Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET
Abstract
Abstract. The ability to monitor, understand, and predict the dynamics of the terrestrial carbon cycle requires the capacity to robustly and coherently synthesize multiple streams of information that each provide partial information about different pools and fluxes. In this study, we introduce 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 “reanalysis” product that harmonizes carbon pools (leaf, wood, soil) and fluxes (GPP, Ra, Rh, NEE) across the contiguous United States from 1986–2019. We first calibrated this system against plant trait and flux tower net ecosystem exchange (NEE) using a novel emulated hierarchical Bayesian approach. Next, we extended the Tobit–Wishart ensemble filter (TWEnF) state data assimilation (SDA) framework, a generalization of the common ensemble Kalman filter which accounts for censored data and provides a fully Bayesian estimate of model process error, to a regional-scale system with a calibrated localization. Combined with additional workflows for propagating parameter, initial condition, and driver uncertainty, this represents the most complete and robust uncertainty accounting available for terrestrial carbon models. Our initial reanalysis was run on an irregular grid of ∼ 500 points selected using a stratified sampling method to efficientlymore »
- Publication Date:
- Research Org.:
- Brookhaven National Laboratory (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE; National Aeronautics and Space Administration (NASA)
- OSTI Identifier:
- 1864062
- Alternate Identifier(s):
- OSTI ID: 1869268
- Report Number(s):
- BNL-223004-2022-JAAM
Journal ID: ISSN 1991-9603
- Grant/Contract Number:
- SC0012704; 80NSSC17K0711
- Resource Type:
- Published Article
- Journal Name:
- Geoscientific Model Development (Online)
- Additional Journal Information:
- Journal Name: Geoscientific Model Development (Online) Journal Volume: 15 Journal Issue: 8; Journal ID: ISSN 1991-9603
- Publisher:
- Copernicus GmbH
- Country of Publication:
- Germany
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES
Citation Formats
Dokoohaki, Hamze, Morrison, Bailey D., Raiho, Ann, Serbin, Shawn P., Zarada, Katie, Dramko, Luke, and Dietze, Michael. Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET. Germany: N. p., 2022.
Web. doi:10.5194/gmd-15-3233-2022.
Dokoohaki, Hamze, Morrison, Bailey D., Raiho, Ann, Serbin, Shawn P., Zarada, Katie, Dramko, Luke, & Dietze, Michael. Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET. Germany. https://doi.org/10.5194/gmd-15-3233-2022
Dokoohaki, Hamze, Morrison, Bailey D., Raiho, Ann, Serbin, Shawn P., Zarada, Katie, Dramko, Luke, and Dietze, Michael. Wed .
"Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET". Germany. https://doi.org/10.5194/gmd-15-3233-2022.
@article{osti_1864062,
title = {Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET},
author = {Dokoohaki, Hamze and Morrison, Bailey D. and Raiho, Ann and Serbin, Shawn P. and Zarada, Katie and Dramko, Luke and Dietze, Michael},
abstractNote = {Abstract. The ability to monitor, understand, and predict the dynamics of the terrestrial carbon cycle requires the capacity to robustly and coherently synthesize multiple streams of information that each provide partial information about different pools and fluxes. In this study, we introduce 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 “reanalysis” product that harmonizes carbon pools (leaf, wood, soil) and fluxes (GPP, Ra, Rh, NEE) across the contiguous United States from 1986–2019. We first calibrated this system against plant trait and flux tower net ecosystem exchange (NEE) using a novel emulated hierarchical Bayesian approach. Next, we extended the Tobit–Wishart ensemble filter (TWEnF) state data assimilation (SDA) framework, a generalization of the common ensemble Kalman filter which accounts for censored data and provides a fully Bayesian estimate of model process error, to a regional-scale system with a calibrated localization. Combined with additional workflows for propagating parameter, initial condition, and driver uncertainty, this represents the most complete and robust uncertainty accounting available for terrestrial carbon models. Our initial reanalysis was run on an irregular grid of ∼ 500 points selected using a stratified sampling method to efficiently capture environmental heterogeneity. Remotely sensed observations of aboveground biomass (Landsat LandTrendr) and leaf area index (LAI) (MODIS MOD15) were sequentially assimilated into the SIPNET model. Reanalysis soil carbon, which was indirectly constrained based on modeled covariances, showed general agreement with SoilGrids, an independent soil carbon data product. Reanalysis NEE, which was constrained based on posterior ensemble weights, also showed good agreement with eddy flux tower NEE and reduced root mean square error (RMSE) compared to the calibrated forecast. Ultimately, PEcAn's new open-source regional data assimilation framework provides a scalable workflow for harmonizing multiple data constraints and providing a uniform synthetic platform for carbon monitoring, reporting, and verification (MRV) as well as accelerating terrestrial carbon cycle research.},
doi = {10.5194/gmd-15-3233-2022},
journal = {Geoscientific Model Development (Online)},
number = 8,
volume = 15,
place = {Germany},
year = {Wed Apr 20 00:00:00 EDT 2022},
month = {Wed Apr 20 00:00:00 EDT 2022}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.5194/gmd-15-3233-2022
https://doi.org/10.5194/gmd-15-3233-2022
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Assimilation of Remotely Sensed Leaf Area Index into the Noah-MP Land Surface Model: Impacts on Water and Carbon Fluxes and States over the Continental United States
journal, July 2019
- Kumar, Sujay V.; M. Mocko, David; Wang, Shugong
- Journal of Hydrometeorology, Vol. 20, Issue 7
Spatial scale affects novel and disappeared climate change projections in Alaska
journal, September 2019
- Morrison, Bailey D.; Heath, Katy; Greenberg, Jonathan A.
- Ecology and Evolution, Vol. 9, Issue 21
Atmospheric inversions for estimating CO2 fluxes: methods and perspectives
book, January 2010
- Ciais, P.; Rayner, P.; Chevallier, F.
- Greenhouse Gas Inventories
A comprehensive uncertainty quantification of large-scale process-based crop modeling frameworks
journal, July 2021
- Dokoohaki, Hamze; Kivi, Marissa S.; Martinez-Feria, Rafael
- Environmental Research Letters, Vol. 16, Issue 8
Non-Gaussian data assimilation of satellite-based leaf area index observations with an individual-based dynamic global vegetation model
journal, January 2017
- Arakida, Hazuki; Miyoshi, Takemasa; Ise, Takeshi
- Nonlinear Processes in Geophysics, Vol. 24, Issue 3
Implementation of the LandTrendr Algorithm on Google Earth Engine
journal, May 2018
- Kennedy, Robert; Yang, Zhiqiang; Gorelick, Noel
- Remote Sensing, Vol. 10, Issue 5
Ecoregions of the Conterminous United States
journal, March 1987
- Omernik, James M.
- Annals of the Association of American Geographers, Vol. 77, Issue 1
BETYdb: a yield, trait, and ecosystem service database applied to second-generation bioenergy feedstock production
journal, January 2017
- LeBauer, David; Kooper, Rob; Mulrooney, Patrick
- GCB Bioenergy, Vol. 10, Issue 1
Joint assimilation of eddy covariance flux measurements and FAPAR products over temperate forests within a process‐oriented biosphere model
journal, September 2015
- Bacour, C.; Peylin, P.; MacBean, N.
- Journal of Geophysical Research: Biogeosciences, Vol. 120, Issue 9
The Land Variational Ensemble Data Assimilation Framework: LAVENDAR v1.0.0
journal, January 2020
- Pinnington, Ewan; Quaife, Tristan; Lawless, Amos
- Geoscientific Model Development, Vol. 13, Issue 1
Probabilistic Forecasting and Bayesian Data Assimilation
journal, May 2015
- Reich, Sebastian; Cotter, Colin
Use of inverse modelling and Bayesian optimization for investigating the effect of biochar on soil hydrological properties
journal, September 2018
- Dokoohaki, Hamze; Miguez, Fernando E.; Archontoulis, Sotirios
- Agricultural Water Management, Vol. 208
An improved state-parameter analysis of ecosystem models using data assimilation
journal, December 2008
- Chen, M.; Liu, S.; Tieszen, L. L.
- Ecological Modelling, Vol. 219, Issue 3-4
Gaps in knowledge and data driving uncertainty in models of photosynthesis
journal, May 2013
- Dietze, Michael C.
- Photosynthesis Research, Vol. 119, Issue 1-2
On the Efficiency of Covariance Localisation of the Ensemble Kalman Filter Using Augmented Ensembles
journal, February 2019
- Farchi, Alban; Bocquet, Marc
- Frontiers in Applied Mathematics and Statistics, Vol. 5
SoilGrids250m: Global gridded soil information based on machine learning
journal, February 2017
- Hengl, Tomislav; Mendes de Jesus, Jorge; Heuvelink, Gerard B. M.
- PLOS ONE, Vol. 12, Issue 2
A New GIS-based Solar Radiation Model and Its Application to Photovoltaic Assessments
journal, April 2004
- Suri, Marcel; Hofierka, Jaroslav
- Transactions in GIS, Vol. 8, Issue 2
A Large and Persistent Carbon Sink in the World's Forests
journal, July 2011
- Pan, Y.; Birdsey, R. A.; Fang, J.
- Science, Vol. 333, Issue 6045
Linking big models to big data: efficient ecosystem model calibration through Bayesian model emulation
journal, January 2018
- Fer, Istem; Kelly, Ryan; Moorcroft, Paul R.
- Biogeosciences, Vol. 15, Issue 19
An open-source database for the synthesis of soil radiocarbon data: International Soil Radiocarbon Database (ISRaD) version 1.0
journal, January 2020
- Lawrence, Corey R.; Beem-Miller, Jeffrey; Hoyt, Alison M.
- Earth System Science Data, Vol. 12, Issue 1
An improved analysis of forest carbon dynamics using data assimilation
journal, January 2005
- Williams, Mathew; Schwarz, Paul A.; Law, Beverly E.
- Global Change Biology, Vol. 11, Issue 1
Evaluation of a Data Assimilation System for Land Surface Models Using CLM4.5
journal, October 2018
- Fox, Andrew M.; Hoar, Timothy J.; Anderson, Jeffrey L.
- Journal of Advances in Modeling Earth Systems, Vol. 10, Issue 10
Improving Yasso15 soil carbon model estimates with ensemble adjustment Kalman filter state data assimilation
journal, January 2020
- Viskari, Toni; Laine, Maisa; Kulmala, Liisa
- Geoscientific Model Development, Vol. 13, Issue 12
Multivariate and Multiscale Data Assimilation in Terrestrial Systems: A Review
journal, November 2012
- Montzka, Carsten; Pauwels, Valentijn; Franssen, Harrie-Jan
- Sensors, Vol. 12, Issue 12
Macro to micro: microwave remote sensing of plant water content for physiology and ecology
journal, April 2019
- Konings, Alexandra G.; Rao, Krishna; Steele‐Dunne, Susan C.
- New Phytologist, Vol. 223, Issue 3
Mapping U.S. forest biomass using nationwide forest inventory data and moderate resolution information
journal, April 2008
- Blackard, J.; Finco, M.; Helmer, E.
- Remote Sensing of Environment, Vol. 112, Issue 4
Vegetation demographics in Earth System Models: A review of progress and priorities
journal, October 2017
- Fisher, Rosie A.; Koven, Charles D.; Anderegg, William R. L.
- Global Change Biology, Vol. 24, Issue 1
Simulating the impacts of disturbances on forest carbon cycling in North America: Processes, data, models, and challenges
journal, January 2011
- Liu, Shuguang; Bond-Lamberty, Ben; Hicke, Jeffrey A.
