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Mansouri, M., Dumont, B., & Destain, M. - F. (2013). Modeling and prediction of nonlinear environmental system using Bayesian methods. Computers and Electronics in Agriculture, 92, 16–31.
Abstract: An environmental dynamic system is usually modeled as a nonlinear system described by a set of nonlinear ODEs. A central challenge in computational modeling of environmental systems is the determination of the model parameters. In these cases, estimating these variables or parameters from other easily obtained measurements can be extremely useful. This work addresses the problem of monitoring and modeling a leaf area index and soil moisture model (LSM) using state estimation. The performances of various conventional and state-of-the-art state estimation techniques are compared when they are utilized to achieve this objective. These techniques include the extended Kalman filter (EKF), particle filter (PF), and the more recently developed technique variational filter (VF). Specifically, two comparative studies are performed. In the first comparative study, the state variables (the leaf-area index LAI, the volumetric water content of the soil layer 1, HUR1 and the volumetric water content of the soil layer 2, HUR2) are estimated from noisy measurements of these variables, and the various estimation techniques are compared by computing the estimation root mean square error (RMSE) with respect to the noise-free data. In the second comparative study, the state variables as well as the model parameters are simultaneously estimated. In this case, in addition to comparing the performances of the various state estimation techniques, the effect of number of estimated model parameters on the accuracy and convergence of these techniques are also assessed. The results of both comparative studies show that the PF provides a higher accuracy than the EKF, which is due to the limited ability of the EKF to handle highly nonlinear processes. The results also show that the VF provides a significant improvement over the PF because, unlike the PF which depends on the choice of sampling distribution used to estimate the posterior distribution, the VF yields an optimum choice of the sampling distribution, which also accounts for the observed data. The results of the second comparative study show that, for all techniques, estimating more model parameters affects the estimation accuracy as well as the convergence of the estimated states and parameters. However, the VF can still provide both convergence as well as accuracy related advantages over other estimation methods. (C) 2013 Elsevier B.V. All rights reserved.
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Malone, R. W., Kersebaum, K. C., Kaspar, T. C., Ma, L., Jaynes, D. B., & Gillette, K. (2017). Winter rye as a cover crop reduces nitrate loss to subsurface drainage as simulated by HERMES. Agric. Water Manage., 184, 156–169.
Abstract: HERMES is a widely used agricultural system model; however, it has never been tested for simulating N loss to subsurface drainage. Here, we integrated a simple drain flbw component into HERMES. We then compared the predictions to four years of data (2002-2005) from central Iowa fields in corn-oybean with winter rye as a cover crop (CC) and without winter rye (NCC). We also compared the HERMES predictions to the more complex Root Zone Water Quality Model (RZWQM) predictions for the same dataset. The average annual observed and simulated N loss to drain flow were 43.8 and 44.4 kg N/ha (NCC) and 17.6 and 18.9 kg N/ha (CC). The slightly over predicted N loss for CC was because of over predicted nitrate concentration, which may be partly caused by slightly under predicted average annual rye shoot N (observed and simulated values were 47.8 and 46.0 kg N/ha). Also, recent research from the site suggests that the soil field capacity may be greater in CC while we used the same soil parameters for both treatments. A local sensitivity analysis suggests that increased field capacity affects HERMES simulations, which includes reduced drain flow nitrate concentrations, increased denitrification, and reduced drain flow volume. HERMES-simulated cumulative monthly drain flow and annual drain flow were reasonable compared to field data and HERMES performance was comparable to other published drainage model tests. Unlike the RZWQM simulations, however, the modified HERMES did riot accurately simulate the year to year variability in nitrate concentration difference between NCC and CC, possibly due in part to the lack of partial mixing and displacement of the soil solution. The results suggest that 1) the relatively simple model HERMES is a promising tool to estimate annual N loss to drain flow under corn-soybean rotations with winter rye as a cover crop and 2) soil field capacity is a critical parameter to investigate to more thoroughly understand and appropriately model denitrification and N losses to subsurface drainage. Published by Elsevier B.V.
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Vilvert, E., Lana, M., Zander, P., & Sieber, S. (2018). Multi-model approach for assessing the sunflower food value chain in Tanzania. Agric. Syst., 159, 103–110.
