Irstea Motive - people:nicolas.dumoulin

Wei W., P. Larrey lassalle, T. Faure, N. Dumoulin, P. Roux, J.D. Mathias
Using the reliability theory for assessing the decision confidence probability for comparative Life Cycle Assessments
Environmental Science & Technology 50 (5), 2016
doi web bib

@article{PUB00046749, author = {Wei W. and Larrey lassalle, P. and Faure, T. and Dumoulin, N. and Roux, P. and Mathias, J.D.}, title = {Using the reliability theory for assessing the decision confidence probability for comparative Life Cycle Assessments}, journal = {Environmental Science & Technology}, volume = {50}, number = {5}, pages = {2272-2280}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00046749}, doi = {http://dx.doi.org/10.1021/acs.est.5b03683}, year = {2016}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA MONTPELLIER UMR ITAP FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA MONTPELLIER UMR ITAP FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {}, }
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J.D. Mathias, A. Alzina, M. Grédiac, P. Michaud, P. Roux, H. De Baynast, C. Delattre, N. Dumoulin, T. Faure, P. Larrey Lassalle, N. Mati Baouche, F. Pennec, S. Sun, N. Tessier Doyen, E. Toussaint, W. Wei
Upcycling sunflower stems as natural fibers for biocomposite applications
Bioresources 10 (4), 2015
abs web bib

One of the big global, environmental, and socioeconomic challenges of today is to make a transition from fossil fuels to biomass as a sustainable supply of renewable raw materials for industry. Growing public awareness of the negative environmental effects of petrochemical-based products adds to the need for alternative production chains, especially in materials science. One option lies in the value-added upcycling of agricultural by-products, which are increasingly being used for biocomposite materials in transport and building sector applications. Here, sunflower by-product (obtained by grinding the stems) is considered as a source of natural fibers for engineered biocomposite material. Recent results are shown for the main mechanical properties of sunflower-based biocomposites and the socioeconomic impact of their use. This paper demonstrates that sunflower stem makes a good candidate feedstock for material applications. This is due not only to its physical and chemical properties, but also to its socioeconomic and environmental rationales.
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@article{PUB00046747, author = {Mathias, J.D. and Alzina, A. and Grédiac, M. and Michaud, P. and Roux, P. and De Baynast, H. and Delattre, C. and Dumoulin, N. and Faure, T. and Larrey Lassalle, P. and Mati Baouche, N. and Pennec, F. and Sun, S. and Tessier Doyen, N. and Toussaint, E. and Wei, W.}, title = {Upcycling sunflower stems as natural fibers for biocomposite applications}, journal = {Bioresources}, volume = {10}, number = {4}, pages = {8076-8088}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00046747}, year = {2015}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; UNIVERSITE DE LIMOGES LABORATOIRE GEMH LIMOGES FRA ; UNIVERSITE DE CLERMONT FERRAND I INSTITUT PASCAL FRA ; UNIVERSITE DE CLERMONT FERRAND I INSTITUT PASCAL FRA ; IRSTEA MONTPELLIER UMR ITAP FRA ; UNIVERSITE DE CLERMONT FERRAND I INSTITUT PASCAL FRA ; UNIVERSITE DE CLERMONT FERRAND I INSTITUT PASCAL FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA MONTPELLIER UMR ITAP FRA ; UNIVERSITE DE CLERMONT FERRAND I INSTITUT PASCAL FRA ; UNIVERSITE DE LIMOGES LABORATOIRE GEMH LIMOGES FRA ; UNIVERSITE DE CLERMONT FERRAND I INSTITUT PASCAL FRA ; UNIVERSITE DE LIMOGES LABORATOIRE GEMH LIMOGES FRA ; UNIVERSITE DE CLERMONT FERRAND I INSTITUT PASCAL FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {One of the big global, environmental, and socioeconomic challenges of today is to make a transition from fossil fuels to biomass as a sustainable supply of renewable raw materials for industry. Growing public awareness of the negative environmental effects of petrochemical-based products adds to the need for alternative production chains, especially in materials science. One option lies in the value-added upcycling of agricultural by-products, which are increasingly being used for biocomposite materials in transport and building sector applications. Here, sunflower by-product (obtained by grinding the stems) is considered as a source of natural fibers for engineered biocomposite material. Recent results are shown for the main mechanical properties of sunflower-based biocomposites and the socioeconomic impact of their use. This paper demonstrates that sunflower stem makes a good candidate feedstock for material applications. This is due not only to its physical and chemical properties, but also to its socioeconomic and environmental rationales.}, }
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T. Rougier, G. Lassalle, H. Drouineau, N. Dumoulin, T. Faure, G. Deffuant, E. Rochard, P. Lambert
The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species
PLoS One 10 (10), 2015
abs doi web bib

Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold temperatures deserved more attention in terms of modelling, but further in conservation planning as well.
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@article{PUB00045248, author = {Rougier, T. and Lassalle, G. and Drouineau, H. and Dumoulin, N. and Faure, T. and Deffuant, G. and Rochard, E. and Lambert, P.}, title = {The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species}, title = {L'utilisation conjointe de modèles de distribution d'espèces mécanistes et corrélatifs bénéficie aux espèces menacées}, journal = {PLoS One}, volume = {10}, number = {10}, pages = {21}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00045248}, doi = {http://dx.doi.org/10.1371/journal.pone.0139194}, year = {2015}, affiliation = {IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA}, abstract = {Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold temperatures deserved more attention in terms of modelling, but further in conservation planning as well.}, }
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W. Wei, P. Larrey Lassalle, T. Faure, N. Dumoulin, P. Roux, J.D. Mathias
How to conduct a proper sensitivity analysis in life cycle assessment: Taking into account correlations within LCI data and interactions within the LCA calculation model
Environmental Science & Technology 49 (1), 2015
abs doi web bib

Sensitivity analysis (SA) is a significant tool for studying the robustness of results and their sensitivity to uncertainty factors in life cycle assessment (LCA). It highlights the most important set of model parameters to determine whether data quality needs to be improved, and to enhance interpretation of results. Interactions within the LCA calculation model and correlations within Life Cycle Inventory (LCI) input parameters are two main issues among the LCA calculation process. Here we propose a methodology for conducting a proper SA which takes into account the effects of these two issues. This study first presents the SA in an uncorrelated case, comparing local and independent global sensitivity analysis. Independent global sensitivity analysis aims to analyze the variability of results because of the variation of input parameters over the whole domain of uncertainty, together with interactions among input parameters. We then apply a dependent global sensitivity approach that makes minor modifications to traditional Sobol indices to address the correlation issue. Finally, we propose some guidelines for choosing the appropriate SA method depending on the characteristics of the model and the goals of the study. Our results clearly show that the choice of sensitivity methods should be made according to the magnitude of uncertainty and the degree of correlation.
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@article{PUB00046736, author = {Wei, W. and Larrey Lassalle, P. and Faure, T. and Dumoulin, N. and Roux, P. and Mathias, J.D.}, title = {How to conduct a proper sensitivity analysis in life cycle assessment: Taking into account correlations within LCI data and interactions within the LCA calculation model}, journal = {Environmental Science & Technology}, volume = {49}, number = {1}, pages = {377-385}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00046736}, doi = {http://dx.doi.org/10.1021/es502128k}, year = {2015}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA MONTPELLIER UMR ITAP FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA MONTPELLIER UMR ITAP FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {Sensitivity analysis (SA) is a significant tool for studying the robustness of results and their sensitivity to uncertainty factors in life cycle assessment (LCA). It highlights the most important set of model parameters to determine whether data quality needs to be improved, and to enhance interpretation of results. Interactions within the LCA calculation model and correlations within Life Cycle Inventory (LCI) input parameters are two main issues among the LCA calculation process. Here we propose a methodology for conducting a proper SA which takes into account the effects of these two issues. This study first presents the SA in an uncorrelated case, comparing local and independent global sensitivity analysis. Independent global sensitivity analysis aims to analyze the variability of results because of the variation of input parameters over the whole domain of uncertainty, together with interactions among input parameters. We then apply a dependent global sensitivity approach that makes minor modifications to traditional Sobol indices to address the correlation issue. Finally, we propose some guidelines for choosing the appropriate SA method depending on the characteristics of the model and the goals of the study. Our results clearly show that the choice of sensitivity methods should be made according to the magnitude of uncertainty and the degree of correlation.}, }
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T. Rougier, H. Drouineau, N. Dumoulin, T. Faure, G. Deffuant, E. Rochard, P. Lambert
The GR3D model, a tool to explore the Global Repositioning Dynamicsof Diadromous fish Distribution
Ecological Modelling 283, 2014
abs doi web bib

Within the context of ongoing environmental changes, the life history of diadromous fish represents areal potential for exploring and colonizing new environments due to high potential dispersal abilities. Theuse of dynamic approaches to assess how these species will respond to climate change is a challenging issue and mechanistic models able to incorporate biological and evolutionary processes are a promising tool. To this end we developed an individual-based model, called GR3D (Global Repositioning Dynamicsfor Diadromous fish Distribution), combining climatic requirements and population dynamics with an explicit dispersal process to evaluate potential evolution of their distribution area in the context of climatic change. This paper describes thoroughly the model structure and presents an exploratory test casewhere the repositioning of a virtual allis shad (Alosa alosa L.) population between two river catchments under a scenario of temperature increase was assessed. The global sensitivity analysis showed that land-scape structure and parameters related to sea lifespan and to survival at sea were crucial to determine the success of colonization. These results were consistent with the ecology of this species. The integration of climatic factors directly into the processes and the explicit dispersal process make GR3D an original and relevant tool to assess the repositioning dynamics and persistence of diadromous fish facing climate change.
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@article{PUB00041011, author = {Rougier, T. and Drouineau, H. and Dumoulin, N. and Faure, T. and Deffuant, G. and Rochard, E. and Lambert, P.}, title = {The GR3D model, a tool to explore the Global Repositioning Dynamicsof Diadromous fish Distribution}, journal = {Ecological Modelling}, volume = {283}, pages = {31-44}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00041011}, doi = {http://dx.doi.org/10.1016/j.ecolmodel.2014.03.019}, year = {2014}, affiliation = {IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA}, abstract = {Within the context of ongoing environmental changes, the life history of diadromous fish represents areal potential for exploring and colonizing new environments due to high potential dispersal abilities. Theuse of dynamic approaches to assess how these species will respond to climate change is a challenging issue and mechanistic models able to incorporate biological and evolutionary processes are a promising tool. To this end we developed an individual-based model, called GR3D (Global Repositioning Dynamicsfor Diadromous fish Distribution), combining climatic requirements and population dynamics with an explicit dispersal process to evaluate potential evolution of their distribution area in the context of climatic change. This paper describes thoroughly the model structure and presents an exploratory test casewhere the repositioning of a virtual allis shad (Alosa alosa L.) population between two river catchments under a scenario of temperature increase was assessed. The global sensitivity analysis showed that land-scape structure and parameters related to sea lifespan and to survival at sea were crucial to determine the success of colonization. These results were consistent with the ecology of this species. The integration of climatic factors directly into the processes and the explicit dispersal process make GR3D an original and relevant tool to assess the repositioning dynamics and persistence of diadromous fish facing climate change.}, }
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F. Jabot, T. Faure, N. Dumoulin
EasyABC: Performing efficient approximate Bayesian computation sampling schemes using R
Methods in Ecology and Evolution 4 (7), 2013
abs doi web bib

