Articles | Volume 15, issue 19
https://doi.org/10.5194/bg-15-5801-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-15-5801-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Linking big models to big data: efficient ecosystem model calibration through Bayesian model emulation
Department of Earth and Environment, Boston University, Boston, MA 02215, USA
Ryan Kelly
RK Analytics, Durham, NC 27712, USA
Paul R. Moorcroft
Department Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Andrew D. Richardson
School of Informatics, Computing and Cyber Systems, Northern Arizona University Flagstaff, AZ 86011, USA
Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA
Elizabeth M. Cowdery
Department of Earth and Environment, Boston University, Boston, MA 02215, USA
Michael C. Dietze
Department of Earth and Environment, Boston University, Boston, MA 02215, USA
Related authors
Hui Tang, Samuli Launianen, Julius Vira, Liisa Kulmala, Taru Palosuo, Hermanni Aaltonen, Olli Nevalainen, Istem Fer, Henriikka Vekuri, Jari-Pekka Nousu, Mika Korkiakoski, and Jari Liski
EGUsphere, https://doi.org/10.5194/egusphere-2025-5972, https://doi.org/10.5194/egusphere-2025-5972, 2025
Short summary
Short summary
We present a modelling approach to study how crops in northern climates deal with water stress. By combining several years of field measurements with the modelling approach, we show that both oat and forage grasses use water cautiously, helping them preserve enough soil water to stay productive during dry periods. Our results highlight the need to better understand how northern crops use water for improving their food production in the future, when more frequent and severe drought will occur.
Toni Viskari, Janne Pusa, Istem Fer, Anna Repo, Julius Vira, and Jari Liski
Geosci. Model Dev., 15, 1735–1752, https://doi.org/10.5194/gmd-15-1735-2022, https://doi.org/10.5194/gmd-15-1735-2022, 2022
Short summary
Short summary
We wanted to examine how the chosen measurement data and calibration process affect soil organic carbon model calibration. In our results we found that there is a benefit in using data from multiple litter-bag decomposition experiments simultaneously, even with the required assumptions. Additionally, due to the amount of noise and uncertainties in the system, more advanced calibration methods should be used to parameterize the models.
Olli Nevalainen, Olli Niemitalo, Istem Fer, Antti Juntunen, Tuomas Mattila, Olli Koskela, Joni Kukkamäki, Layla Höckerstedt, Laura Mäkelä, Pieta Jarva, Laura Heimsch, Henriikka Vekuri, Liisa Kulmala, Åsa Stam, Otto Kuusela, Stephanie Gerin, Toni Viskari, Julius Vira, Jari Hyväluoma, Juha-Pekka Tuovinen, Annalea Lohila, Tuomas Laurila, Jussi Heinonsalo, Tuula Aalto, Iivari Kunttu, and Jari Liski
Geosci. Instrum. Method. Data Syst., 11, 93–109, https://doi.org/10.5194/gi-11-93-2022, https://doi.org/10.5194/gi-11-93-2022, 2022
Short summary
Short summary
Better monitoring of soil carbon sequestration is needed to understand the best carbon farming practices in different soils and climate conditions. We, the Field Observatory Network (FiON), have therefore established a methodology for monitoring and forecasting agricultural carbon sequestration by combining offline and near-real-time field measurements, weather data, satellite imagery, and modeling. To disseminate our work, we built a website called the Field Observatory (fieldobservatory.org).
Konstantin Gregor, Benjamin F. Meyer, Tillmann Gaida, Victor Justo Vasquez, Karina Bett-Williams, Matthew Forrest, João P. Darela-Filho, Sam Rabin, Marcos Longo, Joe R. Melton, Johan Nord, Peter Anthoni, Vladislav Bastrikov, Thomas Colligan, Christine Delire, Michael C. Dietze, George Hurtt, Akihiko Ito, Lasse T. Keetz, Jürgen Knauer, Johannes Köster, Tzu-Shun Lin, Lei Ma, Marie Minvielle, Stefan Olin, Sebastian Ostberg, Hao Shi, Reiner Schnur, Qing Sun, Peter E. Thornton, and Anja Rammig
Geosci. Model Dev., 19, 2407–2436, https://doi.org/10.5194/gmd-19-2407-2026, https://doi.org/10.5194/gmd-19-2407-2026, 2026
Short summary
Short summary
Geoscientific models are crucial for understanding Earth’s processes. However, they sometimes do not adhere to highest software quality standards, and scientific results are often hard to reproduce due to the complexity of the workflows. Here we gather the expertise of 20 modeling groups and software engineers to define best practices for making geoscientific models maintainable, usable, and reproducible. We conclude with an open-source example serving as a reference for modeling communities.
