Helen, Lucas-Moffat, Antje, Trotta, Carlo, Papale, Dario, Vitale, Domenico, Mammarella, Ivan, Alekseychik, Pavel, Aurela, Mika, Avati, Anand, Baldocchi, Dennis, Bansal, Sheel, Bohrer, Gil, Campbell, David I., Chen, Jiquan, Chu, Housen, Dalmagro, Higo J., Delwiche, Kyle B., Desai, Ankur R., Euskirchen, Eugenie, Feron, Sarah, Goeckede, Mathias, Heimann, Martin, Helbig, Manuel, Helfter, Carole, Hemes, Kyle S., Hirano, Takashi, Iwata, Hiroki, Jurasinski, Gerald, Kalhori, Aram, Kondrich, Andrew, Lai, Derrick YF, Lohila, Annalea, Malhotra, Avni, Merbold, Lutz, Mitra, Bhaskar, Ng, Andrew, Nilsson, Mats B., Noormets, Asko, Peichl, Matthias, Rey-Sanchez, A. Camilo, Richardson, Andrew D., Runkle, Benjamin RK, Schäfer, Karina VR, Sonnentag, Oliver, Stuart-Haëntjens, Ellen, Sturtevant, Cove, Ueyama, Masahito, Valach, Alex C., Vargas, Rodrigo, Vourlitis, George L., Ward, Eric J., Wong, Guan Xhuan, Zona, Donatella, Alberto, Ma. R., Billesbach, David P., Celis, Gerardo, Dolman, Han, Friborg, Thomas, Fuchs, Kathrin, Gogo, Sébastien, Gondwe, Mangaliso J., Goodrich, Jordan P., Gottschalk, Pia, Hörtnagl, Lukas, Jacotot, Adrien, Koebsch, Franziska, Kasak, Kuno, Maier, Regine, Morin, Timothy H., Nemitz, Eiko, Oechel, Walter C., Oikawa, Patricia Y., Ono, Keisuke, Sachs, Torsten, Sakabe, Ayaka, Schuur, Edward A., Shortt, Robert, Sullivan, Ryan C., Szutu, Daphne J., Tuittila, Eeva-Stiina, Varlagin, Andrej, Verfaillie, Joeseph G., Wille, Christian, Windham-Myers, Lisamarie, Poulter, Benjamin, and Jackson, Robert B. Fri .
"Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands". United States. https://doi.org/10.1016/j.agrformet.2021.108528. https://www.osti.gov/servlets/purl/1840759.
@article{osti_1840759,
title = {Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands},
author = {Irvin, Jeremy and Zhou, Sharon and McNicol, Gavin and Lu, Fred and Liu, Vincent and Fluet-Chouinard, Etienne and Ouyang, Zutao and Knox, Sara Helen and Lucas-Moffat, Antje and Trotta, Carlo and Papale, Dario and Vitale, Domenico and Mammarella, Ivan and Alekseychik, Pavel and Aurela, Mika and Avati, Anand and Baldocchi, Dennis and Bansal, Sheel and Bohrer, Gil and Campbell, David I. and Chen, Jiquan and Chu, Housen and Dalmagro, Higo J. and Delwiche, Kyle B. and Desai, Ankur R. and Euskirchen, Eugenie and Feron, Sarah and Goeckede, Mathias and Heimann, Martin and Helbig, Manuel and Helfter, Carole and Hemes, Kyle S. and Hirano, Takashi and Iwata, Hiroki and Jurasinski, Gerald and Kalhori, Aram and Kondrich, Andrew and Lai, Derrick YF and Lohila, Annalea and Malhotra, Avni and Merbold, Lutz and Mitra, Bhaskar and Ng, Andrew and Nilsson, Mats B. and Noormets, Asko and Peichl, Matthias and Rey-Sanchez, A. Camilo and Richardson, Andrew D. and Runkle, Benjamin RK and Schäfer, Karina VR and Sonnentag, Oliver and Stuart-Haëntjens, Ellen and Sturtevant, Cove and Ueyama, Masahito and Valach, Alex C. and Vargas, Rodrigo and Vourlitis, George L. and Ward, Eric J. and Wong, Guan Xhuan and Zona, Donatella and Alberto, Ma. R. and Billesbach, David P. and Celis, Gerardo and Dolman, Han and Friborg, Thomas and Fuchs, Kathrin and Gogo, Sébastien and Gondwe, Mangaliso J. and Goodrich, Jordan P. and Gottschalk, Pia and Hörtnagl, Lukas and Jacotot, Adrien and Koebsch, Franziska and Kasak, Kuno and Maier, Regine and Morin, Timothy H. and Nemitz, Eiko and Oechel, Walter C. and Oikawa, Patricia Y. and Ono, Keisuke and Sachs, Torsten and Sakabe, Ayaka and Schuur, Edward A. and Shortt, Robert and Sullivan, Ryan C. and Szutu, Daphne J. and Tuittila, Eeva-Stiina and Varlagin, Andrej and Verfaillie, Joeseph G. and Wille, Christian and Windham-Myers, Lisamarie and Poulter, Benjamin and Jackson, Robert B.},
