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epiABC

swMATH ID: 23334
Software Authors: Kypraios, Theodore; Neal, Peter; Prangle, Dennis
Description: A tutorial introduction to Bayesian inference for stochastic epidemic models using approximate Bayesian computation. Likelihood-based inference for disease outbreak data can be very challenging due to the inherent dependence of the data and the fact that they are usually incomplete. In this paper we review recent Approximate Bayesian Computation (ABC) methods for the analysis of such data by fitting to them stochastic epidemic models without having to calculate the likelihood of the observed data. We consider both non-temporal and temporal-data and illustrate the methods with a number of examples featuring different models and datasets. In addition, we present extensions to existing algorithms which are easy to implement and provide an improvement to the existing methodology. Finally, code to implement the algorithms presented in the paper is available on url{https://github.com/kypraios/epiABC}.
Homepage: https://github.com/kypraios/epiABC
Source Code:  https://github.com/kypraios/epiABC
Keywords: Bayesian inference; epidemics; stochastic epidemic models; approximate Bayesian computation; population Monte Carlo
Related Software: R; BayesDA; abc; GPS-ABC; abcrf; abctools; ABC-SubSim; GitHub; fda (R); CODA; hmer; brlm; AABC; ABCtoolbox; abcpmc; DREAM; onesamp; abc-sde; msABC; DR-ABC
Cited in: 14 Documents

Standard Articles

1 Publication describing the Software, including 1 Publication in zbMATH Year
A tutorial introduction to Bayesian inference for stochastic epidemic models using approximate Bayesian computation. Zbl 1377.92091
Kypraios, Theodore; Neal, Peter; Prangle, Dennis
2017
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Cited by 42 Authors

4 Kypraios, Theodore
2 Prangle, Dennis
1 Andrianakis, Ioannis
1 Aristotelous, Georgios
1 Baggaley, Andrew W.
1 Besser, Thomas E.
1 Blagus, Rok
1 Buckwar, Evelyn
1 Corander, Jukka
1 Dutta, Ritabrata
1 Everitt, Richard Geoffrey
1 Feng, Tao
1 Finkenstädt, Bärbel F.
1 French, Nigel P.
1 Golightly, Andrew
1 Järvenpää, Marko
1 Karabatsos, George
1 Ke, Yuqin
1 Kejžar, Nataša
1 Leisen, Fabrizio
1 Manevski, Damjan
1 McCreesh, Nicky
1 McKinley, Trevelyan J.
1 Mira, Antonietta
1 Neal, Peter J.
1 Nsubuga, Rebecca N.
1 Oakley, Jeremy E.
1 O’Neill, Philip D.
1 Onnela, Jukka-Pekka
1 Parker, Nick G.
1 Qiu, Zhipeng
1 Ružić Gorenjec, Nina
1 Sherlock, Chris
1 Spencer, Simon Edward Frank
1 Tamborrino, Massimiliano
1 Tian, Tianhai
1 Touloupou, Panayiota
1 Tubikanec, Irene
1 Vernon, Ian
1 Wadkin, Laura E.
1 Whitaker, Sam A.
1 White, Richard G.
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Cited in 9 Serials

4 Statistics and Computing
2 Mathematical Biosciences
1 Statistical Science
1 Computational Statistics
1 The Annals of Applied Statistics
1 International Journal of Biomathematics
1 Statistics Surveys
1 Bayesian Analysis
1 Proceedings of the Royal Society of London. A. Mathematical, Physical and Engineering Sciences
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Cited in 6 Fields

13 Statistics (62-XX)
9 Biology and other natural sciences (92-XX)
3 Numerical analysis (65-XX)
2 Probability theory and stochastic processes (60-XX)
1 Game theory, economics, finance, and other social and behavioral sciences (91-XX)
1 Systems theory; control (93-XX)

Citations by Year