Approximate Bayesian computation (ABC), a type of likelihood-free inference, is a family of statistical techniques to perform parameter estimation and model selection. It is increasingly used in ecology and evolution, where the models used can be too complex to be handled with standard likelihood techniques. The essence of ABC techniques is to compare simulation outputs to observed data, in order to select the parameter values of the simulations which best fit the data. ABC techniques are thus computationally demanding. This constitutes a key limitation to their implementation. We introduce the R package 'EasyABC' that enables one to launch a series of simulations from the R platform and to retrieve the simulation outputs in an appropriate format for post-processing. The 'EasyABC' package further implements several efficient parameter sampling schemes to speed up the ABC procedure: on top of the standard prior sampling, it implements various algorithms to perform sequential (ABC-sequential) and Markov chain Monte Carlo (ABC-MCMC) sampling schemes. The package functions can furthermore make use of parallel computing. The R package 'EasyABC' complements the package 'abc' which enables various post-processing of simulation outputs. 'EasyABC' makes several state-of-the-art ABC implementations available to the large community of R users in the fields of ecology and evolution. It is a freely available R package under the GPL license, and it can be downloaded at http://cran.r-project.org/web/packages/EasyABC/index.html.
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@article{PUB00038743, author = {Jabot, F. and Faure, T. and Dumoulin, N.}, title = {EasyABC: Performing efficient approximate Bayesian computation sampling schemes using R }, journal = {Methods in Ecology and Evolution}, volume = {4}, number = {7}, pages = {684-687}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00038743}, doi = {http://dx.doi.org/10.1111/2041-210X.12050}, year = {2013}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {Approximate Bayesian computation (ABC), a type of likelihood-free inference, is a family of statistical techniques to perform parameter estimation and model selection. It is increasingly used in ecology and evolution, where the models used can be too complex to be handled with standard likelihood techniques. The essence of ABC techniques is to compare simulation outputs to observed data, in order to select the parameter values of the simulations which best fit the data. ABC techniques are thus computationally demanding. This constitutes a key limitation to their implementation. We introduce the R package 'EasyABC' that enables one to launch a series of simulations from the R platform and to retrieve the simulation outputs in an appropriate format for post-processing. The 'EasyABC' package further implements several efficient parameter sampling schemes to speed up the ABC procedure: on top of the standard prior sampling, it implements various algorithms to perform sequential (ABC-sequential) and Markov chain Monte Carlo (ABC-MCMC) sampling schemes. The package functions can furthermore make use of parallel computing. The R package 'EasyABC' complements the package 'abc' which enables various post-processing of simulation outputs. 'EasyABC' makes several state-of-the-art ABC implementations available to the large community of R users in the fields of ecology and evolution. It is a freely available R package under the GPL license, and it can be downloaded at http://cran.r-project.org/web/packages/EasyABC/index.html. }, }
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F. Chuffart, N. Dumoulin, T. Faure, G. Deffuant
SimExplorer: programming experimental design on models and managing quality of modelling process
International Journal of Agricultural and Environmental Information Systems IJAEIS 1 (1), 2010
abs doi web bib

This article describes Simexplorer, a computer framework for managing simulation experiments and, to some extent, the scientific quality of the modelling process. An information system, included in the framework, insures the traceability of the experiments and their reproducibility and thus contributes to the modelling process quality management. Moreover, this information system provides facilities for sharing and exchanging components of experiment scenarios. The authors illustrate the use of the framework on a simple example of modelling process.
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@article{PUB00028275, author = {Chuffart, F. and Dumoulin, N. and Faure, T. and Deffuant, G.}, title = {SimExplorer: programming experimental design on models and managing quality of modelling process}, title = {SimExplorer : programmer des plans d'expérience sur les modèles et gérer la traçabilité des expériences}, journal = {International Journal of Agricultural and Environmental Information Systems IJAEIS}, volume = {1}, number = {1}, pages = {55-68}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00028275}, doi = {http://dx.doi.org/10.4018/jaeis.2010101304}, year = {2010}, affiliation = {CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA}, abstract = {This article describes Simexplorer, a computer framework for managing simulation experiments and, to some extent, the scientific quality of the modelling process. An information system, included in the framework, insures the traceability of the experiments and their reproducibility and thus contributes to the modelling process quality management. Moreover, this information system provides facilities for sharing and exchanging components of experiment scenarios. The authors illustrate the use of the framework on a simple example of modelling process. }, }
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N. Dumoulin
SimAquaLife : un cadriciel pour la modélisation de la dynamique spatiale d'organismes aquatiques
Technique et Science Informatiques 26 (6), 2007
abs web bib

