Desirable BUGS in models of infectious diseases

Megan Auzenbergs, Carla Correia-Gomes, Theo Economou, Rachel Lowe, Kathleen M O'Reilly

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Abstract

Bayesian inference using Gibbs sampling (BUGS) is a set of statistical software that uses Markov chain Monte Carlo (MCMC) methods to estimate almost any specified model. Originally developed in the late 1980s, the software is an excellent introduction to applied Bayesian statistics without the need to write a MCMC sampler. The software is typically used for regression-based analyses, but any model that can be specified using graphical nodes are possible. Advanced topics such as missing data, spatial analysis, model comparison and dynamic infectious disease models can be tackled. Three examples are provided; a linear regression model to illustrate parameter estimation, the steps to ensure that the estimates have converged and a comparison of run-times across different computing platforms. The second example describes a model that estimates the probability of being vaccinated from cross-sectional and surveillance data, and illustrates the specification of different models, model comparison and data augmentation. The third example illustrates estimation of parameters within a dynamic Susceptible-Infected-Recovered model. These examples show that BUGS can be used to estimate parameters from models relevant for infectious diseases, and provide an overview of the relative merits of the approach taken.

Original languageEnglish
Article number100361
JournalEpidemics
Early online date17 Oct 2019
DOIs
Publication statusFirst published - 17 Oct 2019

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Communicable Diseases
Markov Chains
Software
Linear Models
Monte Carlo Method
Spatial Analysis
Regression Analysis

Bibliographical note

Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.

Keywords

  • Statistics
  • Modelling
  • Bayesian
  • Spatial
  • Infectious diseases

Cite this

Auzenbergs, M., Correia-Gomes, C., Economou, T., Lowe, R., & O'Reilly, K. M. (2019). Desirable BUGS in models of infectious diseases. Epidemics, [100361]. https://doi.org/10.1016/j.epidem.2019.100361
Auzenbergs, Megan ; Correia-Gomes, Carla ; Economou, Theo ; Lowe, Rachel ; O'Reilly, Kathleen M. / Desirable BUGS in models of infectious diseases. In: Epidemics. 2019.
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Auzenbergs, M, Correia-Gomes, C, Economou, T, Lowe, R & O'Reilly, KM 2019, 'Desirable BUGS in models of infectious diseases', Epidemics. https://doi.org/10.1016/j.epidem.2019.100361

Desirable BUGS in models of infectious diseases. / Auzenbergs, Megan; Correia-Gomes, Carla; Economou, Theo; Lowe, Rachel; O'Reilly, Kathleen M.

In: Epidemics, 17.10.2019.

Research output: Contribution to journalArticle

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N2 - Bayesian inference using Gibbs sampling (BUGS) is a set of statistical software that uses Markov chain Monte Carlo (MCMC) methods to estimate almost any specified model. Originally developed in the late 1980s, the software is an excellent introduction to applied Bayesian statistics without the need to write a MCMC sampler. The software is typically used for regression-based analyses, but any model that can be specified using graphical nodes are possible. Advanced topics such as missing data, spatial analysis, model comparison and dynamic infectious disease models can be tackled. Three examples are provided; a linear regression model to illustrate parameter estimation, the steps to ensure that the estimates have converged and a comparison of run-times across different computing platforms. The second example describes a model that estimates the probability of being vaccinated from cross-sectional and surveillance data, and illustrates the specification of different models, model comparison and data augmentation. The third example illustrates estimation of parameters within a dynamic Susceptible-Infected-Recovered model. These examples show that BUGS can be used to estimate parameters from models relevant for infectious diseases, and provide an overview of the relative merits of the approach taken.

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Auzenbergs M, Correia-Gomes C, Economou T, Lowe R, O'Reilly KM. Desirable BUGS in models of infectious diseases. Epidemics. 2019 Oct 17. 100361. https://doi.org/10.1016/j.epidem.2019.100361