Hui Tang, Samuli Launianen, Julius Vira, Liisa Kulmala, Taru Palosuo, Hermanni Aaltonen, Olli Nevalainen, Istem Fer, Henriikka Vekuri, Jari-Pekka Nousu, Mika Korkiakoski, and Jari Liski
EGUsphere, https://doi.org/10.5194/egusphere-2025-5972, https://doi.org/10.5194/egusphere-2025-5972, 2025
Short summary
Short summary
We present a modelling approach to study how crops in northern climates deal with water stress. By combining several years of field measurements with the modelling approach, we show that both oat and forage grasses use water cautiously, helping them preserve enough soil water to stay productive during dry periods. Our results highlight the need to better understand how northern crops use water for improving their food production in the future, when more frequent and severe drought will occur.
Adam M. Young, Thomas Milliman, Koen Hufkens, Keith L. Ballou, Christopher Coffey, Kai Begay, Michael Fell, Mostafa Javadian, Alison K. Post, Christina Schädel, Zakary Vladich, Oscar Zimmerman, Dawn M. Browning, Christopher R. Florian, Minkyu Moon, Michael D. SanClements, Bijan Seyednasrollah, Mark A. Friedl, and Andrew D. Richardson
Earth Syst. Sci. Data, 17, 6531–6556, https://doi.org/10.5194/essd-17-6531-2025, https://doi.org/10.5194/essd-17-6531-2025, 2025
Short summary
Short summary
Here, we describe the PhenoCam V3.0 public data release, which characterizes vegetation phenology in ecosystems across the US and globally using repeat digital photography. This V3.0 release includes new data records (a camera-derived normalized difference vegetation index and simplified data sets) and provides >4800 site years of phenological time series and transition dates, a 170 % increase relative to the previous release (V2.0). Over 450 of the time series are 5 years or longer in length.
Guohua Liu, Mirco Migliavacca, Christian Reimers, Basil Kraft, Markus Reichstein, Andrew D. Richardson, Lisa Wingate, Nicolas Delpierre, Hui Yang, and Alexander J. Winkler
Geosci. Model Dev., 17, 6683–6701, https://doi.org/10.5194/gmd-17-6683-2024, https://doi.org/10.5194/gmd-17-6683-2024, 2024
Short summary
Short summary
Our study employs long short-term memory (LSTM) networks to model canopy greenness and phenology, integrating meteorological memory effects. The LSTM model outperforms traditional methods, enhancing accuracy in predicting greenness dynamics and phenological transitions across plant functional types. Highlighting the importance of multi-variate meteorological memory effects, our research pioneers unlock the secrets of vegetation phenology responses to climate change with deep learning techniques.
Hamze Dokoohaki, Bailey D. Morrison, Ann Raiho, Shawn P. Serbin, Katie Zarada, Luke Dramko, and Michael Dietze
Geosci. Model Dev., 15, 3233–3252, https://doi.org/10.5194/gmd-15-3233-2022, https://doi.org/10.5194/gmd-15-3233-2022, 2022
Short summary
Short summary
We present a new terrestrial carbon cycle data assimilation system, built on the PEcAn model–data eco-informatics system, and its application for the development of a proof-of-concept carbon
reanalysisproduct that harmonizes carbon pools (leaf, wood, soil) and fluxes (GPP, Ra, Rh, NEE) across the contiguous United States from 1986–2019. Here, we build on a decade of work on uncertainty propagation to generate the most complete and robust uncertainty accounting available to date.
Toni Viskari, Janne Pusa, Istem Fer, Anna Repo, Julius Vira, and Jari Liski
Geosci. Model Dev., 15, 1735–1752, https://doi.org/10.5194/gmd-15-1735-2022, https://doi.org/10.5194/gmd-15-1735-2022, 2022
Short summary
Short summary
We wanted to examine how the chosen measurement data and calibration process affect soil organic carbon model calibration. In our results we found that there is a benefit in using data from multiple litter-bag decomposition experiments simultaneously, even with the required assumptions. Additionally, due to the amount of noise and uncertainties in the system, more advanced calibration methods should be used to parameterize the models.
Olli Nevalainen, Olli Niemitalo, Istem Fer, Antti Juntunen, Tuomas Mattila, Olli Koskela, Joni Kukkamäki, Layla Höckerstedt, Laura Mäkelä, Pieta Jarva, Laura Heimsch, Henriikka Vekuri, Liisa Kulmala, Åsa Stam, Otto Kuusela, Stephanie Gerin, Toni Viskari, Julius Vira, Jari Hyväluoma, Juha-Pekka Tuovinen, Annalea Lohila, Tuomas Laurila, Jussi Heinonsalo, Tuula Aalto, Iivari Kunttu, and Jari Liski
Geosci. Instrum. Method. Data Syst., 11, 93–109, https://doi.org/10.5194/gi-11-93-2022, https://doi.org/10.5194/gi-11-93-2022, 2022
Short summary
Short summary
Better monitoring of soil carbon sequestration is needed to understand the best carbon farming practices in different soils and climate conditions. We, the Field Observatory Network (FiON), have therefore established a methodology for monitoring and forecasting agricultural carbon sequestration by combining offline and near-real-time field measurements, weather data, satellite imagery, and modeling. To disseminate our work, we built a website called the Field Observatory (fieldobservatory.org).
Xin Huang, Dan Lu, Daniel M. Ricciuto, Paul J. Hanson, Andrew D. Richardson, Xuehe Lu, Ensheng Weng, Sheng Nie, Lifen Jiang, Enqing Hou, Igor F. Steinmacher, and Yiqi Luo
Geosci. Model Dev., 14, 5217–5238, https://doi.org/10.5194/gmd-14-5217-2021, https://doi.org/10.5194/gmd-14-5217-2021, 2021
Short summary
Short summary
In the data-rich era, data assimilation is widely used to integrate abundant observations into models to reduce uncertainty in ecological forecasting. However, applications of data assimilation are restricted by highly technical requirements. To alleviate this technical burden, we developed a model-independent data assimilation (MIDA) module which is friendly to ecologists with limited programming skills. MIDA also supports a flexible switch of different models or observations in DA analysis.
Kyle B. Delwiche, Sara Helen Knox, Avni Malhotra, Etienne Fluet-Chouinard, Gavin McNicol, Sarah Feron, Zutao Ouyang, Dario Papale, Carlo Trotta, Eleonora Canfora, You-Wei Cheah, Danielle Christianson, Ma. Carmelita R. Alberto, Pavel Alekseychik, Mika Aurela, Dennis Baldocchi, Sheel Bansal, David P. Billesbach, Gil Bohrer, Rosvel Bracho, Nina Buchmann, David I. Campbell, Gerardo Celis, Jiquan Chen, Weinan Chen, Housen Chu, Higo J. Dalmagro, Sigrid Dengel, Ankur R. Desai, Matteo Detto, Han Dolman, Elke Eichelmann, Eugenie Euskirchen, Daniela Famulari, Kathrin Fuchs, Mathias Goeckede, Sébastien Gogo, Mangaliso J. Gondwe, Jordan P. Goodrich, Pia Gottschalk, Scott L. Graham, Martin Heimann, Manuel Helbig, Carole Helfter, Kyle S. Hemes, Takashi Hirano, David Hollinger, Lukas Hörtnagl, Hiroki Iwata, Adrien Jacotot, Gerald Jurasinski, Minseok Kang, Kuno Kasak, John King, Janina Klatt, Franziska Koebsch, Ken W. Krauss, Derrick Y. F. Lai, Annalea Lohila, Ivan Mammarella, Luca Belelli Marchesini, Giovanni Manca, Jaclyn Hatala Matthes, Trofim Maximov, Lutz Merbold, Bhaskar Mitra, Timothy H. Morin, Eiko Nemitz, Mats B. Nilsson, Shuli Niu, Walter C. Oechel, Patricia Y. Oikawa, Keisuke Ono, Matthias Peichl, Olli Peltola, Michele L. Reba, Andrew D. Richardson, William Riley, Benjamin R. K. Runkle, Youngryel Ryu, Torsten Sachs, Ayaka Sakabe, Camilo Rey Sanchez, Edward A. Schuur, Karina V. R. Schäfer, Oliver Sonnentag, Jed P. Sparks, Ellen Stuart-Haëntjens, Cove Sturtevant, Ryan C. Sullivan, Daphne J. Szutu, Jonathan E. Thom, Margaret S. Torn, Eeva-Stiina Tuittila, Jessica Turner, Masahito Ueyama, Alex C. Valach, Rodrigo Vargas, Andrej Varlagin, Alma Vazquez-Lule, Joseph G. Verfaillie, Timo Vesala, George L. Vourlitis, Eric J. Ward, Christian Wille, Georg Wohlfahrt, Guan Xhuan Wong, Zhen Zhang, Donatella Zona, Lisamarie Windham-Myers, Benjamin Poulter, and Robert B. Jackson
Earth Syst. Sci. Data, 13, 3607–3689, https://doi.org/10.5194/essd-13-3607-2021, https://doi.org/10.5194/essd-13-3607-2021, 2021
Short summary
Short summary
Methane is an important greenhouse gas, yet we lack knowledge about its global emissions and drivers. We present FLUXNET-CH4, a new global collection of methane measurements and a critical resource for the research community. We use FLUXNET-CH4 data to quantify the seasonality of methane emissions from freshwater wetlands, finding that methane seasonality varies strongly with latitude. Our new database and analysis will improve wetland model accuracy and inform greenhouse gas budgets.
Cited articles
Arulampalam, M., Maskell, S., Gordon, N., and Clapp, T.: A tutorial on particle filters for online nonlinear/non-Gaussian Bayesian tracking, IEEE T. Signal. Process., 50, 174–188, https://doi.org/10.1109/78.978374, 2002.
Aslanyan, G., Easther, R., and Price, L. C.: Learn-as-you-go acceleration of cosmological parameter estimates, J. Cosmol. Astropart. P., 2015, 005, 2015.
Bradford, J. B., Weishampel, P., Smith, M.-L., Kolka, R., Birdsey, R. A., Ollinger, S. V., and Ryan, M. G.: Carbon pools and fluxes in small temperate forest landscapes: Variability and implications for sampling design, Forest Ecol. Manag., 259, 1245–1254, https://doi.org/10.1016/j.foreco.2009.04.009, 2010.
Braswell, B. H., Sacks, W. J., Linder, E., and Schimel, D. S.: Estimating diurnal to annual ecosystem parameters by synthesis of a carbon flux model with eddy covariance net ecosystem exchange observations, Global Change Biol., 11, 335–355, https://doi.org/10.1111/j.1365-2486.2005.00897.x, 2005.
Brynjarsdóttir, J. and O'Hagan, A.: Learning about physical parameters: the importance of model discrepancy, Inverse Problems, 30, 114007, 2014.
Clark, J. S.: Why environmental scientists are becoming Bayesians, Ecol. Lett., 8, 2–14, https://doi.org/10.1111/j.1461-0248.2004.00702.x, 2005.
Dancik, G. M.: mlegp: Maximum Likelihood Estimates of Gaussian Processes, R package version 3.1.4, available at: https://CRAN.R-project.org/package=mlegp (last access: 30 September 2018), 2013.
Datta, A., Banerjee, S., Finley, A. O., and Gelfand, A. E.: On nearest-neighbor Gaussian process models for massive spatial data, WIRES Comput. Statistics, 8, 162–171, https://doi.org/10.1002/wics.1383, 2016.
Dietze, M. C.: Ecological Forecasting, https://doi.org/10.1002/eap.1589, 2017a.
Dietze, M. C.: Prediction in ecology: a first-principles framework, Ecol. Appl., 27, 2048–2060, https://doi.org/10.1002/eap.1589, 2017b.
Dietze, M. C. and Moorcroft, P. R.: Tree mortality in the eastern and central United States: patterns and drivers, Global Change Biol., 17, 3312–3326, https://doi.org/10.1111/j.1365-2486.2011.02477.x, 2011.
Dietze, M. C., Shawn, S. P., Davidson, C., Desai, A. R., Feng, X., Kelly, R., Kooper, R., LeBauer, D., Mantooth, J., McHenry, K., and Wang, D.: A quantitative assessment of a terrestrial biosphere model's data needs across North American biomes, J. Geophys. Res.-Biogeosci., 119, 286–300, https://doi.org/10.1002/2013JG002392, 2014.
Erickson, C. B., Ankenman, B. E., and Sanchez, S. M.: Comparison of Gaussian process modeling software, Eur. J. Oper. Res., 266, 179–192, https://doi.org/10.1016/j.ejor.2017.10.002, 2018.
Fisher, J., Huntzinger, D., Schwalm, C., and Sitch, S.: Modeling the terrestrial biosphere, Annu. Rev. Env. Resour., 39, 91–123, https://doi.org/10.1146/annurev-environ-012913-093456, 2014.
Fisher, R. A.: On the mathematical foundations of theoretical statistics, Phil. T. R. Soc. A, 222, https://doi.org/10.1098/rsta.1922.0009, 1922.
Forrester, A. I. and Keane, A. J.: Recent advances in surrogate-based optimization, Prog. Aerosp. Sci., 45, 50–79, https://doi.org/10.1016/j.paerosci.2008.11.001, 2009.
Fox, A., Williams, M., Richardson, A. D., Cameron, D., Gove, J. H., Quaife, T., Ricciuto, D., Reichstein, M., Tomelleri, E., Trudinger, C. M., and Wijk, M. T. V.: The REFLEX project: Comparing different algorithms and implementations for the inversion of a terrestrial ecosystem model against eddy covariance data, Agr. Forest Meteorol., 149, 1597–1615, https://doi.org/10.1016/j.agrformet.2009.05.002, 2009.
Friedlingstein, P., Meinshausen, M., Arora, V. K., Jones, C. D., Anav, A., Liddicoat, S. K., and Knutti, R.: Uncertainties in CMIP5 Climate Projections due to Carbon Cycle Feedbacks, J. Climate, 27, 511–526, https://doi.org/10.1175/JCLI-D-12-00579.1, 2014.
Gong, W. and Duan, Q.: An adaptive surrogate modeling-based sampling strategy for parameter optimization and distribution estimation (ASMO-PODE), Environ. Modell. Softw., 95, 61–75, https://doi.org/10.1016/j.envsoft.2017.05.005, 2017.
Gupta, H. V., Clark, M. P., Jasper, J. A. V., Abramowitz, G., and Ye, M.: Towards a comprehensive assessment of model structural adequacy, Water Resour. Res., 48, W08301, https://doi.org/10.1029/2011WR011044, 2012.
Gutmann, M. U. and Corander, J.: Bayesian Optimization for Likelihood-Free Inference of Simulator-Based Statistical Models, J. Mach. Learn. Res., 17, 1–47, 2016.
Haario, H., Saksman, E., and Tamminen, J.: An adaptive Metropolis algorithm, Bernoulli, 7, 223–242, 2001.
Hartig, F., Dyke, J., Hickler, T., Higgins, S. I., O'Hara, R. B., Scheiter, S., and Huth, A.: Connecting dynamic vegetation models to data – an inverse perspective, J. Biogeogr., 39, 2240–2252, https://doi.org/10.1111/j.1365-2699.2012.02745.x, 2012.
Hartig, F., Minuno, F., and Paul, S.: BayesianTools: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics, R package version 0.1.3, available at: https://CRAN.R-project.org/package=BayesianTools (last access: 30 September 2018, 2017.
Huang, M., Ray, J., Hou, Z., Ren, H., Liu, Y., and Swiler, L.: On the applicability of surrogate-based Markov chain Monte Carlo-Bayesian inversion to the Community Land Model: Case studies at flux tower sites, J. Geophys. Res.-Atmos., 121, 7548–7563, https://doi.org/10.1002/2015JD024339, 2016.
Jandarov, R., Haran, M., Bjørnstad, O., and Grenfell, B.: Emulating a gravity model to infer the spatiotemporal dynamics of an infectious disease, J. R. Stat. Soc. C-Appl., 63, 423–444, https://doi.org/10.1111/rssc.12042, 2014.
Jenkins, J. C., Chojnacky, D. C., Heath, L. S., and Birdsey, R. A.: Comprehensive database of diameter-based biomass regressions for North American tree species, United States Department of Agriculture, available at: https://www.fs.fed.us/ne/durham/4104/papers/ne_gtr319_jenkins_and_others.pdf (last access: 30 September 2018), 2004.
Joyce, P. and Marjoram, P.: Approximately sufficient statistics and Bayesian computation, Stat. Appl. Genet. Mo. B., 7, https://doi.org/10.2202/1544-6115.1389, 2008.
Kandasamy, K., Schneider, J., and Póczos, B.: Bayesian Active Learning for Posterior Estimation, AAAI Publications, Twenty-Fourth International Joint Conference on Artificial Intelligence, Buenos Aires, Argentina, 2015.
Keenan, T. F., Carbone, M. S., Reichstein, M., and Richardson, A. D.: The model-data fusion pitfall: assuming certainty in an uncertain world, Oecologia, 167, 587, https://doi.org/10.1007/s00442-011-2106-x, 2011.
Keenan, T. F., Davidson, E. A., Munger, J. W., and Richardson, A. D.: Rate my data: quantifying the value of ecological data for the development of models of the terrestrial carbon cycle, Ecol. Appl., 23, 273–286, https://doi.org/10.1890/12-0747.1, 2013.
Kennedy, M., Anderson, C., O'Hagan, A., Lomas, M., Woodward, I., Gosling, J. P., and Heinemeyer, A.: Quantifying uncertainty in the biospheric carbon flux for England and Wales, J. R. Stat. Soc. A Stat., 171, 109–135, https://doi.org/10.1111/j.1467-985X.2007.00489.x, 2008.
Kennedy, M. C. and O'Hagan, A.: Bayesian calibration of computer models, J. R. Stat. Soc. B Stat., 63, 425–464, https://doi.org/10.1111/1467-9868.00294, 2001.
Laloy, E. and Vrugt, J. A.: High-dimensional posterior exploration of hydrologic models using multiple-try DREAM(ZS) and high-performance computing, Water Resour. Res., 48, W01526, https://doi.org/10.1029/2011WR010608, 2012.
Lasslop, G., Reichstein, M., Kattge, J., and Papale, D.: Influences of observation errors in eddy flux data on inverse model parameter estimation, Biogeosciences, 5, 1311–1324, https://doi.org/10.5194/bg-5-1311-2008, 2008.
LeBauer, D., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., and Dietze, M. C.: BETYdb: a yield, trait, and ecosystem service database applied to second-generation bioenergy feedstock production, GCB Bioenergy, 10, 61–71, https://doi.org/10.1111/gcbb.12420, 2017.
LeBauer, D. S., Wang, D., Richter, K. T., Davidson, C. C., and Dietze, M. C.: Facilitating feedbacks between field measurements and ecosystem models, Ecol. Monogr., 83, 133–154, https://doi.org/10.1890/12-0137.1, 2013.
Lee, M. S., Hollinger, D. Y., Keenan, T. F., Ouimette, A. P., Ollinger, S. V., and Richardson, A. D.: Model-based analysis of the impact of diffuse radiation on CO2 exchange in a temperate deciduous forest, Agr. Forest Meteorol., 249, 377–389, https://doi.org/10.1016/j.agrformet.2017.11.016, 2018.
Li, J., Duan, Q., Wang, Y.-P., Gong, W., Gan, Y., and Wang, C.: Parameter optimization for carbon and water fluxes in two global land surface models based on surrogate modelling, Int. J. Climatol., 38, e1016–e1031, https://doi.org/10.1002/joc.5428, 2018.
Loeppky, J. L., Sacks, J., and Welch, W. J.: Choosing the Sample Size of a Computer Experiment: A Practical Guide, Technometrics, 51, 366–376, https://doi.org/10.1198/TECH.2009.08040, 2009.
Lu, D., Ricciuto, D., Walker, A., Safta, C., and Munger, W.: Bayesian calibration of terrestrial ecosystem models: a study of advanced Markov chain Monte Carlo methods, Biogeosciences, 14, 4295–4314, https://doi.org/10.5194/bg-14-4295-2017, 2017.
MacBean, N., Peylin, P., Chevallier, F., Scholze, M., and Schürmann, G.: Consistent assimilation of multiple data streams in a carbon cycle data assimilation system, Geosci. Model Dev., 9, 3569–3588, https://doi.org/10.5194/gmd-9-3569-2016, 2016.
