Bayesian Network Modeling Applied to Feline Calicivirus Infection Among Cats in Switzerland

Gilles Kratzer; Fraser I Lewis; Barbara Willi; Marina L Meli; Felicitas S Boretti; Regina Hofmann-Lehmann; Paul Torgerson; Reinhard Furrer; Sonja Hartnack

doi:10.3389/fvets.2020.00073

Bayesian Network Modeling Applied to Feline Calicivirus Infection Among Cats in Switzerland

Front Vet Sci. 2020 Feb 26:7:73. doi: 10.3389/fvets.2020.00073. eCollection 2020.

Authors

Gilles Kratzer¹, Fraser I Lewis², Barbara Willi³, Marina L Meli^{4

5}, Felicitas S Boretti³, Regina Hofmann-Lehmann^{4

5}, Paul Torgerson⁶, Reinhard Furrer^{1

7}, Sonja Hartnack⁶

Affiliations

¹ Department of Mathematics, University of Zurich, Zurich, Switzerland.
² Independent Researcher, Utrecht, Netherlands.
³ Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
⁴ Clinical Laboratory, Department of Clinical Diagnostics and Services, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
⁵ Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
⁶ Section of Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
⁷ Department of Computational Science, University of Zurich, Zurich, Switzerland.

Abstract

Bayesian network (BN) modeling is a rich and flexible analytical framework capable of elucidating complex veterinary epidemiological data. It is a graphical modeling technique that enables the visual presentation of multi-dimensional results while retaining statistical rigor in population-level inference. Using previously published case study data about feline calicivirus (FCV) and other respiratory pathogens in cats in Switzerland, a full BN modeling analysis is presented. The analysis shows that reducing the group size and vaccinating animals are the two actionable factors directly associated with FCV status and are primary targets to control FCV infection. The presence of gingivostomatitis and Mycoplasma felis is also associated with FCV status, but signs of upper respiratory tract disease (URTD) are not. FCV data is particularly well-suited to a network modeling approach, as both multiple pathogens and multiple clinical signs per pathogen are involved, along with multiple potentially interrelated risk factors. BN modeling is a holistic approach-all variables of interest may be mutually interdependent-which may help to address issues, such as confounding and collinear factors, as well as to disentangle directly vs. indirectly related variables. We introduce the BN methodology as an alternative to the classical uni- and multivariable regression approaches commonly used for risk factor analyses. We advise and guide researchers about how to use BNs as an exploratory data tool and demonstrate the limitations and practical issues. We present a step-by-step case study using FCV data along with all code necessary to reproduce our analyses in the open-source R environment. We compare and contrast the findings of the current case study using BN modeling with previous results that used classical regression techniques, and we highlight new potential insights. Finally, we discuss advanced methods, such as Bayesian model averaging, a common way of accounting for model uncertainty in a Bayesian network context.

Keywords: Bayesian network; feline calicivirus; good modeling practice; graphical model; multivariable analysis; reproducible research; risk factor analysis.