Stan for epidemiology
Annibale Cois, Richard Matzopoulos, Victoria Pillay-van Wyk, Debbie Bradshaw. Bayesian modelling of population trends in alcohol consumption provides empirically based country estimates for South Africa Population Health Metrics 19(43). 2021.
Victoire Michal, Laís Picinini Freitas, Alexandra M Schmidt. A Bayesian hierarchical model for disease mapping that accounts for scaling and heavy-tailed latent effects. 2021.
Marnie Downes, Lyle C Gurrin, Dallas R English, Jane Pirkis, Dianne Currier, Matthew J Spittal, John B Carlin. Multilevel Regression and Poststratification: A Modeling Approach to Estimating Population Quantities From Highly Selected Survey Samples American Journal of Epidemiology, Volume 187, Issue 8, August 2018, Pages 1780–1790.
Morris, Mitzi & Wheeler-Martin, Katherine & Simpson, Dan & Mooney, Stephen & Gelman, Andrew & Dimaggio, Charles. Bayesian Hierarchical Spatial Models: Implementing the Besag York Mollié Model in Stan. Spatial and Spatio-temporal Epidemiology. 2019.
Julien Riou, Chiara Poletto, Pierre-Yves Boëlle, A comparative analysis of Chikungunya and Zika transmission, Epidemics, Volume 19, 2017.
MacLehose, R.F., Hamra, G.B. Applications of Bayesian Methods to Epidemiologic Research. Curr Epidemiol Rep 1, 103–109 (2014).
Sreenath Madathil, Lawrence Joseph, Rebecca Hardy, Marie-Claude Rousseau, Belinda Nicolau, A Bayesian approach to investigate life course hypotheses involving continuous exposures, International Journal of Epidemiology, Volume 47, Issue 5, October 2018, Pages 1623–1635.
APA Brilleman, Samuel L.a,b; Howe, Laura D.c,d; Wolfe, Rorya,b; Tilling, Katec,d Bayesian Piecewise Linear Mixed Models With a Random Change Point, Epidemiology: November 2017 - Volume 28 - Issue 6 - p 827-833
Diarra, Issa & Nurtop, Elif & Sangaré, Abdoul & Sagara, Issaka & Pastorino, Boris & Sacko, Souleymane & Zeguimé, Amatigué & Coulibaly, Drissa & Fofana, Bakary & Gallian, Pierre & Priet, Stéphane & Drexler, Jan & Dabo, Abdoulaye & Thera, Mahamadou & Djimdé, Abdoulaye & Kouriba, Bourèma & Cauchemez, Simon & Lamballerie, Xavier & Doumbo, Ogobara. Zika Virus Circulation in Mali. Emerging infectious diseases. 2020.
Jon Brugger, Christian L. Althaus, Transmission of and susceptibility to seasonal influenza in Switzerland from 2003 to 2015, Epidemics, Volume 30, 2020.
Lewis J, White PJ. Estimating Local Chlamydia Incidence and Prevalence Using Surveillance Data. Epidemiology. 2017.
Nyaga, V., Marc, A. & Marc, A. Marginal models for meta-analysis of diagnostic accuracy studies in frequentist and Bayesian framework using rstan and CopulaREMADA. Arch Public Health 73, O4 (2015).
Fernandez-Pujals AM, Adams MJ, Thomson P, et al. Epidemiology and Heritability of Major Depressive Disorder, Stratified by Age of Onset, Sex, and Illness Course in Generation Scotland: Scottish Family Health Study (GS:SFHS). PLoS One. 2015.
Riou J, Poletto C, Boëlle PY. Improving early epidemiological assessment of emerging Aedes-transmitted epidemics using historical data. PLoS Negl Trop Dis. 2018.
Rodriguez-Barraquer I, Salje H, Cummings DA. Opportunities for improved surveillance and control of dengue from age-specific case data. Elife. 2019.
Kiang, Mathew V., Nancy Krieger, Caroline O. Buckee, Jukka Pekka Onnela, and Jarvis T. Chen. Decomposition of the US black/white inequality in premature mortality, 2010–2015: an observational study. BMJ open 9, no. 11 (2019).
