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Ben Touhami, H.; Bellocchi, G. |
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Title |
Bayesian calibration of the Pasture Simulation model (PaSim) to simulate European grasslands under water stress |
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Journal Article |
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Year |
2015 |
Publication |
Ecological Informatics |
Abbreviated Journal |
Ecological Informatics |
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Volume |
30 |
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Pages |
356-364 |
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Keywords  |
Bayesian calibration framework; Grasslands; Pasture Simulation model; (PaSim); integrated assessment models; chain monte-carlo; climate-change; computation; impacts; vulnerability; likelihoods; france |
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Abstract |
As modeling becomes a more widespread practice in the agro-environmental sciences, scientists need reliable tools to calibrate models against ever more complex and detailed data. We present a generic Bayesian computation framework for grassland simulation, which enables parameter estimation in the Bayesian formalism by using Monte Carlo approaches. We outline the underlying rationale, discuss the computational issues, and provide results from an application of the Pasture Simulation model (PaSim) to three European grasslands. The framework was suited to investigate the challenging problem of calibrating complex biophysical models to data from altered scenarios generated by precipitation reduction (water stress conditions). It was used to infer the parameters of manipulated grassland systems and to assess the gain in uncertainty reduction by updating parameter distributions using measurements of the output variables. |
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1574-9541 |
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CropM, LiveM, ft_macsur |
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MA @ admin @ |
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4697 |
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Author |
Makowski, D. |
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Title |
A simple Bayesian method for adjusting ensemble of crop model outputs to yield observations |
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Journal Article |
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Year |
2017 |
Publication |
European Journal of Agronomy |
Abbreviated Journal |
Europ. J. Agron. |
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88 |
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76-83 |
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Bayesian method; Climate change; Ensemble modelling; Uncertainty; Yield; Linear-Approach; Climate-Change; CO2 |
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Multi-model forecasting has drawn some attention in crop science for evaluating effect of climate change on crop yields. The principle is to run several individual process-based crop models under several climate scenarios in order to generate ensembles of output values. This paper describes a simple Bayesian method – called Bayes linear method- for updating ensemble of crop model outputs using yield observations. The principle is to summarize the ensemble of crop model outputs by its mean and variance, and then to adjust these two quantities to yield observations in order to reduce uncertainty. The adjusted mean and variance combine two sources of information, i.e., the ensemble of crop model outputs and the observations. Interestingly, with this method, observations collected under a given climate scenario can be used to adjust mean and variance of the model ensemble under a different scenario. Another advantage of the proposed method is that it does not rely on a separate calibration of each individual crop model. The uncertainty reduction resulting from the adjustment of an ensemble of crop models to observations was assessed in a numerical application. The implementation of the Bayes linear method systematically reduced uncertainty, but the results showed the effectiveness of this method varied in function of several factors, especially the accuracy of the yield observation, and the covariance between the crop model output and the observation. (C) 2015 Elsevier B.V. All rights reserved. |
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2017-08-07 |
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1161-0301 |
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CropM, ft_macsur |
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MA @ admin @ |
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5171 |
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Author |
Hidy, D.; Barcza, Z.; Haszpra, L.; Churkina, G.; Pintér, K.; Nagy, Z. |
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Title |
Development of the Biome-BGC model for simulation of managed herbaceous ecosystems |
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Journal Article |
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Year |
2012 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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226 |
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99-119 |
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biogeochemical model; biome-bgc; grassland; management; soil moisture; bayesian calibration; carbon flux model; regional applications; bayesian calibration; use efficiency; general-model; exchange; balance; climate; grassland; variability |
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Apart from measurements, numerical models are the most convenient instruments to analyze the carbon and water balance of terrestrial ecosystems and their interactions with changing environmental conditions. The process-based Biome-BGC model is widely used to simulate the storage and flux of water, carbon, and nitrogen within the vegetation, litter, and soil of unmanaged terrestrial ecosystems. Considering herbaceous vegetation related simulations with Biome-BGC, soil moisture and growing season control on ecosystem functioning is inaccurate due to the simple soil hydrology and plant phenology representation within the model. Consequently, Biome-BGC has limited applicability in herbaceous ecosystems because (1) they are usually managed; (2) they are sensitive to soil processes, most of all hydrology; and (3) their carbon balance is closely connected with the growing season length. Our aim was to improve the applicability of Biome-BGC for managed herbaceous ecosystems by implementing several new modules, including management. A new index (heatsum growing season index) was defined to accurately estimate the first and the final days of the growing season. Instead of a simple bucket soil sub-model, a multilayer soil sub-model was implemented, which can handle the processes of runoff, diffusion and percolation. A new module was implemented to simulate the ecophysiological effect of drought stress on plant mortality. Mowing and grazing modules were integrated in order to quantify the functioning of managed ecosystems. After modifications, the Biome-BGC model was calibrated and validated using eddy covariance-based measurement data collected in Hungarian managed grassland ecosystems. Model calibration was performed based on the Bayes theorem. As a result of these developments and calibration, the performance of the model was substantially improved. Comparison with measurement-based estimate showed that the start and the end of the growing season are now predicted with an average accuracy of 5 and 4 days instead of 46 and 85 days as in the original model. Regarding the different sites and modeled fluxes (gross primary production, total ecosystem respiration, evapotranspiration), relative errors were between 18-60% using the original model and 10-18% using the developed model; squares of the correlation coefficients were between 0.02-0.49 using the original model and 0.50-0.81 using the developed model. (c) 2011 Elsevier B.V. All rights reserved. |
