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For: Grinsztajn L, Semenova E, Margossian CC, Riou J. Bayesian workflow for disease transmission modeling in Stan. Stat Med 2021;40:6209-6234. [PMID: 34494686 PMCID: PMC8661657 DOI: 10.1002/sim.9164] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/06/2021] [Accepted: 07/29/2021] [Indexed: 12/18/2022]
Number Cited by Other Article(s)
1
Zhang R, Tai J, Yao Q, Yang W, Ruggeri K, Shaman J, Pei S. Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City. PLoS Comput Biol 2025;21:e1012979. [PMID: 40300036 PMCID: PMC12101855 DOI: 10.1371/journal.pcbi.1012979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 05/23/2025] [Accepted: 03/18/2025] [Indexed: 05/01/2025]  Open
2
Loyens DB, Caetano C, Matias-Dias C. Impact of non-pharmacological interventions on the first wave of COVID-19 in Portugal 2020. Heliyon 2025;11:e41569. [PMID: 40028538 PMCID: PMC11868933 DOI: 10.1016/j.heliyon.2024.e41569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 12/23/2024] [Accepted: 12/28/2024] [Indexed: 03/05/2025]  Open
3
Avilov KK, Li Q, Lin L, Demirhan H, Stone L, He D. The 1978 English boarding school influenza outbreak: where the classic SEIR model fails. J R Soc Interface 2024;21:20240394. [PMID: 39563495 PMCID: PMC11576841 DOI: 10.1098/rsif.2024.0394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 08/05/2024] [Accepted: 09/17/2024] [Indexed: 11/21/2024]  Open
4
Jdid T, Benbrahim M, Kabbaj MN, Naji M. A vaccination-based COVID-19 model: Analysis and prediction using Hamiltonian Monte Carlo. Heliyon 2024;10:e38204. [PMID: 39391520 PMCID: PMC11466577 DOI: 10.1016/j.heliyon.2024.e38204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 10/12/2024]  Open
5
Humphreys JM, Pelzel-McCluskey AM, Shults PT, Velazquez-Salinas L, Bertram MR, McGregor BL, Cohnstaedt LW, Swanson DA, Scroggs SLP, Fautt C, Mooney A, Peters DPC, Rodriguez LL. Modeling the 2014-2015 Vesicular Stomatitis Outbreak in the United States Using an SEIR-SEI Approach. Viruses 2024;16:1315. [PMID: 39205289 PMCID: PMC11359999 DOI: 10.3390/v16081315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/02/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]  Open
6
Earn DJD, Park SW, Bolker BM. Fitting Epidemic Models to Data: A Tutorial in Memory of Fred Brauer. Bull Math Biol 2024;86:109. [PMID: 39052140 DOI: 10.1007/s11538-024-01326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/04/2024] [Indexed: 07/27/2024]
7
Schmidt PW. Inference under superspreading: Determinants of SARS-CoV-2 transmission in Germany. Stat Med 2024;43:1933-1954. [PMID: 38422989 DOI: 10.1002/sim.10046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/11/2024] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
8
Chowell G, Bleichrodt A, Luo R. Parameter estimation and forecasting with quantified uncertainty for ordinary differential equation models using QuantDiffForecast: A MATLAB toolbox and tutorial. Stat Med 2024;43:1826-1848. [PMID: 38378161 PMCID: PMC11031352 DOI: 10.1002/sim.10036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/22/2024]
9
Bouman JA, Hauser A, Grimm SL, Wohlfender M, Bhatt S, Semenova E, Gelman A, Althaus CL, Riou J. Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models. PLoS Comput Biol 2024;20:e1011575. [PMID: 38683878 PMCID: PMC11081492 DOI: 10.1371/journal.pcbi.1011575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/09/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]  Open
10
Gibson GC, Reich NG, Sheldon D. REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY. Ann Appl Stat 2023;17:1801-1819. [PMID: 38983109 PMCID: PMC11229176 DOI: 10.1214/22-aoas1671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
11
Simpson MJ, Maclaren OJ. Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models. PLoS Comput Biol 2023;19:e1011515. [PMID: 37773942 PMCID: PMC10566698 DOI: 10.1371/journal.pcbi.1011515] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 10/11/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023]  Open