- Journal of Geophysical Research, Vol. 116
Monitoring of water and carbon fluxes using a land data assimilation system: a case study for southwestern France
journal, January 2010
- Albergel, C.; Calvet, J. -C.; Mahfouf, J. -F.
- Hydrology and Earth System Sciences, Vol. 14, Issue 6
On the Validation of Models
journal, July 1981
- Willmott, Cort J.
- Physical Geography, Vol. 2, Issue 2
Constraining a land-surface model with multiple observations by application of the MPI-Carbon Cycle Data Assimilation System V1.0
journal, January 2016
- Schürmann, Gregor J.; Kaminski, Thomas; Köstler, Christoph
- Geoscientific Model Development, Vol. 9, Issue 9
Assimilation of global MODIS leaf area index retrievals within a terrestrial biosphere model: MODIS LEAF AREA INDEX RETRIEVALS
journal, August 2007
- Demarty, J.; Chevallier, F.; Friend, A. D.
- Geophysical Research Letters, Vol. 34, Issue 15
Cutting out the middleman: calibrating and validating a dynamic vegetation model (ED2-PROSPECT5) using remotely sensed surface reflectance
journal, January 2021
- Shiklomanov, Alexey N.; Dietze, Michael C.; Fer, Istem
- Geoscientific Model Development, Vol. 14, Issue 5
Reviews and syntheses: Systematic Earth observations for use in terrestrial carbon cycle data assimilation systems
journal, January 2017
- Scholze, Marko; Buchwitz, Michael; Dorigo, Wouter
- Biogeosciences, Vol. 14, Issue 14
Global Carbon Sinks and Their Variability Inferred from Atmospheric O2 and δ13C
journal, March 2000
- Battle, M.; Bender, M.L.; Tans, P.P.
- Science, Vol. 287, Issue 5462, p. 2467-2470
The ensemble Kalman filter for combined state and parameter estimation
journal, June 2009
- Evensen, Geir
- IEEE Control Systems, Vol. 29, Issue 3
Ensemble-based data assimilation and the localisation problem
journal, March 2010
- Petrie, Ruth E.; Dance, Sarah L.
- Weather, Vol. 65, Issue 3
Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data‐model integration
journal, November 2020
- Fer, Istem; Gardella, Anthony K.; Shiklomanov, Alexey N.
- Global Change Biology, Vol. 27, Issue 1
Data-driven diagnostics of terrestrial carbon dynamics over North America
journal, October 2014
- Xiao, Jingfeng; Ollinger, Scott V.; Frolking, Steve
- Agricultural and Forest Meteorology, Vol. 197
Improving CLM5.0 Biomass and Carbon Exchange Across the Western United States Using a Data Assimilation System
journal, July 2021
- Raczka, Brett; Hoar, Timothy J.; Duarte, Henrique F.
- Journal of Advances in Modeling Earth Systems, Vol. 13, Issue 7
A large carbon sink in the woody biomass of Northern forests
journal, December 2001
- Myneni, R. B.; Dong, J.; Tucker, C. J.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 26
Model-data assimilation of multiple phenological observations to constrain and predict leaf area index
journal, March 2015
- Viskari, Toni; Hardiman, Brady; Desai, Ankur R.
- Ecological Applications, Vol. 25, Issue 2
Development of a data-assimilation system to forecast agricultural systems: A case study of constraining soil water and soil nitrogen dynamics in the APSIM model
journal, May 2022
- Kivi, Marissa S.; Blakely, Bethany; Masters, Michael
- Science of The Total Environment, Vol. 820
Spatio-temporal topsoil organic carbon mapping of a semi-arid Mediterranean region: The role of land use, soil texture, topographic indices and the influence of remote sensing data to modelling
journal, December 2017
- Schillaci, Calogero; Acutis, Marco; Lombardo, Luigi
- Science of The Total Environment, Vol. 601-602
Three decades of simulated global terrestrial carbon fluxes from a data assimilation system confronted with different periods of observations
journal, January 2019
- Castro-Morales, Karel; Schürmann, Gregor; Köstler, Christoph
- Biogeosciences, Vol. 16, Issue 15
Forest biogeochemistry in response to drought
journal, November 2015
- Schlesinger, William H.; Dietze, Michael C.; Jackson, Robert B.
