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Mixed-Effects Estimation in Dynamic Models of Plant Growth for the Assessment of Inter-individual Variability

Author

Listed:
  • Charlotte Baey

    (Laboratoire Paul Painlevé, Université de Lille, Cité Scientifique)

  • Amélie Mathieu

    (Université Paris-Saclay)

  • Alexandra Jullien

    (Université Paris-Saclay)

  • Samis Trevezas

    (National and Kapodistrian University of Athens)

  • Paul-Henry Cournède

    (Université Paris-Saclay, Grande Voie des Vignes)

Abstract

Modeling inter-individual variability in plant populations is a key issue to understand crop heterogeneity and its variations in response to the environment. Being able to describe the interactions among plants and explain the variability observed in the population could provide useful information on how to control it and improve global plant growth. We propose here a method to model plant variability within a field, by extending the so-called GreenLab functional-structural plant model from the individual to the population scale via nonlinear mixed-effects modeling. Parameter estimation of the population model is achieved using the stochastic approximation expectation maximization algorithm, implemented in the platform for plant growth modeling and analysis PyGMAlion. The method is first applied on a set of simulated data and then on a real dataset from a population of 34 winter oilseed rape plants at the rosette stage. Results show that our method allows for a good characterization of the variability in the population with only a limited number of parameters, which is a key point for plant models. Results on simulated data show that parameters associated with a low sensitivity index are inaccurately estimated by the algorithm when considered as random effects, but a good stability of the results can be obtained by considering them as fixed effects. These results open new ways for the analysis of inter-plant variability within a population and the study of plant–plant competition.Supplementary materials accompanying this paper appear online.

Suggested Citation

  • Charlotte Baey & Amélie Mathieu & Alexandra Jullien & Samis Trevezas & Paul-Henry Cournède, 2018. "Mixed-Effects Estimation in Dynamic Models of Plant Growth for the Assessment of Inter-individual Variability," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 23(2), pages 208-232, June.
    • Handle: RePEc:spr:jagbes:v:23:y:2018:i:2:d:10.1007_s13253-017-0307-4
    DOI: 10.1007/s13253-017-0307-4
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    References listed on IDEAS

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    1. Baey, Charlotte & Didier, Anne & Lemaire, Sébastien & Maupas, Fabienne & Cournède, Paul-Henry, 2013. "Modelling the interindividual variability of organogenesis in sugar beet populations using a hierarchical segmented model," Ecological Modelling, Elsevier, vol. 263(C), pages 56-63.
    2. Marc Lavielle & Adeline Samson & Ana Karina Fermin & France Mentré, 2011. "Maximum Likelihood Estimation of Long-Term HIV Dynamic Models and Antiviral Response," Biometrics, The International Biometric Society, vol. 67(1), pages 250-259, March.
    3. Trevezas, S. & Malefaki, S. & Cournède, P.-H., 2014. "Parameter estimation via stochastic variants of the ECM algorithm with applications to plant growth modeling," Computational Statistics & Data Analysis, Elsevier, vol. 78(C), pages 82-99.
    4. Kuhn, E. & Lavielle, M., 2005. "Maximum likelihood estimation in nonlinear mixed effects models," Computational Statistics & Data Analysis, Elsevier, vol. 49(4), pages 1020-1038, June.
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    Cited by:

    1. D. Logothetis & S. Malefaki & S. Trevezas & P.-H. Cournède, 2022. "Bayesian Estimation for the GreenLab Plant Growth Model with Deterministic Organogenesis," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 27(1), pages 63-87, March.

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