Bayesian calibration of simple forest models with multiplicative mathematical structure: A case study with two Light Use Efficiency models in an alpine forest

Abstract Forest models are increasingly being used to study ecosystem functioning, through simulation of carbon fluxes and productivity in different biomes and plant functional types all over the world. Several forest models based on the concept of Light Use Efficiency (LUE) rely mostly on a simplified mathematical structure and empirical parameters, require little amount of data to be run, and their computations are usually fast. However, possible calibration issues must be investigated in order to ensure reliable results. Here we addressed the important issue of delayed convergence when calibrating LUE models, characterized by a multiplicative structure, with a Bayesian approach. We tested two models (Prelued and the Horn and Schulz (2011a) model), applying three Markov Chain Monte Carlo-based algorithms with different number of iterations, and different sets of prior parameter distributions with increasing information content. The results showed that recently proposed algorithms for adaptive calibration did not confer a clear advantage over the Metropolis–Hastings Random Walk algorithm for the forest models used here, and that a high number of iterations is required to stabilize in the convergence region. This can be partly explained by the multiplicative mathematical structure of the models, with high correlations between parameters, and by the use of empirical parameters with neither ecological nor physiological meaning. The information content of the prior distributions of the parameters did not play a major role in reaching convergence with a lower number of iterations. We conclude that there is a need for a more careful approach to calibration to solve potential problems when applying models characterized by a multiplicative mathematical structure. Moreover, the calibration proved time consuming and mathematically difficult, so advantages of using a computationally fast and user-friendly model were lost due to the calibration process needed to obtain reliable results.

[1]  Christina Eisfelder,et al.  Quantifying the carbon uptake by vegetation for Europe on a 1 km 2 resolution using a remote sensing driven vegetation model , 2013 .

[2]  R. Waring,et al.  A generalised model of forest productivity using simplified concepts of radiation-use efficiency, carbon balance and partitioning , 1997 .

[3]  R. Ceulemans,et al.  Footprint-adjusted net ecosystem CO2 exchange and carbon balance components of a temperate forest , 2006 .

[4]  Cajo J. F. ter Braak,et al.  A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: easy Bayesian computing for real parameter spaces , 2006, Stat. Comput..

[5]  T Vesala,et al.  Contributions of climate, leaf area index and leaf physiology to variation in gross primary production of six coniferous forests across Europe: a model-based analysis. , 2009, Tree physiology.

[6]  Charles J. Geyer,et al.  Practical Markov Chain Monte Carlo , 1992 .

[7]  J. Yeluripati,et al.  A Bayesian framework for model calibration, comparison and analysis: Application to four models for the biogeochemistry of a Norway spruce forest , 2011 .

[8]  David Gustafsson,et al.  Bayesian calibration of a model describing carbon, water and heat fluxes for a Swedish boreal forest stand. , 2008 .

[9]  Karsten Schulz,et al.  Spatial extrapolation of light use efficiency model parameters to predict gross primary production , 2011 .

[10]  Christopher J. Still,et al.  Large‐scale plant light‐use efficiency inferred from the seasonal cycle of atmospheric CO2 , 2004 .

[11]  A. Mäkelä,et al.  Acclimation of photosynthetic capacity in Scots pine to the annual cycle of temperature. , 2004, Tree physiology.

[12]  S. T. Gower,et al.  A cross‐biome comparison of daily light use efficiency for gross primary production , 2003 .

[13]  B. Law,et al.  An improved analysis of forest carbon dynamics using data assimilation , 2005 .

[14]  D. Hollinger,et al.  Uncertainty in eddy covariance measurements and its application to physiological models. , 2005, Tree physiology.

[15]  Tyler Smith,et al.  Bayesian methods in hydrologic modeling: A study of recent advancements in Markov chain Monte Carlo techniques , 2008 .

[16]  A. Mäkelä,et al.  Does canopy mean nitrogen concentration explain variation in canopy light use efficiency across 14 contrasting forest sites? , 2012, Tree physiology.

[17]  H. Haario,et al.  An adaptive Metropolis algorithm , 2001 .

[18]  C. Wirth,et al.  Reconciling Carbon-cycle Concepts, Terminology, and Methods , 2006, Ecosystems.

[19]  Damiano Gianelle,et al.  Bayesian optimization of a light use efficiency model for the estimation of daily gross primary productivity in a range of Italian forest ecosystems , 2015 .

[20]  A. Mäkelä,et al.  Bayesian calibration, comparison and averaging of six forest models, using data from Scots pine stands across Europe , 2013 .

[21]  John Skilling,et al.  Data analysis : a Bayesian tutorial , 1996 .

[22]  Alan R. Ek,et al.  Process-based models for forest ecosystem management: current state of the art and challenges for practical implementation. , 2000, Tree physiology.

[23]  Flavio Manenti,et al.  Better reformulation of kinetic models , 2010, Comput. Chem. Eng..

[24]  Rainer Storn,et al.  Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces , 1997, J. Glob. Optim..

[25]  Ron Smith,et al.  Bayesian calibration of process-based forest models: bridging the gap between models and data. , 2005, Tree physiology.

[26]  Damian Barrett,et al.  Conversion of canopy intercepted radiation to photosynthate: review of modelling approaches for regional scales. , 2003, Functional plant biology : FPB.

[27]  Henry L. Gholz,et al.  Climatic factors controlling the productivity of pine stands: a model-based analysis , 1994 .

[28]  A. Cescatti,et al.  Main determinants of forest soil respiration along an elevation/temperature gradient in the Italian Alps , 2005 .

[29]  Peter C. Young,et al.  The seasonal temperature dependency of photosynthesis and respiration in two deciduous forests , 2004 .

[30]  M. Williams,et al.  Net primary production of forests: a constant fraction of gross primary production? , 1998, Tree physiology.

[31]  Georgios Xenakis,et al.  Sensitivity and uncertainty analysis from a coupled 3-PG and soil organic matter decomposition model , 2008 .

[32]  T. A. Black,et al.  Optimization of ecosystem model parameters through assimilating eddy covariance flux data with an ensemble Kalman filter , 2008 .

[33]  Xinyou Yin,et al.  Extension of a biochemical model for the generalized stoichiometry of electron transport limited C3 photosynthesis , 2004 .

[34]  Yiqi Luo,et al.  Assimilation of multiple data sets with the ensemble Kalman filter to improve forecasts of forest carbon dynamics. , 2011, Ecological applications : a publication of the Ecological Society of America.

[35]  M. Oijen,et al.  Simple equations for dynamic models of the effects of CO2 and O3 on light-use efficiency and growth of crops , 2004 .

[36]  Sylvia Richardson,et al.  Markov Chain Monte Carlo in Practice , 1997 .

[37]  Changbin Li,et al.  Simultaneously assimilating multivariate data sets into the two-source evapotranspiration model by Bayesian approach: application to spring maize in an arid region of northwestern China , 2014 .

[38]  Markus Reichstein,et al.  On the assignment of prior errors in Bayesian inversions of CO2 surface fluxes , 2006 .

[39]  Andreas Huth,et al.  Connecting dynamic vegetation models to data – an inverse perspective , 2012 .

[40]  Keith Beven,et al.  The Predictive Uncertainty of Land Surface Fluxes in Response to Increasing Ambient Carbon Dioxide , 2001 .

[41]  Steven W. Running,et al.  Testing scale dependent assumptions in regional ecosystem simulations , 1994 .

[42]  B. Rannala Identi(cid:142)ability of Parameters in MCMC Bayesian Inference of Phylogeny , 2002 .

[43]  I. Mammarella,et al.  Estimating nocturnal ecosystem respiration from the vertical turbulent flux and change in storage of CO2 , 2009 .

[44]  Kathy Steppe,et al.  Seasonal leaf dynamics for tropical evergreen forests in a process-based global ecosystem model , 2012 .

[45]  Walter R. Gilks,et al.  Strategies for improving MCMC , 1995 .

[46]  Christian P. Robert,et al.  Monte Carlo Statistical Methods , 2005, Springer Texts in Statistics.

[47]  Cosmin Safta,et al.  Bayesian calibration of terrestrial ecosystem models: a study of advanced Markov chain Monte Carlo methods , 2017 .

[48]  Christoph Heinze,et al.  Evaluation of the carbon cycle components in the Norwegian Earth System Model (NorESM) , 2012 .

[49]  T. Vesala,et al.  On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm , 2005 .

[50]  J. Berry,et al.  A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species , 1980, Planta.

[51]  L. M. Berliner,et al.  A Bayesian tutorial for data assimilation , 2007 .

[52]  L. S. Pereira,et al.  Crop evapotranspiration : guidelines for computing crop water requirements , 1998 .

[53]  A. Arneth,et al.  Separation of net ecosystem exchange into assimilation and respiration using a light response curve approach: critical issues and global evaluation , 2010 .

[54]  Shobha Kondragunta,et al.  Estimating forest biomass in the USA using generalized allometric models and MODIS land products , 2006 .

[55]  Keith Beven,et al.  Bayesian estimation of uncertainty in land surface‐atmosphere flux predictions , 1997 .

[56]  S. Running,et al.  Global Terrestrial Gross and Net Primary Productivity from the Earth Observing System , 2000 .

[57]  A. Mäkelä,et al.  Calibration and validation of a semi-empirical flux ecosystem model for coniferous forests in the Boreal region , 2016 .

[58]  Eero Nikinmaa,et al.  Developing an empirical model of stand GPP with the LUE approach: analysis of eddy covariance data at five contrasting conifer sites in Europe , 2007 .

[59]  K. Schulz,et al.  Identification of a general light use efficiency model for gross primary production , 2010 .

[60]  Fiona Steele,et al.  The use of simple reparameterizations to improve the efficiency of Markov chain Monte Carlo estimation for multilevel models with applications to discrete time survival models , 2009, Journal of the Royal Statistical Society. Series A,.

[61]  Jari Liski,et al.  Heterotrophic soil respiration—Comparison of different models describing its temperature dependence , 2008 .