Development of a user-friendly interface version of the Salmonella source-attribution model

Salmonella, source attribution, flexible user-friendly interface version, scenario analysis
First published in EFSA Supporting Publications
25. Juli 2012
6. Juli 2012
External Scientific Report


The objective of the work described in this report was to develop a flexible and user-friendly interface for attributing human cases of food-borne pathogens to the responsible food-animal reservoirs and/or food sources. The interface is based on two existing Salmonella source-attribution models developed in previous EFSA contracts. The developed interface is called the EFSA Source Attribution Model (EFSA_SAM) and the programming language used is Embarcaderos Delphi XE2 Enterprise. Based on the user’s imported data and model selections, the interface generates a WinBUGS code that is executed in WinBUGS and the resulting data are then imported from WinBUGS to the interface software for tabulation and graphical display. This approach ensures consistency in both model and data setup, eliminating the need for user knowledge of WinBUGS syntax. EFSA_SAM requires data by country on reported number of human cases by subtypes, food-source prevalences by subtypes and food production and trade. Users can specify which countries, food sources and subtypes (e.g. Salmonella serovars) to include in the model. The EFSA_SAM also includes the possibility to run different scenario analyses, where the user can explore the effect on human cases by changing the prevalence of specific subtypes in the included food sources. A critical part of all Bayesian models is to check for model convergence and goodness of fit. The EFSA_SAM describes different ways for checking convergence and exploring model fit providing the user with some tools to assess the validity of the model. The EFSA_SAM interface is delivered with a user-manual, which is also part of this report. Users of the interface are recommended to read this report before starting using the interface to become familiar with the model principles and the mathematics behind.

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The present document has been produced and adopted by the bodies identified above as author(s). This task has been carried out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded following a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors.