Using L-systems for modeling source-sink interactions, architecture and physiology of growing trees: the L-PEACH model, New Phytologist, vol.117, issue.3, pp.166-869, 2005. ,
DOI : 10.1111/j.1469-8137.2005.01348.x
The principles of forest yield study, 1970. ,
Architecture, gradients morphogénétiques etâgeet?etâge physiologique chez les végétaux. Modélisation et simulation de l'architecture des végétaux, Sciences Update, pp.89-136, 1997. ,
Plant Architecture: A Dynamic, Multilevel and Comprehensive Approach to Plant Form, Structure and Ontogeny, Annals of Botany, vol.99, issue.3, pp.375-407, 2007. ,
DOI : 10.1093/aob/mcl260
An overview of the crop model stics, European Journal of Agronomy, vol.18, issue.3-4, pp.18-309, 2003. ,
DOI : 10.1016/S1161-0301(02)00110-7
URL : https://hal.archives-ouvertes.fr/hal-01190851
Inference in hidden Markov models, 2005. ,
Dynamic system of plant growth, 2009. ,
Structural Factorization of Plants to Compute Their Functional and Architectural Growth, SIMULATION, vol.82, issue.7, pp.82-427, 2006. ,
DOI : 10.1177/0037549706069341
Computing Competition for Light in the GREENLAB Model of Plant Growth: A Contribution to the Study of the Effects of Density on Resource Acquisition and Architectural Development, Annals of Botany, vol.101, issue.8, pp.1207-1219, 2008. ,
DOI : 10.1093/aob/mcm272
Mathematical methods of statistics, 1946. ,
Calibration of a hydraulic architecture-based growth model of cotton plants, Agronomie, vol.19, issue.3-4, pp.265-280, 1999. ,
DOI : 10.1051/agro:19990307
URL : https://hal.archives-ouvertes.fr/hal-00885929
Growth units construction in trees: A stochastic approach, Acta Biotheoretica, vol.XII, issue.8, pp.325-342, 1991. ,
DOI : 10.3406/jatba.1965.2856
Plant Growth Models, Ecological Models, vol.4, pp.2824-2837, 2008. ,
DOI : 10.1016/B978-008045405-4.00217-2
URL : https://hal.archives-ouvertes.fr/halsde-00341036
Modeling Inter-individual Variability in Sugar Beet Populations, 2009 Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2009. ,
DOI : 10.1109/PMA.2009.56
URL : https://hal.archives-ouvertes.fr/inria-00537646
Maximum Likelihood from incomplete data via the EM algorithm, Journal of the Royal Statistical Society. Series B (Statistical Methodology), pp.39-40, 1977. ,
A tutorial on particle filtering and smoothing: fifteen years later, 2008. ,
GRAAL: a model of GRowth Architecture and carbon ALlocation during the vegetative phase of the whole maize plant, model description and parameterisation, Ecological Modelling, pp.165-147, 2003. ,
Emergent properties modelled with the functional structural tree growth model ALMIS: Computer experiments on resource gain and use, Ecological Modelling, vol.186, issue.4, pp.470-488, 2005. ,
DOI : 10.1016/j.ecolmodel.2005.02.013
Sink strength: What is it and how do we measure it? A summary, Plant, Cell and Environment, vol.16, issue.9, pp.1045-1046, 1993. ,
DOI : 10.1111/j.1365-3040.1996.tb02061.x
Plant Growth Modelling and Applications: The Increasing Importance of Plant Architecture in Growth Models, Annals of Botany, vol.101, issue.8, pp.1053-1063, 2008. ,
DOI : 10.1093/aob/mcn050
URL : https://hal.archives-ouvertes.fr/halsde-00281936
Parameterization of a processbased tree-growth model: Comparison of optimization, MCMC and particle filtering algorithms . Environmental Modelling and Software, pp.1280-1288, 2008. ,
URL : https://hal.archives-ouvertes.fr/inria-00506344
Functional-structural plant modelling, New Phytologist, vol.166, issue.3, pp.705-708, 2005. ,
DOI : 10.1111/j.1469-8137.2005.01445.x
URL : https://hal.archives-ouvertes.fr/hal-01190931
