Data on the 2009 H1N1 influenza pandemic in a school in New York city
This data set gives:
the daily incidence of self-reported and laboratory-confirmed cases of influenza among children in a school in New York city during the 2009 H1N1 influenza pandemic (see source and references),
interval-censored serial interval data from the 2009 outbreak of H1N1 influenza in a New York city school (see references).
A list of two elements:
incidence: a dataframe with 14 lines containing dates in first column, and daily incidence in second column ,
si_data: a dataframe containing data on the generation time for 16
pairs of infector/infected individuals (see references and see argument
si_data of function estimate_R() for details on columns)
Lessler J. et al. (2009) Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school. New Eng J Med 361: 2628-2636.
Lessler J. et al. (2009) Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school. New Eng J Med 361: 2628-2636.
## Not run:
## Note the following examples use an MCMC routine
## to estimate the serial interval distribution from data,
## so they may take a few minutes to run
## load data on pandemic flu in a New York school in 2009
data("flu_2009_NYC_school")
## estimate the reproduction number (method "si_from_data")
res <- estimate_R(flu_2009_NYC_school$incidence, method="si_from_data",
si_data = flu_2009_NYC_school$si_data,
config = make_config(list(
t_start = seq(2, 8),
t_end = seq(8, 14),
si_parametric_distr = "G",
mcmc_control = make_mcmc_control(list(burnin = 1000,
thin = 10, seed = 1)),
n1 = 1000, n2 = 50))
)
plot(res)
## the second plot produced shows, at each each day,
## the estimate of the reproduction number
## over the 7-day window finishing on that day.
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