Bayesian hierarchical models for disease mapping applied to contagious pathologies

Disease mapping aims to determine the underlying disease risk from scattered epidemiological data and to represent it on a smoothed colored map. This methodology is based on Bayesian inference and is classically dedicated to non-infectious diseases whose incidence is low and whose cases distribution is spatially (and eventually temporally) structured. Over the last decades, disease mapping has received many major improvements to extend its scope of application: integrating the temporal dimension, dealing with missing data, taking into account various a prioris (environmental and population covariates, assumptions concerning the repartition and the evolution of the risk), dealing with overdispersion, etc. We aim to adapt this approach to model rare infectious diseases proposing specific and generic variants of this methodology. In the context of a contagious disease, the outcome of a primary case can in addition generate secondary occurrences of the pathology in a close spatial and temporal neighborhood; this can result in local overdispersion and in higher spatial and temporal dependencies due to direct and/or indirect transmission. In consequence, we test models including a Negative Binomial distribution (instead of the usual Poisson distribution) to deal with local overdispersion. We also use a specific spatio-temporal link in order to better model the stronger spatial and temporal dependencies due to the transmission of the disease. We have proposed and tested 60 Bayesian hierarchical models on 400 simulated datasets and bovine tuberculosis real data. This analysis shows the relevance of the CAR (Conditional AutoRegressive) processes to deal with the structure of the risk. We can also conclude that the negative binomial models outperform the Poisson models with a Gaussian noise to handle overdispersion. In addition our study provided relevant maps which are congruent with the real risk (simulated data) and with the knowledge concerning bovine tuberculosis (real data).

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Bayesian hierarchical models for disease mapping applied to contagious pathologies

10.1101/766071 ◽

2019 ◽

Author(s):

Sylvain Coly ◽

Myriam Garrido ◽

David Abrial ◽

Anne-Françoise Yao

Keyword(s):

Infectious Diseases ◽

Bovine Tuberculosis ◽

Negative Binomial ◽

Disease Mapping ◽

Simulated Data ◽

Real Data ◽

Primary Case ◽

Bayesian Hierarchical ◽

Real Risk ◽

Rare Infectious Diseases

AbstractDisease mapping aims to determine the underlying disease risk from scattered epidemiological data and to represent it on a smoothed colored map. This methodology is based on Bayesian inference and is classically dedicated to non-infectious diseases whose incidence is low and whose cases distribution is spatially (and eventually temporally) structured. Over the last decades, disease mapping has received many major improvements to extend its scope of application: integrating the temporal dimension, dealing with missing data, taking into account various a prioris (environmental and population covariates, assumptions concerning the repartition and the evolution of the risk), dealing with overdispersion, etc. We aim to adapt this approach to rare infectious diseases. In the context of a contagious disease, the outcome of a primary case can in addition generate secondary occurrences of the pathology in a close spatial and temporal neighborhood; this can result in local overdispersion and in higher spatial and temporal dependencies due to direct and/or indirect transmission. We have proposed and tested 60 Bayesian hierarchical models on 400 simulated datasets and bovine tuberculosis real data. This analysis shows the relevance of the CAR (Conditional AutoRegressive) processes to deal with the structure of the risk. We can also conclude that the negative binomial models outperform the Poisson models with a Gaussian noise to handle overdispersion. In addition our study provided relevant maps which are congruent with the real risk (simulated data) and with the knowledge concerning bovine tuberculosis (real data).Author summaryDisease mapping is dedicated to non-infectious diseases whose incidence is low and whose distribution is spatially (and eventually temporally) structured. In this paper, we aim to adapt this approach to rare infectious pathologies. In the context of a contagious disease, the outcome of a primary case can in addition generate secondary occurrences of the pathology in a close spatial and temporal neighborhood, resulting in local overdispersion and in high spatial and temporal dependencies. We thus explored different adapted spatial, temporal and spatiotemporal links and highlight the most adapted to likely risk structures for infectious diseases. We also conclude that the negative binomial models outperform the Poisson models with a Gaussian noise to handle overdispersion. Our study also provided relevant maps which are congruent with the real risk (in case of simulated data) and with the knowledge concerning bovine tuberculosis (when applying to real data). Thus disease mapping appears as a promising way to investigate rare infectious diseases.

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