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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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Bernabucci, U., Biffani, S., Buggiotti, L., Vitali, A., Lacetera, N., & Nardone, A. (2014). The effects of heat stress in Italian Holstein dairy cattle. J. Dairy Sci., 97(1), 471–486.
Abstract: The data set for this study comprised 1,488,474 test-day records for milk, fat, and protein yields and fat and protein percentages from 191,012 first-, second-, and third-parity Holstein cows from 484 farms. Data were collected from 2001 through 2007 and merged with meteorological data from 35 weather stations. A linear model (M1) was used to estimate the effects of the temperature-humidity index (THI) on production traits. Least squares means from M1 were used to detect the THI thresholds for milk production in all parities by using a 2-phase linear regression procedure (M2). A multiple-trait repeatability test-model (M3) was used to estimate variance components for all traits and a dummy regression variable (t) was defined to estimate the production decline caused by heat stress. Additionally, the estimated variance components and M3 were used to estimate traditional and heat-tolerance breeding values (estimated breeding values, EBV) for milk yield and protein percentages at parity 1. An analysis of data (M2) indicated that the daily THI at which milk production started to decline for the 3 parities and traits ranged from 65 to 76. These THI values can be achieved with different temperature/humidity combinations with a range of temperatures from 21 to 36°C and relative humidity values from 5 to 95%. The highest negative effect of THI was observed 4 d before test day over the 3 parities for all traits. The negative effect of THI on production traits indicates that first-parity cows are less sensitive to heat stress than multiparous cows. Over the parities, the general additive genetic variance decreased for protein content and increased for milk yield and fat and protein yield. Additive genetic variance for heat tolerance showed an increase from the first to third parity for milk, protein, and fat yield, and for protein percentage. Genetic correlations between general and heat stress effects were all unfavorable (from -0.24 to -0.56). Three EBV per trait were calculated for each cow and bull (traditional EBV, traditional EBV estimated with the inclusion of THI covariate effect, and heat tolerance EBV) and the rankings of EBV for 283 bulls born after 1985 with at least 50 daughters were compared. When THI was included in the model, the ranking for 17 and 32 bulls changed for milk yield and protein percentage, respectively. The heat tolerance genetic component is not negligible, suggesting that heat tolerance selection should be included in the selection objectives.
Keywords: Animals; Breeding; Cattle; Dietary Fats/analysis; Dietary Proteins/analysis; Female; Genetic Variation; Heat Stress Disorders/*veterinary; *Hot Temperature; Humans; Humidity; *Lactation; Linear Models; Milk/chemistry; Parity; Phenotype; Weather; dairy cow; heritability; production trait; temperature-humidity index breaking point
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Jing, Q., Bélanger, G., Baron, V., Bonesmo, H., Virkajärvi, P., & Young, D. (2012). Regrowth simulation of the perennial grass timothy. Ecol. Model., 232, 64–77.
Abstract: Several process-based models for simulating the growth of perennial grasses have been developed but few include the simulation of regrowth. The model CATIMO simulates the primary growth of timothy (Phleum pratense L), an important perennial forage grass species in northern regions of Europe and North America. Our objective was to further develop the model CATIMO to simulate timothy regrowth using the concept of reserve-dependent growth. The performance of this modified CATIMO model in simulating leaf area index (LAI), biomass dry matter (DM) yield, and N uptake of regrowth was assessed with data from four independent field experiments in Norway, Finland, and western and eastern Canada using an approach that combines graphical comparison and statistical analysis. Biomass DM yield and N uptake of regrowth were predicted at the same accuracy as primary growth with linear regression coefficients of determination between measured and simulated values greater than 0.79, model simulation efficiencies greater than 0.78, and normalized root mean square errors (14-30% for biomass and 24-34% for N uptake) comparable with the coefficients of variation of measured data (1-21% for biomass and 1-25% for N uptake). The model satisfactorily simulated the regrowth LAI but only up to a value of about 4.0. The modified CATIMO model with its capacity to simulate regrowth provides a framework to simulate perennial grasses with multiple harvests, and to explore management options for sustainable grass production under different environmental conditions. Crown Copyright (C) 2012 Published by Elsevier B.V. All rights reserved.
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Constantin, J., Raynal, H., Casellas, E., Hoffman, H., Bindi, M., Doro, L., et al. (2019). Management and spatial resolution effects on yield and water balance at regional scale in crop models. Agricultural and Forest Meteorology, 275, 184–195.
Abstract: Due to the more frequent use of crop models at regional and national scale, the effects of spatial data input resolution have gained increased attention. However, little is known about the influence of variability in crop management on model outputs. A constant and uniform crop management is often considered over the simulated area and period. This study determines the influence of crop management adapted to climatic conditions and input data resolution on regional-scale outputs of crop models. For this purpose, winter wheat and maize were simulated over 30 years with spatially and temporally uniform management or adaptive management for North Rhine-Westphalia ((similar to)34 083 km(2)), Germany. Adaptive management to local climatic conditions was used for 1) sowing date, 2) N fertilization dates, 3) N amounts, and 4) crop cycle length. Therefore, the models were applied with four different management sets for each crop. Input data for climate, soil and management were selected at five resolutions, from 1 x 1 km to 100 x 100 km grid size. Overall, 11 crop models were used to predict regional mean crop yield, actual evapotranspiration, and drainage. Adaptive management had little effect (< 10% difference) on the 30-year mean of the three output variables for most models and did not depend on soil, climate, and management resolution. Nevertheless, the effect was substantial for certain models, up to 31% on yield, 27% on evapotranspiration, and 12% on drainage compared to the uniform management reference. In general, effects were stronger on yield than on evapotranspiration and drainage, which had little sensitivity to changes in management. Scaling effects were generally lower than management effects on yield and evapotranspiration as opposed to drainage. Despite this trend, sensitivity to management and scaling varied greatly among the models. At the annual scale, effects were stronger in certain years, particularly the management effect on yield. These results imply that depending on the model, the representation of management should be carefully chosen, particularly when simulating yields and for predictions on annual scale.
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