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0304-3800 |
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LiveM |
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MA @ admin @ |
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4472 |
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Author |
Höglind, M.; Van Oijen, M.; Cameron, D.; Persson, T. |
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Title |
Process-based simulation of growth and overwintering of grassland using the BASGRA model |
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Journal Article |
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2016 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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335 |
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1-15 |
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Keywords |
Cold hardening; Frost injury; Phleum pratense L.; Process-based; modelling; Winter survival; Yield; low-temperature tolerance; perennial forage crops; dry-matter; production; climate-change; nutritive-value; snow-cover; bayesian; calibration; timothy regrowth; phleum-pratense; lolium-perenne |
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Process-based models (PBM) for simulation of weather dependent grass growth can assist farmers and plant breeders in addressing the challenges of climate change by simulating alternative roads of adaptation. They can also provide management decision support under current conditions. A drawback of existing grass models is that they do not take into account the effect of winter stresses, limiting their use for full-year simulations in areas where winter survival is a key factor for yield security. Here, we present a novel full-year PBM for grassland named BASGRA. It was developed by combining the LINGRA grassland model (Van Oijen et al., 2005a) with models for cold hardening and soil physical winter processes. We present the model and show how it was parameterized for timothy (Phleum pratense L.), the most important forage grass in Scandinavia and parts of North America and Asia. Uniquely, BASGRA simulates the processes taking place in the sward during the transition from summer to winter, including growth cessation and gradual cold hardening, and functions for simulating plant injury due to low temperatures, snow and ice affecting regrowth in spring. For the calibration, we used detailed data from five different locations in Norway, covering a wide range of agroclimatic regions, day lengths (latitudes from 59 degrees to 70 degrees N) and soil conditions. The total dataset included 11 variables, notably above-ground dry matter, leaf area index, tiller density, content of C reserves, and frost tolerance. All data were used in the calibration. When BASGRA was run with the maximum a-posteriori (MAP) parameter vector from the single, Bayesian calibration, nearly all measured variables were simulated to an overall normalized root mean squared error (NRMSE) <0.5. For many site x experiment combinations, NRMSE was <0.3. The temporal dynamics were captured well for most variables, as evaluated by comparing simulated time courses versus data for the individual sites. The results may suggest that BASGRA is a reasonably robust model, allowing for simulation of growth and several important underlying processes with acceptable accuracy for a range of agroclimatic conditions. However, the robustness of the model needs to be tested further using independent data from a wide range of growing conditions. Finally we show an example of application of the model, comparing overwintering risks in two climatically different sites, and discuss future model applications. Further development work should include improved simulation of the dynamics of C reserves, and validation of winter tiller dynamics against independent data. (C) 2016 Elsevier B.V. All rights reserved. |
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2016-07-28 |
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0304-3800 |
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CropM, LiveM, ft_macsur |
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MA @ admin @ |
Serial |
4764 |
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Author |
Mansouri, M.; Dumont, B.; Leemans, V.; Destain, M.-F. |
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Title |
Bayesian methods for predicting LAI and soil water content |
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Journal Article |
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Year |
2014 |
Publication |
Precision Agriculture |
Abbreviated Journal |
Precision Agric. |
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Volume |
15 |
Issue |
2 |
Pages |
184-201 |
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Keywords |
crop model; bayes; data assimilation; extended kalman filtering; particle filtering; variational filtering; leaf-area index; parameter-estimation; crop models; moisture; instruments; management; sensors; state |
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LAI of winter wheat (Triticum aestivum L.) and soil water content of the topsoil (200 mm) and of the subsoil (500 mm) were considered as state variables of a dynamic soil-crop system. This system was assumed to progress according to a Bayesian probabilistic state space model, in which real values of LAI and soil water content were daily introduced in order to correct the model trajectory and reach better future evolution. The chosen crop model was mini STICS which can reduce the computing and execution times while ensuring the robustness of data processing and estimation. To predict simultaneously state variables and model parameters in this non-linear environment, three techniques were used: extended Kalman filtering (EKF), particle filtering (PF), and variational filtering (VF). The significantly improved performance of the VF method when compared to EKF and PF is demonstrated. The variational filter has a low computational complexity and the convergence speed of states and parameters estimation can be adjusted independently. Detailed case studies demonstrated that the root mean square error of the three estimated states (LAI and soil water content of two soil layers) was smaller and that the convergence of all considered parameters was ensured when using VF. Assimilating measurements in a crop model allows accurate prediction of LAI and soil water content at a local scale. As these biophysical properties are key parameters in the crop-plant system characterization, the system has the potential to be used in precision farming to aid farmers and decision makers in developing strategies for site-specific management of inputs, such as fertilizers and water irrigation. |
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1385-2256 |
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CropM, ftnotmacsur |
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MA @ admin @ |
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4629 |
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