EpiEstim (version 1.1-2)

Flu2009: Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania

Description

This data set gives

1/ the daily incidence of onset of acute respiratory illness (ARI, defined as at least two symptoms among fever, cough, sore throat, and runny nose) amongst children in a school in Pennsylvania during the 2009 H1N1 influenza pandemic (see source and references),

2/ the discrete daily distribution of the serial interval for influenza, assuming a shifted Gamma distribution with mean 2.6 days, standard deviation 1.5 days and shift 1 day (see references).

Usage

Flu2009

Format

A list of two elements:

1/ "Incidence": a vector containing 32 days of observation,

2/ "SI.Distr": a vector containing a set of 12 probabilities.

References

Cauchemez S. et al. (2011) Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza. Proc Natl Acad Sci U S A 108(7), 2825-2830.

Ferguson N.M. et al. (2005) Strategies for containing an emerging influenza pandemic in Southeast Asia. Nature 437(7056), 209-214.

Examples

# NOT RUN {
		## load data on pandemic flu in a school in 2009
		data("Flu2009")

		## estimate the instantaneous reproduction number (method "NonParametricSI")
		EstimateR(Flu2009$Incidence, T.Start=2:26, T.End=8:32, method="NonParametricSI", 
			SI.Distr=Flu2009$SI.Distr, plot=TRUE, leg.pos=xy.coords(1,3))
		# 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.

	
# }