flu_2009_NYC_school: Data on the 2009 H1N1 influenza pandemic in a school in New...

In annecori/EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Data on the 2009 H1N1 influenza pandemic in a school in New York city

Description

This data set gives:

1. 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),

2. interval-censored serial interval data from the 2009 outbreak of H1N1 influenza in a New York city school (see references).

Format

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)

Source

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.

References

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.

Examples

## 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.

## End(Not run)

annecori/EpiEstim documentation built on Oct. 14, 2023, 1:54 a.m.