Individual-based modelling of ecosystems necessitates a multi-disciplinary approach, making tough the development and the maintenance of these models. Several individual-based modelling platforms exist and make possible to simplify the design and maintenance tasks, however we consider that we could improve by isolating aspects related to modeling from the other aspects mainly related to the simulation techniques and to the display of results. Without taking into account aspect-oriented programming, we propose a software framework which makes an intensive use of metadatas to simplify the use and development of models, and also to produce automatically graphical user interfaces for data settings and results display. This approach is based on the metamodelling concept of model engineering. The software framework has been mainly developed for the spatialized and individual-centered simulation of aquatic organisms movements, mainly river fresh water fishes and eels at different development stages. / a modélisation individu-centrée d'écosystèmes fait intervenir plusieurs disciplines, ce qui a pour effet de compliquer le développement et la maintenance de ces modèles. Plusieurs plate-formes de modélisation individu-centrée existent et permettent de faciliter ces tâches. Nous considérons qu'elles pourraient être encore plus efficaces en isolant les aspects liés à la modélisation des autres aspects principalement liés à la simulation et à la visualisation des résultats. Sans faire appel à la programmation par aspects, nous proposons un cadriciel qui utilise intensivement les métadonnées pour faciliter l'écriture et l'utilisation modèles, et pour produire automatiquement les interfaces utilisateurs de saisie des données et d'affichage des résultats. Cette approche repose sur le concept de métamodélisation de l'ingénierie des modèles. Le cadriciel proposé a été développé principalement .pour la simulation spatialisée et individu-centrée des déplacements d'organismes aquatiques tels que les poissons et les anguilles d'eau douce à différents stades de leur développement.
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@article{PUB00022542, author = {Dumoulin, N.}, title = {SimAquaLife : un cadriciel pour la modélisation de la dynamique spatiale d'organismes aquatiques}, title = {SimAquaLife: a framework for aquatic organisms spatial dynamics modelling}, journal = {Technique et Science Informatiques}, volume = {26}, number = {6}, pages = {701-721}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00022542}, year = {2007}, affiliation = {CEMAGREF CLERMONT FERRAND LISC}, abstract = {Individual-based modelling of ecosystems necessitates a multi-disciplinary approach, making tough the development and the maintenance of these models. Several individual-based modelling platforms exist and make possible to simplify the design and maintenance tasks, however we consider that we could improve by isolating aspects related to modeling from the other aspects mainly related to the simulation techniques and to the display of results. Without taking into account aspect-oriented programming, we propose a software framework which makes an intensive use of metadatas to simplify the use and development of models, and also to produce automatically graphical user interfaces for data settings and results display. This approach is based on the metamodelling concept of model engineering. The software framework has been mainly developed for the spatialized and individual-centered simulation of aquatic organisms movements, mainly river fresh water fishes and eels at different development stages. / a modélisation individu-centrée d'écosystèmes fait intervenir plusieurs disciplines, ce qui a pour effet de compliquer le développement et la maintenance de ces modèles. Plusieurs plate-formes de modélisation individu-centrée existent et permettent de faciliter ces tâches. Nous considérons qu'elles pourraient être encore plus efficaces en isolant les aspects liés à la modélisation des autres aspects principalement liés à la simulation et à la visualisation des résultats. Sans faire appel à la programmation par aspects, nous proposons un cadriciel qui utilise intensivement les métadonnées pour faciliter l'écriture et l'utilisation modèles, et pour produire automatiquement les interfaces utilisateurs de saisie des données et d'affichage des résultats. Cette approche repose sur le concept de métamodélisation de l'ingénierie des modèles. Le cadriciel proposé a été développé principalement .pour la simulation spatialisée et individu-centrée des déplacements d'organismes aquatiques tels que les poissons et les anguilles d'eau douce à différents stades de leur développement.}, }
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S. Huet, N. Dumoulin, G. Deffuant
A calibration to properly design a model integrating residential mobility and migration in rural area
Advances in Social Simulation 2015, Advances in Intelligent Systems and Computing 528 (p. 163-179), Springer, 2017
abs web bib