12
Andrade J, Duggan J. Anchoring the mean generation time in the SEIR to mitigate biases in ℜ0 estimates due to uncertainty in the distribution of the epidemiological delays. ROYAL SOCIETY OPEN SCIENCE 2023;10:230515. [PMID: 37538746 PMCID: PMC10394422 DOI: 10.1098/rsos.230515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023]
13
Akuno AO, Ramírez-Ramírez LL, Espinoza JF. Inference on a Multi-Patch Epidemic Model with Partial Mobility, Residency, and Demography: Case of the 2020 COVID-19 Outbreak in Hermosillo, Mexico. ENTROPY (BASEL, SWITZERLAND) 2023;25:968. [PMID: 37509915 PMCID: PMC10378648 DOI: 10.3390/e25070968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023]
14
Lison A, Banholzer N, Sharma M, Mindermann S, Unwin HJT, Mishra S, Stadler T, Bhatt S, Ferguson NM, Brauner J, Vach W. Effectiveness assessment of non-pharmaceutical interventions: lessons learned from the COVID-19 pandemic. Lancet Public Health 2023;8:e311-e317. [PMID: 36965985 PMCID: PMC10036127 DOI: 10.1016/s2468-2667(23)00046-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 03/27/2023]
15
Emmenegger M, De Cecco E, Lamparter D, Jacquat RP, Riou J, Menges D, Ballouz T, Ebner D, Schneider MM, Morales IC, Doğançay B, Guo J, Wiedmer A, Domange J, Imeri M, Moos R, Zografou C, Batkitar L, Madrigal L, Schneider D, Trevisan C, Gonzalez-Guerra A, Carrella A, Dubach IL, Xu CK, Meisl G, Kosmoliaptsis V, Malinauskas T, Burgess-Brown N, Owens R, Hatch S, Mongkolsapaya J, Screaton GR, Schubert K, Huck JD, Liu F, Pojer F, Lau K, Hacker D, Probst-Müller E, Cervia C, Nilsson J, Boyman O, Saleh L, Spanaus K, von Eckardstein A, Schaer DJ, Ban N, Tsai CJ, Marino J, Schertler GF, Ebert N, Thiel V, Gottschalk J, Frey BM, Reimann RR, Hornemann S, Ring AM, Knowles TP, Puhan MA, Althaus CL, Xenarios I, Stuart DI, Aguzzi A. Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region. iScience 2023;26:105928. [PMID: 36619367 PMCID: PMC9811913 DOI: 10.1016/j.isci.2023.105928] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/18/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]  Open
16
Dai C, Heng J, Jacob PE, Whiteley N. An Invitation to Sequential Monte Carlo Samplers. J Am Stat Assoc 2022. [DOI: 10.1080/01621459.2022.2087659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
17
Andrade J, Duggan J. Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data. PLoS Comput Biol 2022;18:e1010206. [PMID: 35759506 PMCID: PMC9269962 DOI: 10.1371/journal.pcbi.1010206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 07/08/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022]  Open
18
Grolimund CM, Bärenbold O, Hatz CF, Vennervald BJ, Mayombana C, Mshinda H, Utzinger J, Vounatsou P. Infection intensity-dependent accuracy of reagent strip for the diagnosis of Schistosoma haematobium and estimation of treatment prevalence thresholds. PLoS Negl Trop Dis 2022;16:e0010332. [PMID: 35468129 PMCID: PMC9071146 DOI: 10.1371/journal.pntd.0010332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 05/05/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]  Open
19
Prieto K, Chávez–Hernández MV, Romero–Leiton JP. On mobility trends analysis of COVID-19 dissemination in Mexico City. PLoS One 2022;17:e0263367. [PMID: 35143548 PMCID: PMC8830699 DOI: 10.1371/journal.pone.0263367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/18/2022] [Indexed: 01/04/2023]  Open
20
Prieto K. Current forecast of COVID-19 in Mexico: A Bayesian and machine learning approaches. PLoS One 2022;17:e0259958. [PMID: 35061688 PMCID: PMC8782335 DOI: 10.1371/journal.pone.0259958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022]  Open
21
Grinsztajn L, Semenova E, Margossian CC, Riou J. Bayesian workflow for disease transmission modeling in Stan. Stat Med 2021;40:6209-6234. [PMID: 34494686 PMCID: PMC8661657 DOI: 10.1002/sim.9164] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/06/2021] [Accepted: 07/29/2021] [Indexed: 12/18/2022]
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