Info
Hi! I'm Jean-François Rey, computer scientist, R&D engineer @INRA. I'm passionate about Computer Science, Development, IT and Geeks stuffs ;-).
I define myself as curious, enthusiastic, and independent in my work. I like to discover, test and apply new technologies to answer scientific problems.
Currently I work for the Plant Health and Environment department (@SPE) in the Biostatistique et Processus Spatiaux laboratory (@BioSP).
I mainly involved in the development and deployment of applications and statistical methods for epidemiology.
Quote
"The theory is when you know everything and nothing works.
Practice is when everything works and nobody knows why.
Here we gathered theory and practice: Nothing works ... and no one knows why!"
Projects
Are listed here projects on which I currently work on and which can be shared.
- MEMM (Mixed Effect Mating Model)
MEMM is a computer program implementing a bayesian statistic method presented in Klein et al.(2008). It estimates the pollen dispersal kernel and the variance in male fecundity from spatial and genetic data concerning adult plants and sampled seeds.
More details here
Version 2.0 and fork - Landsepi (Landscape Epidemiology and Evolution)
Landsepi is a R package implementing a spatio-temporal stochastic model to assess resistance deployment strategies against plant pathogens.
I am mainly involved in the developement (C/C++) and R packaging of the model.
GitLab repository
Plos Biology paper
landespi on cran - BriskaR (Biological risk assment in R)
BriskaR (was known as SEHModel) is a R package implementing a spatio-temporal exposure-hazard model for assessing biological risk and impact.
The R package SEHmodel was developed for the european project AMIGA (Assessing and Monitoring the Impact of Genetically modified plants on Agro-ecosystems).
GitLab repository
Risk Analysis paper
More details here
briskaR on cran - Gitlab and Gitlab CI
I one of the administrators of https://gitlab.paca.inra.fr (GitLab CE, a free opensource repository manager and much more). This including Gitlab-ci pipeline ( mainly managing kubernetes cluster and runners, Docker, VM, ...).
And as a developer I use it for my projects management. - ShinyProxy and Shiny Apps
I one of the administrators of https://shiny.biosp.inra.fr (a container proxy for shiny applications). This including server administration and container built (via GitLab CI/CD).
- SMITID (Statistical Methods to Infer Transmissions of Infectious Diseases From Deep Sequencing Data)
SMITID is an ANR project.
The aim of the project is to carry out advanced research on the statistical analysis of pathogen sequence data to infer transmission links.
More details here
Shiny app demonstration here
GitLab projects group
SMITIDstruct R package on CRAN
SMITIDvisu R HTMLwidget package on CRAN - APIMODEL extended by Innov'Api project
APIMODEL is a project funded by France Agrimer and le Programme Apicole Européen.
The aim of the project is an observatory of the honeydew of apiaries on lavender.
Innov'Api is an Europeen project that focus on the damage caused by the Varroa parasite and seeking effective and sustainable control methods.
I'm involved in the development of the Information System APIMODEL
More details here - JAGS MecaStat Module
MecaStat Module implements a plugin for JAGS (Just Another Gibbs Sampler) to integrate mecanico-statistical approaches.
GitLab repository
Networks
@INRA networks :
- R ecosystem Group
Tools and GitLab CI/CD pipelines templates for R ecosystem (Packaging and RShiny).
Main maintainer
The group
Cookbooks
User! 2019, Toulouse, poster R package development using GitLab CI/CD pipeline, JF Rey, L Houde, 2019 - GeOpen4S
GeOpen4S is a platform for management and process of spatialized data.
I intervene in the users committee and the system architecture
More details here
Platform services - Cati IMOTEP 𓇍𓅓𓊵
The Centre automatisé de traitement de l'information (Cati) Informations, MOdèles et Traitement des données en Epidémiologie et dynamique des Populations (IMOTEP) is a regroup of INRA IT staff responsible for managing and developing projects. These projects concern the epidemiological field (animal and plant) and the dynamics of population in the agricultural landscapes
More details here
- Cati CaSciSDI (past)
The Centre automatisé de traitement de l'information (Cati) Calcul Scientifique, Statistique et Développement Informatique pour la recherche à l'INRA (CaSciSDI) is a regrouping of IT personal from INRA around scientific processing, statisitic and Development.
I mainly participate in the exchange platform around R R4CIAM.
More details here
R4CIAM - ModStatSAP
Modeling and statistics for animal and crop health (ModStatSAP) is a network that it main objective is to bring together modellers and statisticians from research structures to study plant / pest and host / pathogen systems.
ModStatSAP
Others networks :
Skills
Some stuff I do currently. It was mostly to try D3JS :-D
CV