We propose a hybrid microsimulation and agent-based model of mobility integrating migration and residential mobility. We tested it on the evolution of the population of the Cantal, a French “département” with 150,000 inhabitants. We calibrated it using various data sources from 1990 to 2006, and tested its predictions on other data of the same period and on the period 2007-2012. The spatial heterogeneity of the evolution is well reproduced and the model makes surprisingly correct predictions despite numerous simplifying assumptions. From this calibration we learnt more about how to model residential mobility and migration considering an agent-based model approach.
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@book{PUB00054555, author = {Huet, S. and Dumoulin, N. and Deffuant, G.}, author = {Jager, W. and Verbrugge, R. and Flache, A. and De Roo, G. and Hoogduin, L. and Hemelrijkn C.}, title = {A calibration to properly design a model integrating residential mobility and migration in rural area}, title = {Une calibration pour une modélisation pertinente de la mobilité résidentielle et de la migration en zone rurale}, bookTitle = {Advances in Social Simulation 2015, Advances in Intelligent Systems and Computing 528}, publisher = {Springer}, pages = {163-179}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00054555}, year = {2017}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {We propose a hybrid microsimulation and agent-based model of mobility integrating migration and residential mobility. We tested it on the evolution of the population of the Cantal, a French “département” with 150,000 inhabitants. We calibrated it using various data sources from 1990 to 2006, and tested its predictions on other data of the same period and on the period 2007-2012. The spatial heterogeneity of the evolution is well reproduced and the model makes surprisingly correct predictions despite numerous simplifying assumptions. From this calibration we learnt more about how to model residential mobility and migration considering an agent-based model approach.}, }
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H. Richard, H. Monod, J. Wang, J. Couteau, N. Dumoulin, B. Poussin, J.C. Soulié, É. Ramat
La boîte à outils Mexico, un environnement générique pour piloter l'exploration numérique de modèles ( Chapitre 9)
Analyse de sensibilité et exploration de modèles : application aux sciences de la nature et de l'environnement (p. 233-253), Quae, 2013
abs web bib

This chapter is about the development of a generic software environment for managing the explorations of numerical models. / Ce chapitre s’intéresse au développement d’un environnement informatique générique pour piloter l’exploration de modèles.
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@book{PUB00038239, author = {Richard, H. and Monod, H. and Wang, J. and Couteau, J. and Dumoulin, N. and Poussin, B. and Soulié, J.C. and Ramat, É.}, author = {Faivre, R. and Iooss, B. and Mahévas, S. and Makowski, D. and Monod, H.}, title = {La boîte à outils Mexico, un environnement générique pour piloter l'exploration numérique de modèles ( Chapitre 9)}, title = {Mexico Toolbox: A generic software environment for managing the explorations of numerical models}, bookTitle = {Analyse de sensibilité et exploration de modèles : application aux sciences de la nature et de l'environnement}, series = {Savoir faire}, publisher = {Quae}, pages = {233-253}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00038239 / http://www.quae.com/fr/r2142-analyse-de-sensibilite-et-exploration-de-modeles.html}, year = {2013}, affiliation = {INRA AVIGNON FRA ; INRA JOUY EN JOSAS FRA ; INRA JOUY EN JOSAS FRA ; CODE LUTIN SAINT SEBASTIEN SUR LOIRE FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; CODE LUTIN SAINT SEBASTIEN SUR LOIRE FRA ; CIRAD MONTPELLIER FRA ; UNIVERSITE DU LITTORAL CALAIS FRA}, ISBNISSN = {ISBN 978-2-7592-1906-3}, abstract = {This chapter is about the development of a generic software environment for managing the explorations of numerical models. / Ce chapitre s’intéresse au développement d’un environnement informatique générique pour piloter l’exploration de modèles. }, }
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S. Huet, N. Dumoulin, G. Deffuant
A calibration to properly design a model integrating residential mobility and migration in a rural area
11th Conference of the European Social Simulation Association: Social Simulation Conference, 14/09/2015-18/09/2015, Groningen, NLD , 2015
abs web bib

We propose a hybrid microsimulation and agent-based model of mobility integrating migration and residential mobility. We tested it on the evolution of the population of the Cantal, a French “département” with 150,000 inhabitants. We calibrated it using various data sources from 1990 to 2006, and tested its predictions on other data of the same period and on the period 2007-2012. The spatial heterogeneity of the evolution is well reproduced and the model makes surprisingly correct predictions despite numerous simplifying assumptions. From this calibration we learnt more about how to model residential mobility and migration considering an agent-based model approach.
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@inproceedings{PUB00046433, author = {Huet, S. and Dumoulin, N. and Deffuant, G.}, title = {A calibration to properly design a model integrating residential mobility and migration in a rural area}, title = {Une calibration pour la conception pertinente d'un modèle intégrant mobilité résidentielle et migration dans l'espace rural}, bookTitle = {11th Conference of the European Social Simulation Association: Social Simulation Conference, 14/09/2015-18/09/2015, Groningen, NLD}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00046433}, year = {2015}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {We propose a hybrid microsimulation and agent-based model of mobility integrating migration and residential mobility. We tested it on the evolution of the population of the Cantal, a French “département” with 150,000 inhabitants. We calibrated it using various data sources from 1990 to 2006, and tested its predictions on other data of the same period and on the period 2007-2012. The spatial heterogeneity of the evolution is well reproduced and the model makes surprisingly correct predictions despite numerous simplifying assumptions. From this calibration we learnt more about how to model residential mobility and migration considering an agent-based model approach.}, }
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G. Lassalle, T. Rougier, H. Drouineau, N. Dumoulin, T. Faure, G. Deffuant, P. Jatteau, E. Rochard, P. Lambert
Allis shad: A concrete example of how niche shift modelling studies could help in the definition of conservation measures
Aquatic Biodiversity and Ecosystems Conference, 30/08/2015-05/09/2015, Liverpool, GBR (p. 19), 2015
abs web bib

