Publications

• Jacquez, J. A. and O'Neill, P. D. (1991) Reproduction numbers and thresholds in stochastic epidemic models I. Homogeneous populations. Mathematical Biosciences 107, 161-186.
• Ball, F. G. and O'Neill, P. D. (1993) A modification of the general stochastic epidemic motivated by AIDS modelling. Advances in Applied Probability 25, 39-62.
• Ball, F. G. and O' Neill, P. D. (1994) Strong convergence of stochastic epidemics. Advances in Applied Probability 26, 629-655.
• O'Neill, P. D. (1995) Epidemic models featuring behaviour change. Advances in Applied Probability 27, 960-979.
• O'Neill, P. D. (1996) Strong approximations for some open population epidemic models. Journal of Applied Probability 33, 448-457.
• O'Neill, P. D. and Bunday, B. D. (1997) The transient state probabilities of the M/M/1/ queue via a random walk approach. The Mathematical Scientist 22, 32-36.
• O'Neill, P. D. (1997) An epidemic model with removal-dependent infection rate. Annals of Applied Probability 7, 90-109.
• Clancy, D. and O'Neill, P. D. (1998) Approximation of epidemics by time-inhomogeneous birth-and-death processes. Stochastic Processes and Their Applications 73, 233-245.
• Ball, F. G. and O'Neill, P. D. (1999) The distribution of general final state random variables for stochastic epidemic models. Journal of Applied Probability 36, 473-491.
• O'Neill, P. D. and Roberts, G. O. (1999) Bayesian inference for partially observed stochastic epidemics. Journal of the Royal Statistical Society Series A 162, 121-129.
• O'Neill, P. D. (1999) On a branching model of division-within-division. I.M.A. Journal of Mathematics Applied in Medicine and Biology 16, 395-405.
• O'Neill, P. D., Balding, D. J., Becker, N. G., Eerola, M. and Mollison, D. (2000) Analyses of infectious disease data from household outbreaks by Markov Chain Monte Carlo methods. Applied Statistics 49, 517-542.
• O'Neill, P. D. and Becker, N. G. (2001) Inference for an epidemic when susceptibility varies. Biostatistics 2, 99-108.
• Clancy, D. and O'Neill, P. D. and Pollett, P. K. (2001) Approximations for the long- term behaviour of an open-population epidemic model.Methodology and Computing in Applied Probability 3, 75-95.
• Ball, F. G., Britton, T. and O'Neill, P. D. (2001) Empty confidence sets for epidemics, branching processes and Brownian motion. Biometrika 89, 211-224.
• Britton, T. and O'Neill, P. D. (2002) Bayesian inference for stochastic epidemics in populations with random social structure. Scandinavian Journal of Statistics 29, 375-390.
• O'Neill, P. D. (2002) A tutorial introduction to Bayesian inference for stochastic epidemic models using Markov chain Monte Carlo methods. Mathematical Biosciences 180, 103-114.
• O'Neill, P. D. (2002) MCMC methods for stochastic epidemic models. In Models and Inference in HSSS: Recent Developments and Perspectives, eds. Green, P. J., Lauritzen, S., and Richardson, S. Oxford University Press.
• O'Neill, P. D. (2003) Perfect simulation for Reed-Frost epidemic models. Statistics and Computing 13, 37-44.
• Hayakawa, Y., O'Neill, P. D., Upton, D., and Yip, P. S. F. (2003) Bayesian inference for a stochastic epidemic model with uncertain numbers of susceptibles of several types. Australian and New Zealand Journal of Statistics 45, 491-502.
• Clough, H., Clancy, D., O'Neill, P. D. and French, N. P. (2003) Bayesian methods for estimating pathogen prevalence within groups of animals from faecal pat sampling. Preventive Veterinary Medicine 58, 145-169.
• Becker, N. G., Britton, T. and O'Neill, P. D. (2003) Estimating vaccine effects on transmission of infection from household outbreak data. Biometrics 59, 467-475.
• O'Neill, P. D. (2005) Epidemic models, structured population. In The Encyclopedia of Biostatistics, 2nd edition.
