EpiEstim (version 1.1-0)

SARS2003: Data on the 2003 SARS epidemic in Hong Kong

Description

This data set gives 1/ the daily incidence of onset of symptoms in Hong Kong during the 2003 severe acute respiratory syndrome (SARS) epidemic (see source and references), 2/ the discrete daily distribution of the serial interval for SARS, assuming a shifted Gamma distribution with mean 8.4 days, standard deviation 3.8 days and shift 1 day (see references).

Usage

SARS2003

format

A list of two elements: 1/ "Incidence": a vector containing 107 days of observation, 2/ "SI.Distr": a vector containing a set of 25 probabilities.

source

Cori A. et al. (2009) Temporal variability and social heterogeneity in disease transmission: the case of SARS in Hong Kong. PLoS Comput Biol 5(8): e1000471.

References

Cori A. et al. (2009) Temporal variability and social heterogeneity in disease transmission: the case of SARS in Hong Kong. PLoS Comput Biol 5(8): e1000471. Lipsitch M. et al. (2003) Transmission dynamics and control of severe acute respiratory syndrome. Science 300(5627): 1966-1970.

Examples

## load data on SARS in Hong Kong in 2003
		data("SARS2003")

		## estimate the instantaneous reproduction number (method "NonParametricSI")
		EstimateR(SARS2003$Incidence, T.Start=14:101, T.End=20:107, method="NonParametricSI", 
			SI.Distr=SARS2003$SI.Distr, plot=TRUE, leg.pos=xy.coords(1,7))
		# the second plot produced shows, at each each day, 
		# the estimate of the instantaneous reproduction number over the 7-day window finishing on that day.