abstractNote = {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).},
doi = {10.1016/j.agrformet.2021.108528},
journal = {Agricultural and Forest Meteorology},
number = ,
volume = 308-309,
place = {United States},
year = {Fri Oct 01 00:00:00 EDT 2021},
month = {Fri Oct 01 00:00:00 EDT 2021}
}
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Effects of seasonality, transport pathway, and spatial structure on greenhouse gas fluxes in a restored wetland
journal, January 2017
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Hot-Moments of Soil CO2 Efflux in a Water-Limited Grassland
journal, August 2018
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Methane fluxes show consistent temperature dependence across microbial to ecosystem scales
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A Multi-Year Record of Methane Flux at the Mer Bleue Bog, Southern Canada
journal, April 2011
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Present state of global wetland extent and wetland methane modelling: methodology of a model inter-comparison project (WETCHIMP)
journal, January 2013
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Biophysical controls on interannual variability in ecosystem-scale CO 2 and CH 4 exchange in a California rice paddy : INTERANNUAL VARIABILITY RICE CH
journal, March 2016
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Revisiting the partitioning of net ecosystem exchange of CO2 into photosynthesis and respiration with simultaneous flux measurements of 13CO2 and CO2, soil respiration and a biophysical model, CANVEG
journal, March 2017
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Comparisons of gap-filling methods for carbon flux dataset: A combination of a genetic algorithm and an artificial neural network
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Evaluating the Classical Versus an Emerging Conceptual Model of Peatland Methane Dynamics: Peatland Methane Dynamics
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Biophysical drivers of net ecosystem and methane exchange across phenological phases in a tidal salt marsh
journal, April 2021
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FLUXNET-CH4 FI-Lom Lompolojankka
dataset, January 2020
- Lohila, Annalea; Aurela, Mika; Tuovinen, Juha-Pekka
- FluxNet; Finnish Meteorological Institute
FLUXNET-CH4 FI-Si2 Siikaneva-2 Bog
dataset, January 2020
- Vesala, Timo; Tuittila, Eeva-Stiina; Mammarella, Ivan
- FluxNet; University of Eastern Finland; University of Helsinki
FLUXNET-CH4 FI-Sii Siikaneva
dataset, January 2020
- Vesala, Timo; Tuittila, Eeva-Stiina; Mammarella, Ivan
- FluxNet; University of Eastern Finland; University of Helsinki
FLUXNET-CH4 JP-BBY Bibai bog
dataset, January 2020
- Ueyama, Masahito; Hirano, Takashi; Kominami, Yasuhiro
- FluxNet; Osaka Prefecture Univeristy
FLUXNET-CH4 JP-Mse Mase rice paddy field
dataset, January 2020
- Iwata, Hiroki
- FluxNet; National Agriculture and Food Research Organization
FLUXNET-CH4 NZ-Kop Kopuatai
dataset, January 2020
- Campbell, David; Goodrich, Jordan
- FluxNet; University of Waikato
FLUXNET-CH4 SE-Deg Degero
dataset, January 2020
- Nilsson, Mats; Peichl, Matthias
- FluxNet; Department of Forest Ecology and Management; Swedish University of Agricultural Sciences