McMahon, S. M., Dietze, M. C., Hersh, M. H., Moran, E. V., and Clark, J. S.: A Predictive Framework to Understand Forest Responses to Global Change, Ann. NY Acad. Sci., 1162, 221–236, https://doi.org/10.1111/j.1749-6632.2009.04495.x, 2009.
Medlyn, B. E., Zaehle, S., De Kauwe, M. G., Walker, A. P., Dietze, M. C., Hanson, P. J., Hickler, T., Jain, A. K., Luo, Y., Parton, W., Prentice, I. C., Thornton, P. E., Wang, S., Wang, Y.-P., Weng, E., Iversen, C. M., McCarthy, H. R., Warren, J. M., Oren, R., and Norby, R. J.: Using ecosystem experiments to improve vegetation models, Nat. Clim. Change, 5, 528–534, https://doi.org/10.1038/nclimate2621, 2015.
Medvigy, D., Wofsy, S. C., Munger, J. W., Hollinger, D. Y., and Moorcroft, P. R.: Mechanistic scaling of ecosystem function and dynamics in space and time: Ecosystem Demography model version 2, J. Geophys. Res.-Biogeosci., 114, G01002, https://doi.org/10.1029/2008JG000812, 2009.
Moorcroft, P. R., Hurtt, G. C., and Pacala, S. W.: A method for scaling vegetation dynamics: The Ecosystem Demography model (ED), Ecol. Monogr., 71, 557–586, https://doi.org/10.1890/0012-9615(2001)071[0557:AMFSVD]2.0.CO;2, 2001.
Oakley, J. E. and Youngman, B. D.: Calibration of Stochastic Computer Simulators Using Likelihood Emulation, Technometrics, 59, 80–92, https://doi.org/10.1080/00401706.2015.1125391, 2017.
Phillips, C. L., Bond-Lamberty, B., Desai, A. R., Lavoie, M., Risk, D., Tang, J., Todd-Brown, K., and Vargas, R.: The value of soil respiration measurements for interpreting and modeling terrestrial carbon cycling, Plant Soil, 413, 1–25, https://doi.org/10.1007/s11104-016-3084-x, 2017.
Post, H., Vrugt, J. A., Fox, A., Vereecken, H., and Hendricks, F. H.: Estimation of Community Land Model parameters for an improved assessment of net carbon fluxes at European sites, J. Geophys. Res.-Biogeosci., 122, 661–689, https://doi.org/10.1002/2015JG003297, 2017.
Rasmussen, C. E. and Williams, C. K. I.: Gaussian processes for machine learning, available at: http://www.gaussianprocess.org/gpml/chapters/RW.pdf (last access: 30 September 2018), 2006.
Raupach, M. R., Rayner, P. J., Barrett, D. J., DeFries, R. S., Heimann, M., Ojima, D. S., Quegan, S., and Schmullius, C. C.: Model–data synthesis in terrestrial carbon observation: methods, data requirements and data uncertainty specifications, Global Change Biol., 11, 378–397, https://doi.org/10.1111/j.1365-2486.2005.00917.x, 2005.
Ray, J., Hou, Z., Huang, M., Sargsyan, K., and Swiler, L.: Bayesian calibration of the Community Land Model using surrogates, SIAM/ASA J. Uncertain. Quantif., 3, 199–233, https://doi.org/10.1137/140957998, 2015.
Ricciuto, D. M., Davis, K. J., and Keller, K.: A Bayesian calibration of a simple carbon cycle model: The role of observations in estimating and reducing uncertainty, Global Biogeochem. Cy., 22, https://doi.org/10.1029/2006GB002908, 2008.
Richardson, A. D., Hollinger, D. Y., Burba, G. G., Davis, K. J., Flanagan, L. B., Katul, G. G., Munger, J. W., Ricciuto, D. M., Stoy, P. C., Suyker, A. E., Verma, S. B., and Wofsy, S. C.: A multi-site analysis of random error in tower-based measurements of carbon and energy fluxes, Agr. Forest Meteorol., 136, 1–18, https://doi.org/10.1016/j.agrformet.2006.01.007, 2006.
Richardson, A. D., Williams, M., Hollinger, D. Y., Moore, D. J. P., Dail, D. B., Davidson, E. A., Scott, N. A., Evans, R. S., Hughes, H., Lee, J. T., Rodrigues, C., and Savage, K.: Estimating parameters of a forest ecosystem C model with measurements of stocks and fluxes as joint constraints, Oecologia, 164, 25–40, https://doi.org/10.1007/s00442-010-1628-y, 2010.
Sacks, J., Welch, W. J., Mitchell, T. J., and Wynn, H. P.: Design and Analysis of Computer Experiments, Stat. Sci., 4, 409–423, https://doi.org/10.1214/ss/1177012413, 1989.
Sacks, W. J., Schimel, D. S., Monson, R. K., and Braswell, B. H.: Model-data synthesis of diurnal and seasonal CO2 fluxes at Niwot Ridge, Colorado, Global Change Biol., 12, 240–259, https://doi.org/10.1111/j.1365-2486.2005.01059.x, 2006.
Thomas, R. Q., Brooks, E. B., Jersild, A. L., Ward, E. J., Wynne, R. H., Albaugh, T. J., Dinon-Aldridge, H., Burkhart, H. E., Domec, J.-C., Fox, T. R., Gonzalez-Benecke, C. A., Martin, T. A., Noormets, A., Sampson, D. A., and Teskey, R. O.: Leveraging 35 years of Pinus taeda research in the southeastern US to constrain forest carbon cycle predictions: regional data assimilation using ecosystem experiments, Biogeosciences, 14, 3525–3547, https://doi.org/10.5194/bg-14-3525-2017, 2017.
Trudinger, C. M., Raupach, M. R., Rayner, P. J., Kattge, J., Liu, Q., Pak, B., Reichstein, M., Renzullo, L., Richardson, A. D., Roxburgh, S. H., Styles, J., Wang, Y. Y., Briggs, P., Barrett, D., and Nikolova, S.: OptIC project: An intercomparison of optimization techniques for parameter estimation in terrestrial biogeochemical models, J. Geophys. Res.-Biogeosci., 112, G02027, https://doi.org/10.1029/2006JG000367, 2007.
van Oijen, M.: Bayesian Methods for Quantifying and Reducing Uncertainty and Error in Forest Models, Current Forestry Reports, 3, 269–280, https://doi.org/10.1007/s40725-017-0069-9, 2017.
van Oijen, M., Cameron, D. R., Butterbach-Bahl, K., Farahbakhshazad, N., Jansson, P.-E., Kiese, R., Rahn, K.-H., Werner, C., and Yeluripati, J. B.: A Bayesian framework for model calibration, comparison and analysis: Application to four models for the biogeochemistry of a Norway spruce forest, Agr. Forest Meteorol., 151, 1609–1621, https://doi.org/10.1016/j.agrformet.2011.06.017, 2011.
Walker, A. P., Ye, M., Lu, D., De Kauwe, M. G., Gu, L., Medlyn, B. E., Rogers, A., and Serbin, S. P.: The multi-assumption architecture and testbed (MAAT v1.0): R code for generating ensembles with dynamic model structure and analysis of epistemic uncertainty from multiple sources, Geosci. Model Dev., 11, 3159–3185, https://doi.org/10.5194/gmd-11-3159-2018, 2018.
Wang, C., Duan, Q., Gong, W., Ye, A., Di, Z., and Miao, C.: An evaluation of adaptive surrogate modeling based optimization with two benchmark problems, Environ. Modell. Softw., 60, 167–179, https://doi.org/10.1016/j.envsoft.2014.05.026, 2014.
Williams, M., Richardson, A. D., Reichstein, M., Stoy, P. C., Peylin, P., Verbeeck, H., Carvalhais, N., Jung, M., Hollinger, D. Y., Kattge, J., Leuning, R., Luo, Y., Tomelleri, E., Trudinger, C. M., and Wang, Y.-P.: Improving land surface models with FLUXNET data, Biogeosciences, 6, 1341–1359, https://doi.org/10.5194/bg-6-1341-2009, 2009.
Short summary
The computer models we use to understand and forecast the ecosystem changes have multiple components that determine their outcomes. Due to our limited observation capacities, these components bear uncertainties that in return affect our predictions. While there are techniques for reducing these uncertainties, they are not applicable to every model due to computational and statistical barriers. This research presents a method that lowers those barriers and allows us to improve model predictions.
The computer models we use to understand and forecast the ecosystem changes have multiple...
Altmetrics
Final-revised paper
Preprint