    2009, 6(2): 261-282. doi: 10.3934/mbe.2009.6.261

## The estimation of the effective reproductive number from disease outbreak data

 1 Center for Research in Scientific Computation, Center for Quantitative Sciences in Biomedicine, North Carolina State University, Raleigh, NC 27695, United States 2 Department of Mathematics and Statistics, Arizona State University, P.O. Box 871804, Tempe, AZ 85287-1804, United States 3 Theoretical Division, Mathematical Modeling and Analysis (T-7), Los Alamos National Laboratory, Mail Stop B284, Los Alamos, NM 87545, United States 4 Center for Research in Scientific Computation, Biomathematics Graduate Program, Department of Mathematics, North Carolina State University, Raleigh, NC 27695, United States 5 Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC 27695-8212

Received  April 2008 Revised  August 2008 Published  March 2009

We consider a single outbreak susceptible-infected-recovered (SIR) model and corresponding estimation procedures for the effective reproductive number $\mathcal{R}(t)$. We discuss the estimation of the underlying SIR parameters with a generalized least squares (GLS) estimation technique. We do this in the context of appropriate statistical models for the measurement process. We use asymptotic statistical theories to derive the mean and variance of the limiting (Gaussian) sampling distribution and to perform post statistical analysis of the inverse problems. We illustrate the ideas and pitfalls (e.g., large condition numbers on the corresponding Fisher information matrix) with both synthetic and influenza incidence data sets.
Citation: Ariel Cintrón-Arias, Carlos Castillo-Chávez, Luís M. A. Bettencourt, Alun L. Lloyd, H. T. Banks. The estimation of the effective reproductive number from disease outbreak data. Mathematical Biosciences & Engineering, 2009, 6 (2) : 261-282. doi: 10.3934/mbe.2009.6.261
  Nicolas Bacaër, Xamxinur Abdurahman, Jianli Ye, Pierre Auger. On the basic reproduction number $R_0$ in sexual activity models for HIV/AIDS epidemics: Example from Yunnan, China. Mathematical Biosciences & Engineering, 2007, 4 (4) : 595-607. doi: 10.3934/mbe.2007.4.595  Tom Burr, Gerardo Chowell. The reproduction number $R_t$ in structured and nonstructured populations. Mathematical Biosciences & Engineering, 2009, 6 (2) : 239-259. doi: 10.3934/mbe.2009.6.239  Gerardo Chowell, R. Fuentes, A. Olea, X. Aguilera, H. Nesse, J. M. Hyman. The basic reproduction number $R_0$ and effectiveness of reactive interventions during dengue epidemics: The 2002 dengue outbreak in Easter Island, Chile. Mathematical Biosciences & Engineering, 2013, 10 (5&6) : 1455-1474. doi: 10.3934/mbe.2013.10.1455  Cameron J. Browne, Sergei S. Pilyugin. Minimizing $\mathcal R_0$ for in-host virus model with periodic combination antiviral therapy. Discrete & Continuous Dynamical Systems - B, 2016, 21 (10) : 3315-3330. doi: 10.3934/dcdsb.2016099  Nitu Kumari, Sumit Kumar, Sandeep Sharma, Fateh Singh, Rana Parshad. Basic reproduction number estimation and forecasting of COVID-19: A case study of India, Brazil and Peru. Communications on Pure & Applied Analysis, , () : -. doi: 10.3934/cpaa.2021170  David Burguet. Examples of $\mathcal{C}^r$ interval map with large symbolic extension entropy. Discrete & Continuous Dynamical Systems, 2010, 26 (3) : 873-899. doi: 10.3934/dcds.2010.26.873  Hui Cao, Yicang Zhou. The basic reproduction number of discrete SIR and SEIS models with periodic parameters. Discrete & Continuous Dynamical Systems - B, 2013, 18 (1) : 37-56. doi: 10.3934/dcdsb.2013.18.37  Zhilan Feng, Qing Han, Zhipeng Qiu, Andrew N. Hill, John W. Glasser. Computation of $\mathcal R$ in age-structured epidemiological models with maternal and temporary immunity. Discrete & Continuous Dynamical Systems - B, 2016, 21 (2) : 399-415. doi: 10.3934/dcdsb.2016.21.399  Wenjun Liu, Yukun Xiao, Xiaoqing Yue. Classification of finite irreducible conformal modules over Lie conformal algebra $\mathcal{W}(a, b, r)$. Electronic Research Archive, 2021, 29 (3) : 2445-2456. doi: 10.3934/era.2020123  Salvador Addas-Zanata, Fábio A. Tal. Support of maximizing measures for typical $\mathcal{C}^0$ dynamics on compact manifolds. Discrete & Continuous Dynamical Systems, 2010, 26 (3) : 795-804. doi: 10.3934/dcds.2010.26.795  Xiao-Wen Chang, David Titley-Peloquin. An improved algorithm for generalized least squares estimation. Numerical Algebra, Control & Optimization, 2020, 10 (4) : 451-461. doi: 10.3934/naco.2020044  Hisashi Inaba. The Malthusian parameter and $R_0$ for heterogeneous populations in periodic environments. Mathematical Biosciences & Engineering, 2012, 9 (2) : 313-346. doi: 10.3934/mbe.2012.9.313  Tianhui Yang, Ammar Qarariyah, Qigui Yang. The effect of spatial variables on the basic reproduction ratio for a reaction-diffusion epidemic model. Discrete & Continuous Dynamical Systems - B, 2021  doi: 10.3934/dcdsb.2021170  Timothy C. Reluga, Jan Medlock, Alison Galvani. The discounted reproductive number for epidemiology. Mathematical Biosciences & Engineering, 2009, 6 (2) : 377-393. doi: 10.3934/mbe.2009.6.377  Alonso sepúlveda Castellanos. Generalized Hamming weights of codes over the $\mathcal{GH}$ curve. Advances in Mathematics of Communications, 2017, 11 (1) : 115-122. doi: 10.3934/amc.2017006  Qiang Li. A kind of generalized transversality theorem for $C^r$ mapping with parameter. Discrete & Continuous Dynamical Systems - S, 2017, 10 (5) : 1043-1050. doi: 10.3934/dcdss.2017055  Gerardo Chowell, Catherine E. Ammon, Nicolas W. Hengartner, James M. Hyman. Estimating the reproduction number from the initial phase of the Spanish flu pandemic waves in Geneva, Switzerland. Mathematical Biosciences & Engineering, 2007, 4 (3) : 457-470. doi: 10.3934/mbe.2007.4.457  Ling Xue, Caterina Scoglio. Network-level reproduction number and extinction threshold for vector-borne diseases. Mathematical Biosciences & Engineering, 2015, 12 (3) : 565-584. doi: 10.3934/mbe.2015.12.565  Yu-Ming Chu, Saima Rashid, Fahd Jarad, Muhammad Aslam Noor, Humaira Kalsoom. More new results on integral inequalities for generalized $\mathcal{K}$-fractional conformable Integral operators. Discrete & Continuous Dynamical Systems - S, 2021, 14 (7) : 2119-2135. doi: 10.3934/dcdss.2021063  Agnieszka Badeńska. No entire function with real multipliers in class $\mathcal{S}$. Discrete & Continuous Dynamical Systems, 2013, 33 (8) : 3321-3327. doi: 10.3934/dcds.2013.33.3321

2018 Impact Factor: 1.313