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Van Oijen, M., & Höglind, M. (2016). Toward a Bayesian procedure for using process-based models in plant breeding, with application to ideotype design. Euphytica, 207(3), 627–643.
Abstract: Process-based grassland models (PBMs) simulate growth and development of vegetation over time. The models tend to have a large number of parameters that represent properties of the plants. To simulate different cultivars of the same species, different parameter values are required. Parameter differences may be interpreted as genetic variation for plant traits. Despite this natural connection between PBMs and plant genetics, there are only few examples of successful use of PBMs in plant breeding. Here we present a new procedure by which PBMs can help design ideotypes, i.e. virtual cultivars that optimally combine properties of existing cultivars. Ideotypes constitute selection targets for breeding. The procedure consists of four steps: (1) Bayesian calibration of model parameters using data from cultivar trials, (2) Estimating genetic variation for parameters from the combination of cultivar-specific calibrated parameter distributions, (3) Identifying parameter combinations that meet breeding objectives, (4) Translating model results to practice, i.e. interpreting parameters in terms of practical selection criteria. We show an application of the procedure to timothy (Phleum pratense L.) as grown in different regions of Norway.
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Persson, T., Kværnø, S., & Höglind, M. (2015). Impact of soil type extrapolation on timothy grass yield under baseline and future climate conditions in southeastern Norway. Clim. Res., 65, 71–86.
Abstract: Interactions between soil properties and climate affect forage grass productivity. Dynamic models, simulating crop performance as a function of environmental conditions, are valid for a specific location with given soil and weather conditions. Extrapolations of local soil properties to larger regions can help assess the requirement for soil input in regional yield estimations. Using the LINGRA model, we simulated the regional yield level and variability of timothy, a forage grass, in Akershus and Ostfold counties, Norway. Soils were grouped according to physical similarities according to 4 sets of criteria. This resulted in 66, 15, 5 and 1 groups of soils. The properties of the soil with the largest area was extrapolated to the other soils within each group and input to the simulations. All analyses were conducted for 100 yr of generated weather representing the period 1961-1990, and climate projections for the period 2046-2065, the Intergovernmental Panel on Climate Change greenhouse gas emission scenario A1B, and 4 global climate models. The simulated regional seasonal timothy yields were 5-13% lower on average and had higher inter-annual variability for the least detailed soil extrapolation than for the other soil extrapolations, across climates. There were up to 20% spatial intra-regional differences in simulated yield between soil extrapolations. The results indicate that, for conditions similar to these studied here, a few representative profiles are sufficient for simulations of average regional seasonal timothy yield. More spatially detailed yield analyses would benefit from more detailed soil input.
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Hjelkrem, A. - G. R., Höglind, M., van Oijen, M., Schellberg, J., Gaiser, T., & Ewert, F. (2017). Sensitivity analysis and Bayesian calibration for testing robustness of the BASGRA model in different environments. Ecol. Model., 359, 80–91.
Abstract: Highlights • The parameters to be fixed were consistent across sites. • Model calibration must be performed separately for each specific case. • Possible to reduce model parameters from 66 to 45. • Strong model reductions must be avoided. • The error term for the training data were characterised by timing (phase shift). Abstract Proper parameterisation and quantification of model uncertainty are two essential tasks in improvement and assessment of model performance. Bayesian calibration is a method that combines both tasks by quantifying probability distributions for model parameters and outputs. However, the method is rarely applied to complex models because of its high computational demand when used with high-dimensional parameter spaces. We therefore combined Bayesian calibration with sensitivity analysis, using the screening method by Morris (1991), in order to reduce model complexity by fixing parameters to which model output was only weakly sensitive to a nominal value. Further, the robustness of the model with respect to reduction in the number of free parameters were examined according to model discrepancy and output uncertainty. The process-based grassland model BASGRA was examined in the present study on two sites in Norway and in Germany, for two grass species (Phleum pratense and Arrhenatherum elatius). According to this study, a reduction of free model parameters from 66 to 45 was possible. The sensitivity analysis showed that the parameters to be fixed were consistent across sites (which differed in climate and soil conditions), while model calibration had to be performed separately for each combination of site and species. The output uncertainty decreased slightly, but still covered the field observations of aboveground biomass. Considering the training data, the mean square error for both the 66 and the 45 parameter model was dominated by errors in timing (phase shift), whereas no general pattern was found in errors when using the validation data. Stronger model reduction should be avoided, as the error term increased and output uncertainty was underestimated.
