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Paul Miller. Photo.

Paul Miller

Senior lecturer

Paul Miller. Photo.

Optimising CH4 simulations from the LPJ-GUESS model v4.1 using an adaptive Markov chain Monte Carlo algorithm


  • Jalisha T. Kallingal
  • Johan Lindström
  • Paul A. Miller
  • Janne Rinne
  • Maarit Raivonen
  • Marko Scholze

Summary, in English

The processes responsible for methane (CH4) emissions from boreal wetlands are complex; hence, their model representation is complicated by a large number of parameters and parameter uncertainties. The arctic-enabled dynamic global vegetation model LPJ-GUESS (Lund-Potsdam-Jena General Ecosystem Simulator) is one such model that allows quantification and understanding of the natural wetland CH4 fluxes at various scales, ranging from local to regional and global, but with several uncertainties. The model contains detailed descriptions of the CH4 production, oxidation, and transport controlled by several process parameters. Complexities in the underlying environmental processes, warming-driven alternative paths of meteorological phenomena, and changes in hydrological and vegetation conditions highlight the need for a calibrated and optimised version of LPJ-GUESS. In this study, we formulated the parameter calibration as a Bayesian problem, using knowledge of reasonable parameters values as priors. We then used an adaptive Metropolis-Hastings (MH)-based Markov chain Monte Carlo (MCMC) algorithm to improve predictions of CH4 emission by LPJ-GUESS and to quantify uncertainties. Application of this method on uncertain parameters allows for a greater search of their posterior distribution, leading to a more complete characterisation of the posterior distribution with a reduced risk of the sample impoverishment that can occur when using other optimisation methods. For assimilation, the analysis used flux measurement data gathered during the period from 2005 to 2014 from the Siikaneva wetlands in Southern Finland with an estimation of measurement uncertainties. The data are used to constrain the processes behind the CH4 dynamics, and the posterior covariance structures are used to explain how the parameters and the processes are related. To further support the conclusions, the CH4 flux and the other component fluxes associated with the flux are examined. The results demonstrate the robustness of MCMC methods to quantitatively assess the interrelationship between objective function choices, parameter identifiability, and data support. The experiment using real observations from Siikaneva resulted in a reduction in the root-mean-square error (RMSE), from 0.044 to 0.023 gC m-2 d-1, and a 93.89 % reduction in the cost function value. As a part of this work, knowledge about how CH4 data can constrain the parameters and processes is derived. Although the optimisation is performed based on a single site's flux data from Siikaneva, the algorithm is useful for larger-scale multi-site studies for a more robust calibration of LPJ-GUESS and similar models, and the results can highlight where model improvements are needed.


  • MERGE: ModElling the Regional and Global Earth system
  • BECC: Biodiversity and Ecosystem services in a Changing Climate
  • eSSENCE: The e-Science Collaboration
  • Dept of Physical Geography and Ecosystem Science
  • LTH Profile Area: Aerosols
  • Mathematical Statistics
  • LU Profile Area: Nature-based future solutions
  • Centre for Environmental and Climate Science (CEC)

Publishing year







Geoscientific Model Development





Document type

Journal article


Copernicus GmbH


  • Probability Theory and Statistics




  • ISSN: 1991-959X