Dynamic system identification: Experiment design and data analysis, 1977. ,
Pattern Analysis in Branching and Axillary Flowering Sequences, Journal of Theoretical Biology, vol.212, issue.4, pp.481-520, 2001. ,
DOI : 10.1006/jtbi.2001.2392
Adaptation of the Greenlab model for analyzing sink-source relationships in Chinese pine saplings. Plant growth Modeling, simulation, visualization and their Applications (PMA06), 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00576583
Parameter Optimization and Field Validation of the Functional-Structural Model GREENLAB for Maize, Annals of Botany, vol.97, issue.2, pp.97-217, 2006. ,
DOI : 10.1093/aob/mcj033
URL : https://hal.archives-ouvertes.fr/hal-00018867
Essai sur l'architecture et la dynamique de croissance des arbres tropicaux, 1970. ,
Models for navigating biological complexity in breeding improved crop plants, Trends in Plant Science, vol.11, issue.12, pp.587-593, 2006. ,
DOI : 10.1016/j.tplants.2006.10.006
Evaluation of a Dynamic Simulation Model for Tomato Crop Growth and Development, Annals of Botany, vol.83, issue.4, pp.413-422, 1999. ,
DOI : 10.1006/anbo.1998.0832
Ceres -Maize : A simulation model of Maize growth and development, 1986. ,
A new method for the nonlinear transformation of means and covariances in filters and estimators, IEEE Transactions on Automatic Control, vol.45, issue.3, pp.477-482, 2000. ,
DOI : 10.1109/9.847726
Analytical study of a stochastic plant growth model: Application to the GreenLab model, Mathematics and Computers in Simulation, vol.78, issue.1, pp.78-57, 2008. ,
DOI : 10.1016/j.matcom.2007.06.003
URL : https://hal.archives-ouvertes.fr/halsde-00306691
Optimization by Simulated Annealing, Science, issue.4598, pp.220-671, 1983. ,
Carbon allocation among tree organs: A review of basic processes and representation in
functional-structural tree models, Annals of Forest Science, vol.57, issue.5, pp.521-533, 2000. ,
DOI : 10.1051/forest:2000139
URL : https://hal.archives-ouvertes.fr/hal-01191058
A morphogenetic crop model for sugarbeet (Beta Vulgaris l.). Crop Modeling and Decision Support, pp.116-129, 2009. ,
URL : https://hal.archives-ouvertes.fr/inria-00336415
Multi-scale analysis of source-sink relationships in plant growth models for parameter identification. Case of the Greenlab model, 2008. ,
), Functional Plant Biology, vol.35, issue.10, pp.1243-1254, 2008. ,
DOI : 10.1071/FP08065
Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization, Annals of Botany, vol.101, issue.8, pp.951-963, 2008. ,
DOI : 10.1093/aob/mcm197
URL : https://hal.archives-ouvertes.fr/inria-00529529
Asymptotic behavior of the extended Kalman filter as a parameter estimator for linear systems, IEEE Transactions on Automatic Control, vol.24, issue.1, pp.643-652, 1979. ,
DOI : 10.1109/TAC.1979.1101943
System identification: Theory for the user, 1999. ,
Theory and practice of recursive identification, 1983. ,
Generating functions of stochastic L-systems and application to models of plant development, Discrete Mathematics and Theoretical Computer Science Proceedings, pp.325-338, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-01194661
A Symbolic Method to Analyse Patterns in Plant Structure, Combinatorics, Probability and Computing, vol.26, issue.05, 2011. ,
DOI : 10.1007/s00285-008-0193-z
URL : https://hal.archives-ouvertes.fr/inria-00546309
, a model of morphogenesis and competition among sinks in rice. 1. Concept, validation and sensitivity analysis, Functional Plant Biology, vol.33, issue.4, pp.309-323, 2007. ,
DOI : 10.1071/FP05266