For most species, only the realized climate niche can realistically be estimated through correlative distribution models. For some species, it has become possible to determine the fundamental niche based on physiological information and a mechanistic understanding. Predicting the future species distributions using both correlative and mechanistic distribution models under climate change scenarios remains as such a rare application. The Allis shad (Alosa alosa) benefited from the attention of the scientific community given its dramatically decreasing trend in all Western European fresh waters. Conservation and restoration measures for the species are undertaken in two key systems of its distribution range where the species was formally a highly abundant exploited natural resource. Both types of distribution models were developed for allis shad and used for predictions but conclusions were never confronted. In the present study, a joint analysis of their results were undertaken to refine conservation actions in the light of climate change impacts. We raised two main concerns regarding: (i) the potential local adaptation of northern populations and (2) the importance of managing a target watershed considering potential existing neighbouring sources of migrants.
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@inproceedings{PUB00045764, author = {Lassalle, G. and Rougier, T. and Drouineau, H. and Dumoulin, N. and Faure, T. and Deffuant, G. and Jatteau, P. and Rochard, E. and Lambert, P.}, title = {Allis shad: A concrete example of how niche shift modelling studies could help in the definition of conservation measures}, bookTitle = {Aquatic Biodiversity and Ecosystems Conference, 30/08/2015-05/09/2015, Liverpool, GBR}, pages = {19}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00045764}, year = {2015}, affiliation = {IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA ; IRSTEA BORDEAUX UR EABX FRA}, abstract = {For most species, only the realized climate niche can realistically be estimated through correlative distribution models. For some species, it has become possible to determine the fundamental niche based on physiological information and a mechanistic understanding. Predicting the future species distributions using both correlative and mechanistic distribution models under climate change scenarios remains as such a rare application. The Allis shad (Alosa alosa) benefited from the attention of the scientific community given its dramatically decreasing trend in all Western European fresh waters. Conservation and restoration measures for the species are undertaken in two key systems of its distribution range where the species was formally a highly abundant exploited natural resource. Both types of distribution models were developed for allis shad and used for predictions but conclusions were never confronted. In the present study, a joint analysis of their results were undertaken to refine conservation actions in the light of climate change impacts. We raised two main concerns regarding: (i) the potential local adaptation of northern populations and (2) the importance of managing a target watershed considering potential existing neighbouring sources of migrants.}, }
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S. Westrelin, N. Dumoulin, I. Pauwels
Premiers pas vers la modélisation de la dynamique spatiale d’une population de brochets dans une retenue hydro-électrique
Journées de la Modélisation, 02/06/2015-03/06/2015, Clermont-Ferrand, FRA (p. 17), 2015
abs web bib

Présentation d'une démarche de modélisation initiée sur les déplacements de brochets adultes suivis par télémétrie acoustique dans un réservoir.
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@inproceedings{PUB00047038, author = {Westrelin, S. and Dumoulin, N. and Pauwels, I.}, title = {Premiers pas vers la modélisation de la dynamique spatiale d’une population de brochets dans une retenue hydro-électrique}, title = {First steps towards the modelling of the spatial dynamics of a pike population in a reservoir.}, bookTitle = {Journées de la Modélisation, 02/06/2015-03/06/2015, Clermont-Ferrand, FRA}, pages = {17}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00047038}, year = {2015}, affiliation = {IRSTEA AIX EN PROVENCE UR HYAX FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; INBO BRUXELLES BEL}, abstract = {Présentation d'une démarche de modélisation initiée sur les déplacements de brochets adultes suivis par télémétrie acoustique dans un réservoir.}, }
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S. Bimonte, N. Dumoulin
SimOLAP: A system for the semi-automatic implementation of simulation datawarehouses
10èmes journées francophones sur les Entrepôts de Données et l’Analyse en ligne EDA, 05/06/2014-06/06/2014, Vichy (p. 4), RNTI, 2014
abs web bib

Data Warehouses and OLAP systems allow decision-makers exploring and analyzing huge volumes of data modeled according the multidimensional model, and extracted from heterogeneous data sources. Usually, DW design is a complex, and time and resources consuming task. Then, DWexperts are necessary during design and implementation phases. In this paper, we present a new methodology and a tool allowing modelers (DW unskilled users) to design and implement DWs for analyzing simulation results data by themselves, without any intervention of DW experts.
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@inproceedings{PUB00040995, author = {Bimonte, S. and Dumoulin, N.}, title = {SimOLAP: A system for the semi-automatic implementation of simulation datawarehouses}, title = {SimOLAP : un système pour l'implémentation semi-automatique d'entrepôts de données de simulation}, bookTitle = {10èmes journées francophones sur les Entrepôts de Données et l’Analyse en ligne EDA, 05/06/2014-06/06/2014, Vichy}, publisher = {RNTI}, pages = {4}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00040995}, year = {2014}, affiliation = {IRSTEA CLERMONT FERRAND UR TSCF FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {Data Warehouses and OLAP systems allow decision-makers exploring and analyzing huge volumes of data modeled according the multidimensional model, and extracted from heterogeneous data sources. Usually, DW design is a complex, and time and resources consuming task. Then, DWexperts are necessary during design and implementation phases. In this paper, we present a new methodology and a tool allowing modelers (DW unskilled users) to design and implement DWs for analyzing simulation results data by themselves, without any intervention of DW experts.}, }
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F. Jabot, T. Faure, N. Dumoulin
EasyABC: performing efficient approximate Bayesian computation sampling schemes using R
ABC (Approximate Bayesian Computation), 30/05/2013-31/05/2013, Rome, ITA , 2013
abs web bib

1.Approximate Bayesian computation (ABC), also called likelihood-free inference, is a family of statistical techniques to perform parameter inference and model comparison. It is increasingly used in ecology and evolution, where the models used can be too complex to be handled with standard likelihood techniques. The essence of ABC techniques is to compare model simulation outputs to observed data, in order to select the model simulations (and their associated parameter values) which best fit the data. ABC techniques therefore require a large number of model simulations. 2.We introduce the R package 'EasyABC' that enables to launch a series of simulations of a computer code from the R platform and to retrieve the simulation outputs in an appropriate format for post-processing treatments. The 'EasyABC' package further implements several efficient parameter sampling schemes to speed up the ABC procedure: on top of the standard prior sampling, it implements various algorithms to perform sequential (ABC-sequential) and Markov chain Monte Carlo (ABC-MCMC) sampling schemes. The package functions can furthermore make use in parallel of several cores of a multi-core computer. 3.The R package 'EasyABC' complements the package 'abc' which enables various post-processing treatments of simulation outputs. 'EasyABC' will make the up-to-date ABC implementations available to the large community of R users in the fields of ecology and evolution. It is a freely available R package under the GPL license, and it can be downloaded at http://cran.r-project.org/web/packages/EasyABC/index.html .
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@inproceedings{PUB00040536, author = {Jabot, F. and Faure, T. and Dumoulin, N.}, title = {EasyABC: performing efficient approximate Bayesian computation sampling schemes using R}, title = {EasyABC : effectuer des protocoles d'échantillonnages efficaces pour le calcul Bayésien approché avec R}, bookTitle = {ABC (Approximate Bayesian Computation), 30/05/2013-31/05/2013, Rome, ITA}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00040536}, year = {2013}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA}, abstract = {1.Approximate Bayesian computation (ABC), also called likelihood-free inference, is a family of statistical techniques to perform parameter inference and model comparison. It is increasingly used in ecology and evolution, where the models used can be too complex to be handled with standard likelihood techniques. The essence of ABC techniques is to compare model simulation outputs to observed data, in order to select the model simulations (and their associated parameter values) which best fit the data. ABC techniques therefore require a large number of model simulations. 2.We introduce the R package 'EasyABC' that enables to launch a series of simulations of a computer code from the R platform and to retrieve the simulation outputs in an appropriate format for post-processing treatments. The 'EasyABC' package further implements several efficient parameter sampling schemes to speed up the ABC procedure: on top of the standard prior sampling, it implements various algorithms to perform sequential (ABC-sequential) and Markov chain Monte Carlo (ABC-MCMC) sampling schemes. The package functions can furthermore make use in parallel of several cores of a multi-core computer. 3.The R package 'EasyABC' complements the package 'abc' which enables various post-processing treatments of simulation outputs. 'EasyABC' will make the up-to-date ABC implementations available to the large community of R users in the fields of ecology and evolution. It is a freely available R package under the GPL license, and it can be downloaded at http://cran.r-project.org/web/packages/EasyABC/index.html . }, }
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R. Reuillon, F. Chuffart, M. Leclaire, T. Faure, N. Dumoulin, D. Hill
Declarative task delegation in OpenMOLE
High Performance Computing and Simulation (HPCS), 28/06/2010-02/07/2010, Caen, FRA (p. 55-62), 2010
abs doi web bib

In this paper we present OpenMOLE, a scientific framework providing a virtualized runtime environment for distributed computing. Current distributed execution systems do not hide the hardware and software heterogeneity of computing and data resources whereas OpenMOLE provides generic services to develop distributed scientific algorithms independently from the execution environment architecture. OpenMOLE uses abstraction layers to delegate computing tasks with the same high level interface for the major underlying architectures: local processors, batch systems, computational grids, Internet computing and cloud computing. The file access abstraction layer is another key feature helping a generic usage of the computation power provided by grids and clusters. The OpenMOLE framework has been tested with the exploration of a bacterial biofilm simulation with an individual-based model.
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@inproceedings{PUB00031905, author = {Reuillon, R. and Chuffart, F. and Leclaire, M. and Faure, T. and Dumoulin, N. and Hill, D.}, title = {Declarative task delegation in OpenMOLE}, title = {Délégation déclarative de tâche avec OpenMOLE}, bookTitle = {High Performance Computing and Simulation (HPCS), 28/06/2010-02/07/2010, Caen, FRA}, pages = {55-62}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00031905}, doi = {http://dx.doi.org/10.1109/HPCS.2010.5547155}, year = {2010}, affiliation = {INSTITUT DES SYSTEMES COMPLEXES PARIS FRA ; LABORATOIRE DE L'INFORMATIQUE DU PARALLELISME LYON FRA ; INSTITUT DES SYSTEMES COMPLEXES PARIS FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA ; UNIVERSITE BLAISE PASCAL CLERMONT FERRAND LIMOS CNRS UMR 6158 FRA}, ISBNISSN = {ISBN 978-1-4244-6827-0 }, abstract = {In this paper we present OpenMOLE, a scientific framework providing a virtualized runtime environment for distributed computing. Current distributed execution systems do not hide the hardware and software heterogeneity of computing and data resources whereas OpenMOLE provides generic services to develop distributed scientific algorithms independently from the execution environment architecture. OpenMOLE uses abstraction layers to delegate computing tasks with the same high level interface for the major underlying architectures: local processors, batch systems, computational grids, Internet computing and cloud computing. The file access abstraction layer is another key feature helping a generic usage of the computation power provided by grids and clusters. The OpenMOLE framework has been tested with the exploration of a bacterial biofilm simulation with an individual-based model.}, }
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F. Chuffart, T. Faure, N. Dumoulin, R. Reuillon, G. Deffuant
Design and analysis of computer experiments with SimExplorer
ESM'2008 European Simulation and Modelling Conference, 27/10/2008-29/10/2008, Le Havre, FRA (p. 575-577), EUROSIS, 2008
abs web bib