• Höhle, M., Jørgensen, E. and O'Neill, P. D. (2005) Inference in disease transmission experiments by using stochastic epidemic models. Applied Statistics 54, 349-366.
• Demiris, N. and O'Neill, P. D. (2005) Bayesian inference for stochastic epidemic models with two levels of mixing. Scandinavian Journal of Statistics 32, 265-280.
• Clough, H. E., Clancy, D., French, N. P., O'Neill, P. D. and Robinson, S. E. (2005) A Bayesian method for quantifying uncertainty associated with numbers of E. Coli 0157 present in faecal samples. Biometrics 61, 610-616.
• O'Neill, P. D. and Marks, P. J. (2005) Bayesian model choice and infection route modelling in an outbreak of Norovirus. Statistics in Medicine 24, 2011-2024.
• Demiris, N. and O'Neill, P. D. (2005) Bayesian inference for stochastic multitype epidemics in structured populations via random graphs. Journal of the Royal Statistical Society, Series B 67, 731-746.
• Demiris, N. and O'Neill, P. D. (2006) Computation of final outcome probabilities for the generalised stochastic epidemic. Statistics and Computing 16, 309-317.
• Becker, N. G., Britton, T. and O'Neill, P. D. (2006) Estimating vaccine effects from studies of outbreaks in household pairs. Statistics in Medicine 25, 1079-1093.
• Clancy, D. and O'Neill, P. D. (2007) Exact Bayesian inference and model selection for stochastic models of epidemics among a community of households. Scandinavian Journal of Statistics 34, 259-274.
• O'Neill, P. D. (2007) Constructing population processes with specified quasi-stationary distributions. Stochastic Models 23, 439-449.
• Ball, F. G., O'Neill, P. D. and Pike, J. (2007) Stochastic epidemic models in structured populations featuring dynamic vaccination and isolation. Journal of Applied Probability 44, 571-585.
• Clancy, D. and O'Neill, P.D. (2008) Bayesian estimation of the basic reproduction number in stochastic epidemic models. Bayesian Analysis 3, No. 4, 737-758.
• Ball, F. G., Knock, E. S. and O'Neill, P. D. (2008) Control of emerging infectious diseases using responsive imperfect vaccination and isolation. Mathematical Biosciences 216, 100-113.
• O'Neill, P.D. (2009) Bayesian inference for stochastic multitype epidemics in structured populations using sample data. Biostatistics 10(4), 779-791.
• Kypraios, T., O'Neill, P. D., Huang, S. S., Rifas-Shiman, S. L. and Cooper, B. S. (2010) Assessing the role of undetected colonization and isolation precautions in reducing Methicillin-Resistant Staphylococcus aureus transmission in intensive care units. BMC Infectious Diseases 10(29).
• van Boven, M., Kretzschmar, M., Wallinga, J., O'Neill, P. D., Wichmann, O. and Hahne, S. (2010) Estimation of measles vaccine efficacy and cricital vaccination coverage in a highly vaccinated population. Journal of the Royal Society Interface 7, 1537-1544.
• O'Neill, P.D. (2010) Introduction and snapshot review: Relating infectious disease transmission models to data. Statistics in Medicine 29, 2069-2077.
• Britton, T., Kypraios, T. and O'Neill, P.D. (2011) Inference for epidemics with three levels of mixing: methodology and application to a measles outbreak. Scandinavian Journal of Statistics 38, 578-599.
• Spencer, S. E. F. and O'Neill, P. D. (2011) The probability of containment for multitype branching process models for emerging epidemics. Journal of Applied Probability 48, 173-188.
• Kypraios, T., O'Neill, P. D., Jones, D. E., Ware, J., Batra, R., Edgeworth, D. E. and Cooper, B. S. (2011) Effect of systemic antibiotics and topical chlorhexidine on methicillin-resistant Staphylococcus aureus (MRSA) carriage in intensive care unit patients. Journal of Hospital Infection 7, 222-226.
• Ball, F. G., Knock, E. S. and O'Neill, P. D. (2011) Threshold behaviour of emerging epidemics featuring contact tracing. Advances in Applied Probability 43, 1048-1065.
