Skip to content

Preloaded Datasets

robin-thompson edited this page Jul 12, 2017 · 6 revisions

A number of preloaded datasets are included in the EpiEstim web application to illustrate its usage, and are described below. Three types of dataset are available: time series of disease incidence data from historical outbreaks (incidence data); interval-censored data on the appearance of symptoms in known donor-recipient pairs from historical outbreaks (serial interval data); or probability distributions for the length of the serial interval estimated in historical outbreaks (serial interval distribution estimates). The incidence data can be used in combination with either the serial interval data or the serial interval distribution estimates to generate an estimate of the reproduction number.

Incidence Data

H1N1 Pennsylvania 2009

These data were taken from the first version of the package, EpiEstim 1.0. For details, see the paper below.

Cori A, Ferguson NM, Fraser C, Cauchemez S. 2013. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidem 178: 1505-1512.

H1N1 New York 2009

These data underlie Figure 1 of the publication below. Thanks to the authors for their permission to use the original data.

Lessler J, Reich NG, Cummings DA. 2009. Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school. New Eng J Med 361: 2628-2636.

Rotavirus Kiribati 2013

These data were approximated from Figure 2 of the citation below.

Tabunga T, Utiera M, Tekoaua R, Tibwe T, Tira T, Toatu T, Duituturaga SE, Nilles E, Craig A. 2014. Response to a large rotavirus outbreak on South Tarawa, Kiribati, 2013. Western Pac Surveill Response J 5: 9-14.

H1N1 Maryland 1918

These data were taken from the first version of the package, EpiEstim 1.0. For details, see the paper below.

Cori A, Ferguson NM, Fraser C, Cauchemez S. 2013. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidem 178: 1505-1512.

Measles Germany 1861

These data were taken from the first version of the package, EpiEstim 1.0. For details, see the paper below.

Cori A, Ferguson NM, Fraser C, Cauchemez S. 2013. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidem 178: 1505-1512.

SARS Hong Kong 2003

These data were taken from the first version of the package, EpiEstim 1.0. For details, see the paper below.

Cori A, Ferguson NM, Fraser C, Cauchemez S. 2013. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidem 178: 1505-1512.

Smallpox Kosovo 1972

These data were taken from the first version of the package, EpiEstim 1.0. For details, see the paper below.

Cori A, Ferguson NM, Fraser C, Cauchemez S. 2013. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidem 178: 1505-1512.

Serial Interval Data

Rotavirus Ecuador 2011

These data were taken from households with two infections, in which the individuals involved were assumed to represent a single donor-recipient pair. The data are shown in Figure 2 of the citation below.

Lopman B, Vicuña Y, Salazar F, Broncano N, Esona MD, Sandoval C, Gregoricus N, Bowen MD, Payne D, Vaca M, Chico M. 2013. Household transmission of rotavirus in a community with rotavirus vaccination in Quininde, Ecuador. PLoS One 8: e67763.

H1N1 New York 2009

These data have been compiled from Table 2 of the supplementary material in the paper below.

Lessler J, Reich NG, Cummings DA. 2009. Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school. New Eng J Med 361: 2628-36.

H1N1 USA 2009

These data were approximated from Figure 1(c) of the reference below. The data are compiled from a number of studies of the serial interval from throughout USA during the 2009 pandemic of H1N1 influenza.

Donnelly CA, Finelli L, Cauchemez S, Olsen SJ, Doshi S, Jackson ML, Kennedy ED, Kamimoto L, Marchbanks TL, Morgan OW, Patel M. 2011. Serial intervals and the temporal distribution of secondary infections within households of 2009 pandemic influenza A (H1N1): implications for influenza control recommendations. Clin Inf Dis 52: S123-130.

Serial Interval Distribution Estimates

All of these data were taken from the first version of the package, EpiEstim 1.0. For details, see the paper below. Note that the methods used to construct these distribution estimates may not be consistent with how EpiEstim 2.0 would construct them given some serial interval patient data. In particular, the raw patient data may not be explicitly available.

Cori A, Ferguson NM, Fraser C, Cauchemez S. 2013. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidem 178: 1505-1512.

H1N1 Maryland 1918

H1N1 Pennsylvania 2009

Measles Germany 1861

SARS Hong Kong 2003

Smallpox Kosovo 1972

You can’t perform that action at this time.