Keywords: Metropolis-hasting; Morris method; Reducing complexity; Robustness
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Mittenzwei, K., Persson, T., Höglind, M., & Kværnø, S. (2017). Combined effects of climate change and policy uncertainty on the agricultural sector in Norway. Agric. Syst., 153, 118–126.
Abstract: Highlights • A framework to study climate and policy uncertainty in agriculture is presented. • Combining both sources of uncertainty has ambiguous effects on agriculture. • Uncertainty needs to be highlighted in modelling tools for policy analysis. Abstract Farmers are exposed to climate change and uncertainty about how that change will develop. As farm incomes, in Norway and elsewhere, greatly depend on government subsidies, the risk of a policy change constitutes an additional uncertainty source. Hence, climate and policy uncertainty could substantially impact agricultural production and farm income. However, these sources of uncertainty have, so far, rarely been combined in food production analyses. The aim of this study was to determine the effects of a combination of policy and climate uncertainty on agricultural production, land use, and social welfare in Norway. Output yield distributions of spring wheat and timothy, a major forage grass, from simulations with the weather-driven crop models, CSM-CERES-Wheat and, LINGRA, were processed in the a stochastic version Jordmod, a price-endogenous spatial economic sector model of the Norwegian agriculture. To account for potential effects of climate uncertainty within a given future greenhouse gas emission scenario on farm profitability, effects on conditions that represented the projected climate for 2050 under the emission scenario A1B from the 4th assessment report of the Intergovernmental Panel on Climate Change and four Global Climate Models (GCM) was investigated. The uncertainty about the level of payment rates at the time farmers make their management decisions was handled by varying the distribution of payment rates applied in the Jordmod model. These changes were based on the change in the overall level of agricultural support in the past. Three uncertainty scenarios were developed and tested: one with climate change uncertainty, another with payment rate uncertainty, and a third where both types of uncertainty were combined. The three scenarios were compared with results from a deterministic scenario where crop yields and payment rates were constant. Climate change resulted in on average 9% lower cereal production, unchanged grass production and more volatile crop yield as well as 4% higher farm incomes on average compared to the deterministic scenario. The scenario with a combination of climate change and policy uncertainty increased the mean farm income more than a scenario with only one source of uncertainty. On the other hand, land use and farm labour were negatively affected under these conditions compared to the deterministic case. Highlighting the potential influence of climate change and policy uncertainty on the performance of the farm sector our results underline the potential error in neglecting either of these two uncertainties in studies of agricultural production, land use and welfare.
Keywords: Climate change; Norway; Agriculture; Policy uncertainty; Modelling; LINGRA; CSM-CERES-Wheat; DSSAT
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Kipling, R. P., Virkajärvi, P., Breitsameter, L., Curnel, Y., De Swaef, T., Gustavsson, A. - M., et al. (2016). Key challenges and priorities for modelling European grasslands under climate change. Science of the Total Environment, 566-567, 851–864.
Abstract: Grassland-based ruminant production systems are integral to sustainable food production in Europe, converting plant materials indigestible to humans into nutritious food, while providing a range of environmental and cultural benefits. Climate change poses significant challenges for such systems, their productivity and the wider benefits they supply. In this context, grassland models have an important role in predicting and understanding the impacts of climate change on grassland systems, and assessing the efficacy of potential adaptation and mitigation strategies. In order to identify the key challenges for European grassland modelling under climate change, modellers and researchers from across Europe were consulted via workshop and questionnaire. Participants identified fifteen challenges and considered the current state of modelling and priorities for future research in relation to each. A review of literature was undertaken to corroborate and enrich the information provided during the horizon scanning activities. Challenges were in four categories relating to: 1) the direct and indirect effects of climate change on the sward 2) climate change effects on grassland systems outputs 3) mediation of climate change impacts by site, system and management and 4) cross-cutting methodological issues. While research priorities differed between challenges, an underlying theme was the need for accessible, shared inventories of models, approaches and data, as a resource for stakeholders and to stimulate new research. Developing grassland models to effectively support efforts to tackle climate change impacts, while increasing productivity and enhancing ecosystem services, will require engagement with stakeholders and policy-makers, as well as modellers and experimental researchers across many disciplines. The challenges and priorities identified are intended to be a resource 1) for grassland modellers and experimental researchers, to stimulate the development of new research directions and collaborative opportunities, and 2) for policy-makers involved in shaping the research agenda for European grassland modelling under climate change.
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