SimExplorer is a framework that includes an API and an IDE dedicated to design and analysis of computer experiments. SimExplorer combines blind computing on demand service access, traceability and reporting features and sensitivity analysis tools. This tutorial provides the concepts and exemplifies a typical use of SimExplorer, performing a global sensitivity analysis of a given individual-based predator prey model.
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@inproceedings{PUB00024933, author = {Chuffart, F. and Faure, T. and Dumoulin, N. and Reuillon, R. and Deffuant, G.}, title = {Design and analysis of computer experiments with SimExplorer}, title = {Conception et analyse de plans d'expériences avec SimExplorer}, bookTitle = {ESM'2008 European Simulation and Modelling Conference, 27/10/2008-29/10/2008, Le Havre, FRA}, publisher = {EUROSIS}, pages = {575-577}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00024933}, year = {2008}, affiliation = {CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA ; CEMAGREF CLERMONT FERRAND UR LISC FRA}, abstract = {SimExplorer is a framework that includes an API and an IDE dedicated to design and analysis of computer experiments. SimExplorer combines blind computing on demand service access, traceability and reporting features and sensitivity analysis tools. This tutorial provides the concepts and exemplifies a typical use of SimExplorer, performing a global sensitivity analysis of a given individual-based predator prey model. }, }
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S. Huet, N. Dumoulin, G. Deffuant, F. Gargiulo, M. Lenormand, O. Baqueiro Espinosa, S. Ternes
Micro-simulation model of municipality network in the Auvergne case study
2012
abs web bib

How do European rural areas evolve? Some tend to decrease dramatically, as in the Netherlands or in the United Kingdom, where the urban areas tend to spread all over the country. Their population can also be drastically depleting through a large rural exodus, as observed in for instance France, Bulgaria or Croatia in the first part of the last Century. They can also keep steady population densities occupied in leisure services offered to urban people and agriculture with various proportions of inhabitants commuting to the cities for their work. Better understanding these evolutions is what the PRIMA simulation model presented in this report is interested in. / Ce document décrit un modèle de micro-simulation de communes développé dans le cadre du projet européen PRIMA (EU ENV 2007-1). Ce modèle permet d'étudier l'évolution des populations rurales sous l'effet des interactions spatiales et des dynamiques économiques locales.
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@techreport{PUB00036510, author = {Huet, S. and Dumoulin, N. and Deffuant, G. and Gargiulo, F. and Lenormand, M. and Baqueiro Espinosa, O. and Ternes, S.}, title = {Micro-simulation model of municipality network in the Auvergne case study }, title = {Modèle de micro-simulation d'un réseau de communes : étude de cas en Auvergne}, pages = {66}, url = {http://irsteadoc.irstea.fr/cemoa/PUB00036510}, year = {2012}, affiliation = {IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IRSTEA CLERMONT FERRAND UR LISC FRA ; IAMO INSTITUTE OF AGRICULTURAL DEVELOPMENT IN CENTRAL AND EASTERN EUROPE LEIBNITZ DEU ; IAMO INSTITUTE OF AGRICULTURAL DEVELOPMENT IN CENTRAL AND EASTERN EUROPE LEIBNITZ DEU}, abstract = {How do European rural areas evolve? Some tend to decrease dramatically, as in the Netherlands or in the United Kingdom, where the urban areas tend to spread all over the country. Their population can also be drastically depleting through a large rural exodus, as observed in for instance France, Bulgaria or Croatia in the first part of the last Century. They can also keep steady population densities occupied in leisure services offered to urban people and agriculture with various proportions of inhabitants commuting to the cities for their work. Better understanding these evolutions is what the PRIMA simulation model presented in this report is interested in. / Ce document décrit un modèle de micro-simulation de communes développé dans le cadre du projet européen PRIMA (EU ENV 2007-1). Ce modèle permet d'étudier l'évolution des populations rurales sous l'effet des interactions spatiales et des dynamiques économiques locales.}, }
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Dumoulin Nicolas

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