• O'Neill, P. D. and Wen, C. H. (2012) Modelling and inference for epidemic models featuring non-linear infection pressure. Mathematical Biosciences 238, 36-48.
• Spencer, S. E. F. and O'Neill, P. D. (2012) Assessing the impact of intervention delays on stochastic epidemics. Methodology and Computing in Applied Probability, 15, 803-820.
• van Boven, M., Ruijs, W.L., Wallinga, J., O'Neill, P. D. and Hahne, S. (2013) Estimation of mumps vaccine efficacy and critical vaccination coverage. Public Library of Science Computational Biology 9(5): e1003061.
• Worby, C., Jeyaratnam, D., Robotham, J. V., Kypraios, T., O.Neill, P. D., De Angelis, D., French, G. and Cooper, B. S. (2013) Estimating the effectiveness of isolation and decolonization measures in reducing transmission of methicillin-resistant Staphylococcus aureus in hospital general wards. American Journal of Epidemiology 177 (11), 1306-1313.
• Knock, E.S. and O'Neill, P.D. (2014) Bayesian model choice for epidemic models with two levels of mixing. Biostatistics, 15, 46-59.
• Ball, F. G., Knock, E. S. and O'Neill, P. D. (2015) Stochastic epidemic models featuring contact tracing with delays. Mathematical Biosciences 266, 23-35.
• Verykouki, E., Kypraios, T. and O'Neill, P. D. (2016) Modelling the effect of antimicrobial treatment on carriage of hospital pathogens with application to MRSA. Biostatistics 17, 65-78.
• Worby, C. J., O'Neill, P. D., Kypraios, T., Robotham, J. V., De Angelis, D., Cartwright, E. J. P., Peacock, S. J. and Cooper, B. S. (2016) Reconstructing transmission trees for communicable diseases using densely sampled genetic data. Annals of Applied Statistics 10(1), 395-417. arXiv paper
• Xu, X. Kypraios, T. and O'Neill, P. D. (2016) Bayesian nonparametric inference for stochastic epidemic models using Gaussian processes. Biostatistics 17(4), 619-633.
• Stockdale, J. E., Kypraios, T. and O'Neill, P. D. (2017) Modelling and Bayesian analysis of the Abakaliki Smallpox Data. Epidemics 19, 13-23.
• Kypraios, T. and O'Neill, P. D. (2018) Bayesian nonparametrics for stochastic epidemic models. Statistical Science 33(1), 44-56.
• Wei, Y., Kypraios, T., O'Neill, P. D., Huang, S. S., Rifas-Shiman, S. L. and Cooper, B. S. (2018) Evaluating hospital infection control measures for antimicrobial-resistant pathogens using stochastic transmission models: application to Vancomycin Resistant Enterococci in Intensive Care Units. Statistical Methods in Medical Research 27(1), 269-285. arXiv paper
• Alharthi, M., Kypraios, T. and O'Neill, P. D. (2019) Bayes Factors for Partially Observed Stochastic Epidemic Models Bayesian Analysis 14(3), 927-956.
• Stockdale, J. E., Kypraios, T. and O'Neill, P. D. (2019) Pair-based likelihood approximations for stochastic epidemic models Biostatistics 22(3), 575-597.
• Thompson, R. N. et al. (2020) Key questions for modelling COVID-19 exit strategies Proceedings of the Royal Society B 287:20201405.
• Seymour, R., Kypraios, T., O'Neill P. D. and Hagenaars, T. J. (2021) A Bayesian nonparametric analysis of the 2003 outbreak of highly pathogenic Avian Influenza in the Netherlands Journal of the Royal Statistical Society, Series C 70, 1323-1343.
• Seymour, R. G., Kypraios, T., and O'Neill, P. D. (2022) Bayesian nonparametric inference for heterogeneously-mixing infectious disease models Proceedings of the National Academy of Sciences of the United States of America 119(10):e2118425119
• Aristoleous, G., Kypraios, T. and O’Neill, P.D. (2022) Posterior predictive checking for partially observed stochastic epidemic models. Bayesian Analysis, to appear.

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