- Global Change Biology, Vol. 22, Issue 7
The Data Assimilation Research Testbed: A Community Facility
journal, September 2009
- Anderson, Jeffrey; Hoar, Tim; Raeder, Kevin
- Bulletin of the American Meteorological Society, Vol. 90, Issue 9
Comparing soil carbon estimates in glaciated soils at a farm scale using geospatial analysis of field and SSURGO data
journal, November 2016
- Mikhailova, E. A.; Altememe, A. H.; Bawazir, A. A.
- Geoderma, Vol. 281
A Method for Scaling Vegetation Dynamics: the Ecosystem Demography Model (ed)
journal, November 2001
- Moorcroft, P. R.; Hurtt, G. C.; Pacala, S. W.
- Ecological Monographs, Vol. 71, Issue 4
Programming With Models: Writing Statistical Algorithms for General Model Structures With NIMBLE
journal, October 2016
- de Valpine, Perry; Turek, Daniel; Paciorek, Christopher J.
- Journal of Computational and Graphical Statistics, Vol. 26, Issue 2
Facilitating feedbacks between field measurements and ecosystem models
journal, May 2013
- LeBauer, David S.; Wang, Dan; Richter, Katherine T.
- Ecological Monographs, Vol. 83, Issue 2
Assimilation of multiple data sets with the ensemble Kalman filter to improve forecasts of forest carbon dynamics
journal, July 2011
- Gao, Chao; Wang, Han; Weng, Ensheng
- Ecological Applications, Vol. 21, Issue 5
Actual evapotranspiration and deficit: biologically meaningful correlates of vegetation distribution across spatial scales
journal, September 1998
- Stephenson, Nathan
- Journal of Biogeography, Vol. 25, Issue 5
Estimating diurnal to annual ecosystem parameters by synthesis of a carbon flux model with eddy covariance net ecosystem exchange observations
journal, February 2005
- Braswell, Bobby H.; Sacks, William J.; Linder, Ernst
- Global Change Biology, Vol. 11, Issue 2
L-band vegetation optical depth and effective scattering albedo estimation from SMAP
journal, September 2017
- Konings, Alexandra G.; Piles, Maria; Das, Narendra
- Remote Sensing of Environment, Vol. 198
Mechanistic scaling of ecosystem function and dynamics in space and time: Ecosystem Demography model version 2
journal, January 2009
- Medvigy, D.; Wofsy, S. C.; Munger, J. W.
- Journal of Geophysical Research, Vol. 114, Issue G1
Detecting trends in forest disturbance and recovery using yearly Landsat time series: 1. LandTrendr — Temporal segmentation algorithms
journal, December 2010
- Kennedy, Robert E.; Yang, Zhiqiang; Cohen, Warren B.
- Remote Sensing of Environment, Vol. 114, Issue 12
Temporal and spatial patterns in vegetation and atmospheric properties from AVIRIS
journal, December 1997
- Roberts, D. A.; Green, R. O.; Adams, J. B.
- Remote Sensing of Environment, Vol. 62, Issue 3
Steering operational synergies in terrestrial observation networks: opportunity for advancing Earth system dynamics modelling
journal, January 2018
- Baatz, Roland; Sullivan, Pamela L.; Li, Li
- Earth System Dynamics, Vol. 9, Issue 2
A new stepwise carbon cycle data assimilation system using multiple data
streams to constrain the simulated land surface carbon cycle
journal, January 2016
- Peylin, Philippe; Bacour, Cédric; MacBean, Natasha
- Geoscientific Model Development, Vol. 9, Issue 9
Satellite-derived LAI products exhibit large discrepancies and can lead to substantial uncertainty in simulated carbon and water fluxes
journal, March 2018
- Liu, Yibo; Xiao, Jingfeng; Ju, Weimin
- Remote Sensing of Environment, Vol. 206