Calibration of GREENLAB Model for Maize with Sparse Experimental Data, 2006 Second International Symposium on Plant Growth Modeling and Applications, 2007. ,
DOI : 10.1109/PMA.2006.27
Parameter estimation for crop models. Working with Dynamic Crop Models, pp.55-100, 2006. ,
A dynamic model of plant growth with interactions between development and functional mechanisms to study plant structural plasticity related to trophic competition, Annals of Botany, vol.103, issue.8, pp.1173-1186, 2009. ,
DOI : 10.1093/aob/mcp054
URL : https://hal.archives-ouvertes.fr/halsde-00418643
Calibration of fruit cyclic patterns in cucumber plants as a function of source-sink ratio with the Greenlab model, Proceedings of the 5th international workshop on FSPM, 2007. ,
Stem Growth and Epicormic Branch Formation in Understorey Beech Trees (Fagus sylvatica L.), Annals of Botany, vol.87, issue.6, pp.737-750, 2001. ,
DOI : 10.1006/anbo.2001.1398
Sequential Monte Carlo smoothing with application to parameter estimation in nonlinear state space models, Bernoulli, vol.14, issue.1, pp.155-179, 2008. ,
DOI : 10.3150/07-BEJ6150
URL : https://hal.archives-ouvertes.fr/hal-00096080
Using a mathematical model to evaluate the trophic and non-trophic determinants of axis development in grapevine, Functional Plant Biology, vol.36, issue.2, pp.156-170, 2009. ,
DOI : 10.1071/FP08178
URL : https://hal.archives-ouvertes.fr/hal-00872383
Modeling plant growth and development, Current Opinion in Plant Biology, vol.7, issue.1, pp.79-84, 2004. ,
DOI : 10.1016/j.pbi.2003.11.007
Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference, Bioinformatics, vol.23, issue.23, pp.3209-3216, 2007. ,
DOI : 10.1093/bioinformatics/btm510
URL : https://hal.archives-ouvertes.fr/hal-00341950
A tutorial on hidden Markov models and selected applications in speech recognition, Proc. IEEE, pp.77-257, 1989. ,
Contemporary statistical models for the plant and soil sciences, 2001. ,
DOI : 10.1201/9781420040197
Components of a functional-structural tree model, Annals of Forest Sciences, pp.57-399, 2000. ,
Small Sample Properties of a Class of Two Stage Aitken Estimators, Econometrica, vol.45, issue.2, pp.45-497, 1977. ,
DOI : 10.2307/1911224
Développement du hêtre commun Morphologie et architecture de l'arbre. RevueForestì ere Française, pp.45-58, 1984. ,
Identification de modèles paramétriques, 2006. ,
Simulation of the structure and function of young Mongolian scots pine trees using the stochastic Greenlab model, Annals of Botany, 2010. ,
Ecological data on dry matter production by plants and plant communities. The collection and processing of field data, pp.77-123, 1967. ,
The virtual crop modelling system VICA specified for Barley. Functional-structural plant modelling in crop production, pp.58-69, 2007. ,
Assessment of non-linearity in functional-structural plant models. 6th international workshop on Functional-Structural Plant Models (FSPM10, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01192293
Sensitivity Analysis of GreenLab Model for Maize, 2009 Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2009. ,
DOI : 10.1109/PMA.2009.37
URL : https://hal.archives-ouvertes.fr/inria-00532950
A Dynamic, Architectural Plant Model Simulating Resource-dependent Growth, Annals of Botany, vol.93, issue.5, pp.591-602, 2004. ,
DOI : 10.1093/aob/mch078
URL : https://hal.archives-ouvertes.fr/inria-00122497
Fitting a structural-functional model with plant architectural data. Plant Growth Models and Applications, pp.236-249, 2003. ,
URL : https://hal.archives-ouvertes.fr/inria-00122502
Hidden Markov models for time series -An introduction using R, 2009. ,