Samuel Soubeyrand

Contact   
samuel.soubeyrand@inrae.fr   
+33 4.32.72.21.85   
INRAE - BioSP - 228 rte de l'aérodrome   
84914 Avignon Cedex 9 - France   
Follow @s_soubeyrand

Lannou et al. (2023) - Editions QUAE                   
 

The issue of health crises caused by invasive pests is essential in agriculture. This book deals with various questions on the subject, including: How do invasions occur? How do they spread? Why are they so frequent? What detection and identification tools are available to track these populations and trace their origins? Which models allow to analyze the risk, to predict it and to optimize the monitoring accordingly? Finally, how is society organized in the face of these crises?

Collectif BIOBAYES (2015) - Editions Ellipses  

BIOBAYES website

ModStatSAP network - funded by the SPE, MathNum and SA departments of INRAE - Modeling and statistics for animal and crop health

Richard et al. (2023) - GeoHealth - As air masses move within the troposphere, they transport a multitude of components including gases and particles such as pollen and microorganisms. These movements generate atmospheric highways that connect geographic areas at distant, local, and global scales that particles can ride depending on their aerodynamic properties and their reaction to environmental conditions. In this article we present an approach and an accompanying web application called tropolink for measuring the extent to which distant locations are potentially connected by air-mass movement... https://doi.org/10.1029/2023GH000885

Roques et al. (2023) - Biological Invasions - France has a latitudinal range for the expansion of Aedes albopictus invasive populations that is not yet completely colonized providing a critical opportunity to address key invasion processes. We propose a spatio-temporal model (DISTIGRI) to describe and predict current and future expansions at intra- and inter-annual scales of A. albopictus... doi:10.1007/s10530-023-03062-y

Soubeyrand et al. (2020) - PLoS ONE - Discrepancies in population structures, decision making, health systems and numerous other factors result in various COVID-19-mortality dynamics at country scale [...]. Mortality dynamics of countries that are ahead of time implicitly include these factors and can be used as real-life competing predicting models. We precisely propose such a data-driven approach implemented in a publicly available web app timely providing mortality curves comparisons and real-time short-term forecasts... doi:10.1371/journal.pone.0238410

Baudrot et al. (2020) - Ecotoxicology and Environmental Safety - Field cultivation of Genetically Modified (GM) Bt-plants has a potential environmental risk toward non-target Lepidoptera (NTLs) larvae through the consumption of Bt-maize pollen. The Bt-maize Cry protein targeting Lepidoptera species detrimental to the crop is also expressed in pollen which is dispersed by wind and can thus reach habitats of NTLs. To better assess the current ecological risk of Bt-maize at landscape scales, we developed a spatially-explicit exposure-hazard model... doi:10.1016/j.ecoenv.2020.111215

SMITID project (2016-2020) - ANR grant ANR-16-CE35-0006 - Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data

Soubeyrand (2016) - Journal de la SFdS - Identifying transmission links of an infectious disease through a host population is critical to understanding its epidemiology and informing measures for its control. To infer more reliably who-transmitted-to-whom [...], we present [an approach] that combines (i) an individual-based, spatial, semi-Markov SEIR model for the spatio-temporal dynamics of the pathogen, and (ii) a Markovian evolutionary model for the temporal evolution of genetic sequences of the pathogen... http://journal-sfds.fr/article/view/524

Soubeyrand and Haon-Lasportes (2015) - Statistics and Probability Letters - The weak convergence of posterior distributions conditional on maximum pseudo-likelihood estimates (MPLE) is studied and exploited to justify the use of MPLE as summary statistics in approximate Bayesian computation (ABC). Our study could be generalized by replacing the pseudo-likelihood by other estimating functions (e.g. quasi-likelihoods and contrasts)... doi:10.1016/j.spl.2015.08.003

Mollentze et al. (2014) - Proceedings of the Royal Society B  - We describe a statistical framework for reconstructing the sequence of transmission events between observed cases of an endemic infectious disease using genetic, temporal and spatial information... doi:10.1098/rspb.2013.3251 

Soubeyrand et al. (2014) - Environmental Modelling & Software  - Identifying and characterizing feedbacks in environmental processes may help in improving predictions for some environmental systems. The statistical study of time series is a manner to approach these feedbacks... doi:10.1016/j.envsoft.2014.07.003                   
See also the R package FeedbackTS and the web tool RainfallFeedbackMaps 

Soubeyrand et al. (2024) - CABI Agriculture and Bioscience - In an era marked by rapid global changes, the reinforcement and modernization of plant health surveillance systems have become imperative. Sixty-five scientists present here a research agenda for an enhanced and modernized plant health surveillance to anticipate and mitigate disease and pest emergence... https://doi.org/10.1186/s43170-024-00273-8

Ribaud et al. (2023) - Statistics in Medicine - Classical supervised methods like linear regression and decision trees are not completely adapted for identifying impacting factors on a response variable corresponding to zero-inflated proportion data (ZIPD) that are dependent, continuous and bounded. In this article we propose a within-block permutation-based methodology to identify factors (discrete or continuous) that are significantly correlated with ZIPD... https://doi.org/10.1002/sim.9814

Abboud et al. (2023) - Bulletin of Mathematical Biology - Forecasting invasive-pathogen dynamics is paramount to anticipate eradication and containment strategies. [...] To avoid drawing a forecast grounded on a single PDE-based model that would be prone to errors, we propose to apply Bayesian model averaging (BMA), which allows us to account for both parameter and model uncertainties. [...] This approach is applied to predict the extent of Xylella fastidiosa in South Corsica... https://doi.org/10.1007/s11538-023-01169-w

Eck et al. (2022) - The American Naturalist - The inherently variable nature of epidemics renders predictions of when and where infection is expected to occur challenging. Differences in pathogen strain composition, diversity, fitness, and spatial distribution are generally ignored in epidemiological modeling and are rarely studied in natural populations, yet they may be important drivers of epidemic trajectories... doi:10.1086/717179

Choufany et al. (2021) - Frontiers in Applied Mathematics and Statistics - The movement of atmospheric air masses [...] can be locally simplified by means of three-dimensional trajectories. These trajectories can hence be seen as a way of connecting distant areas [...]. In this paper we present a mathematical formalism to construct spatial and spatiotemporal networks [...] inferred from sampled trajectories of air masses [...] with potential implications in aerobiology and plant epidemiology... doi:10.3389/fams.2020.602621

Dvorak et al. (2019) - Spatial Statistics - For point patterns observed in natura, spatial heterogeneity is more the rule than the exception [...]. We propose parametric and semiparametric models of non-stationary LGCPs where the non-stationarity is included in both the mean function and the covariance function of the GRF... doi:10.1111/risa.12941

Alamil et al. (2019) - Philosophical Transactions B - Here, we propose a statistical learning approach for estimating epidemiological links from deep sequencing data (called SLAFEEL), which is based on a parsimonious semiparametric pseudo-evolutionary model... doi:10.1098/rstb.2018.0258

Soubeyrand et al. (2009) - The American Naturalist - The ecological and evolutionary dynamics of species are influenced by spatiotemporal variation in population size. Unfortunately, we are usually limited in our ability to investigate the numerical dynamics of natural populations across large spatial scales and over long periods of time. Here we combine mechanistic and statistical approaches to reconstruct continuous‐time infection dynamics of an obligate fungal pathogen... doi:10.1086/603624