All models are wrong but some are useful...

Plus un système vivant est autonome, plus il est dépendant à l’égard de l’écosystème ; en effet, l’autonomie suppose la complexité, laquelle suppose une très grande richesse de relations de toutes sortes avec l’environnement, c’est-à-dire dépend d’interrelations, lesquelles constituent très exactement les dépendances qui sont les conditions de la relative indépendance1.

Edgar Morin - Le paradigme perdu : la nature humaine (1973)

  1. A translation could be: The more autonomous a living system is, the more it is dependent on the ecosystem. Indeed, autonomy assumes complexity, which presupposes a very great richness of interactions of all kinds with the environment, that is to say depends on interconnections, which constitute very exactly the dependencies which are the conditions of relative independence. ^


  • Effects of contaminants and trophic cascade regulation on food chain stability: application to cadmium soil pollution on small mammals-raptor systems

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  • Fit GUTS reduced models online: from theory to practice

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  • morse: Modelling Tools for Reproduction and Survival Data in Ecotoxicology

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  • New insights to compare and choose TKTD models for survival based on an inter-laboratory study for *Lymnaea stagnalis* exposed to Cd

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  • Rising variance and abrupt shifts of subfossil chironomids due to eutrophication in a deep sub-alpine lake

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  • Modélisation des interactions trophiques impliquant des transferts de contaminants biologiques et chimiques. Application à *Echinococcus multilocularis* et aux éléments traces métalliques.

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  • The adaptation of generalist predators diet in a multi-prey context: insights from new functional responses

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  • Competence of hosts and complex foraging behavior are two cornerstones in the dynamics of trophically transmitted parasites

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Note: the following post is supposed to be updated regularly Style guides Some references are unavoidable, the Hadley’s style guide, the Google’s R style guide, and also The R Inferno by Patrick Burns As Hadley wrote, the most important is to have a consistent and clear style. Notations Starting with variable, choices doesn’t really matters. I use this style of notation: # GOOD variableName # camelCasing style variable_Name # Not that good (personnal taste) variable.



Fitting Functional Reponses

trophicR is an R package to facilitate model-fitting of functional responses (trophic interactions) using a Bayesian approach with Stan.


[…] a vital next step will be to promote the training of scientists with expertise in both mathematics and biology.

Alan Hastings and Margaret A. Palmer (2003) - A Bright Future for Biologists and Mathematicians? Science 299, pp. 2003-2004

Université de Franche-Comté

2014-2015 | 64 h

Lecture Subject Hours
Licence 1 - Starter ST C2I - produire, traiter, diffuser des documents numériques 14 h
Licence 2 - Biologie Biostatistiques 22 h
Licence Pro - MINA Analyse de données multidimensionnelles 11 h
Licence 3 - Biologie Biologie numérique et statistique 9 h
Master 1 - ECoS Modélisation des dynamiques spatiales 8 h

2015-2016 | 17 h

Lecture Subject Hours
Licence 1 - Starter ST Mathématiques - équations différentielles 14 h
2014 - Quentin Richard
UCB Lyon 1 - M2 Mathématiques Appliquées et Statistiques
Co-supervising with Antoine Perasso (MCF - UBFC)
Étude du comportement de prédation par analyse mathématique et simulations numériques de systèmes proies-prédateur


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