Claire Donnat and Susan Holmes, Modeling the Heterogeneity in COVID-19’s Reproductive Number and Its Impact on Predictive Scenarios, 2020.
Henrik Salje, Cécile Tran Kiem, Noémie Lefrancq, Noémie Courtejoie, Paolo Bosetti, et al.. Estimating the burden of SARS-CoV-2 in France., 2020.
Du Z, Wang L, Cauchemez S, et al. Risk for Transportation of Coronavirus Disease from Wuhan to Other Cities in China. Emerging Infectious Diseases.2020.
Kubinec, Robert, and Luiz Carvalho. “A Retrospective Bayesian Model for Measuring Covariate Effects on Observed COVID-19 Test and Case Counts.” SocArXiv, 1 Apr. 2020. Web.
Woody, Spencer and Garcia Tec, Mauricio and Dahan, Maytal and Gaither, Kelly and Lachmann, Michael and Fox, Spencer and Meyers, Lauren Ancel and Scott, James G, Projections for first-wave COVID-19 deaths across the US using social-distancing measures derived from mobile phones, Cold Spring Harbor Laboratory Press, 2020.
Kucinskas, Simas, Tracking R of COVID-19, 2020.
Yoriyuki Yamagata, Bayesian modeling of Covid-19 epidemic: Japanese case, 2020.
Stefano Cabras, El Virus de la corona, 2020.
Gostic et al., Practical considerations for measuring the effective reproductive number, Rt, 2020.
Hiroshi Nishiura, Natalie M. Linton, Andrei R. Akhmetzhanov, Serial interval of novel coronavirus (COVID-19) infections, International Journal of Infectious Diseases, 2020. Stan code here
Mizumoto Kenji, Kagaya Katsushi, Zarebski Alexander, Chowell Gerardo. Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020. Euro Surveill. 2020.
Campbell et al., Bayesian adjustment for preferential testing in estimating the COVID-19 infection fatality rate: Theory and methods, 2020.
Jérôme Levesque and David W. Maybury, A note on COVID-19 seroprevalence studies: a meta-analysis using hierarchical modelling, 2020.
Andrew Gelman and Bob Carpenter, Bayesian analysis of tests with unknown specificity and sensitivity, 2020. Code and more here.
Andrew Gelman, Simple Bayesian analysis inference of coronavirus infection rate from the Stanford study in Santa Clara county, 2020.
Andrew Gelman, Bayesian analysis of Santa Clara study: Run it yourself in Google Collab, play around with the model, etc!, 2020.
Frank Harrel and Ben Goodrich (?), Sequential Bayesian Designs for Rapid Learning in COVID-19 Clinical Trials, 2020.
Resources for COVID-19 Randomized Clinical Trial Design
Fischer et al., Assessment of N95 respirator decontamination and re-use for SARS-CoV-2, 2020.
van Doremalen, Neeltje and Bushmaker, Trenton and Morris, Dylan H. and Holbrook, Myndi G. and Gamble, Amandine and Williamson, Brandi N. and Tamin, Azaibi and Harcourt, Jennifer L. and Thornburg, Natalie J. and Gerber, Susan I. and Lloyd-Smith, James O. and de Wit, Emmie and Munster, Vincent J., Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1, 2020.
Robert Kubinec, Luiz Carvalho, Joan Barceló, Cindy Cheng, Luca Messerschmidt, Derek Duba, Matthew Cottrell, Fear, Partisanship and the Spread of COVID-19 in the United States, 2020.
Julien Riou, Matthias Egger, Christian Althaus - The emergence of HIV resistance to antiretroviral therapy in southern Africa: a mechanistic meta-analysis of survey data., StanCon 2019.
Christopher Jackson, Anne Presanis - Estimating the prevalence of HIV infection in England using Bayesian evidence synthesis., StanCon 2019.
Anastasia Chatzilena, Edwin van Leeuwen, Oliver Ratmann, Marc Baguelin, Nikolaos Demiris, Contemporary statistical inference for infectious disease models using Stan, Epidemics, Volume 29, 2019.