Abstract: Sunflower is one of the major oilseeds produced in Tanzania, but due to insufficient domestic production more than half of the country’s demand is imported. The improvement of the sunflower food value chain (FVC) understanding is important to ensure an increase in the production, availability, and quality of edible oil. In order to analyse causes and propose solutions to increase the production of sunflower oil, a conceptual framework that proposes the combined use of different models to provide insights about the sunflower FVC was developed. This research focus on the identification of agricultural models that can provide a better understanding of the sunflower FVC in Tanzania, especially within the context of food security improvement. A FVC scheme was designed considering the main steps of sunflower production. Thereafter, relevant models were selected and placed along each step of the FVC. As result, the sunflower FVC model in Tanzania is organized in five steps, namely (1) natural resources; (2) crop production; (3) oil processing; (4) trade; and (5) consumption. Step 1 uses environmental indicators to analyse soil parameters on soil-water models (SWAT, LPJmL, APSIM or CroSyst), with outputs providing data for step 2 of the FVC. In the production step, data from step 1, together with other inputs, is used to run crop models (DSSAT, HERMES, MONICA, STICS, EPIC or AquaCrop) that analyse the impact on sunflower yields. Thereafter, outputs from crop models serve as input for bio-economic farm models (FSSIM or MODAM) to estimate production costs and farm income by optimizing resource allocation planning for step 2. In addition, outputs from crop models are used as inputs for macro-economic models (GTAP, MAGNET or MagPie) by adjusting supply functions and environmental impacts within steps 3, 4, and 5. These models simulate supply and demand, including the processing of products to determine prices and trade volumes at market equilibrium. In turn, these data is used by bio-economic farm models to assess sunflower returns for different farm types and agro-environmental conditions. Due to the large variety of models, it is possible to assess significant parts of the FVC, reducing the need to make assumptions, while improving the understanding of the FVC.
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Hoffmann, H., Zhao, G., Asseng, S., Bindi, M., Biernath, C., Constantin, J., et al. (2016). Impact of spatial soil and climate input data aggregation on regional yield simulations. PLoS One, 11(4), e0151782.
Abstract: We show the error in water-limited yields simulated by crop models which is associated with spatially aggregated soil and climate input data. Crop simulations at large scales (regional, national, continental) frequently use input data of low resolution. Therefore, climate and soil data are often generated via averaging and sampling by area majority. This may bias simulated yields at large scales, varying largely across models. Thus, we evaluated the error associated with spatially aggregated soil and climate data for 14 crop models. Yields of winter wheat and silage maize were simulated under water-limited production conditions. We calculated this error from crop yields simulated at spatial resolutions from 1 to 100 km for the state of North Rhine-Westphalia, Germany. Most models showed yields biased by <15% when aggregating only soil data. The relative mean absolute error (rMAE) of most models using aggregated soil data was in the range or larger than the inter-annual or inter-model variability in yields. This error increased further when both climate and soil data were aggregated. Distinct error patterns indicate that the rMAE may be estimated from few soil variables. Illustrating the range of these aggregation effects across models, this study is a first step towards an ex-ante assessment of aggregation errors in large-scale simulations.
Keywords: systems simulation; nitrogen dynamics; winter-wheat; crop models; data resolution; scale; water; variability; calibration; weather
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Bressan, R. A., Park, H. C., Orsini, F., Oh, D. -ha, Dassanayake, M., Inan, G., et al. (2013). Biotechnology for mechanisms that counteract salt stress in extremophile species: a genome-based view. Plant Biotechnol. Rep., 7(1), 27–37.
Abstract: Molecular genetics has confirmed older research and generated new insights into the ways how plants deal with adverse conditions. This body of research is now being used to interpret stress behavior of plants in new ways, and to add results from most recent genomics-based studies. The new knowledge now includes genome sequences of species that show extreme abiotic stress tolerances, which enables new strategies for applications through either molecular breeding or transgenic engineering. We will highlight some physiological features of the extremophile lifestyle, outline emerging features about halophytism based on genomics, and discuss conclusions about underlying mechanisms.
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