EpiEstim (version 2.2-4)

MockRotavirus: Mock data on a rotavirus epidemic.

Description

This data set gives:

1. the daily incidence of onset of symptoms in a mock outbreak of rotavirus,

2. mock observations of symptom onset dates for 19 pairs of infector/infected individuals.

Format

A list of two elements:

• incidence: a vector containing 53 days of observation,

• si_distr: a dataframe containing a set of 19 observations; each observation corresponds to a pair of infector/infected individuals. EL and ER columns contain the lower an upper bounds of the dates of symptoms onset in the infectors. SL and SR columns contain the lower an upper bounds of the dates of symptoms onset in the infected individuals. The type column has entries 0, 1, or 2, corresponding to doubly interval-censored, single interval-censored or exact observations, respectively, see Reich et al. Statist. Med. 2009

Examples

# NOT RUN {
## Note the following example uses an MCMC routine
## to estimate the serial interval distribution from data,
## so may take a few minutes to run

## load data
data("MockRotavirus")

## estimate the reproduction number (method "si_from_data")
res <- estimate_R(MockRotavirus$incidence,
          method = "si_from_data",
          si_data = MockRotavirus$si_data,
          config = make_config(list(
            si_parametric_distr = "G",
            mcmc_control = make_mcmc_control(list(burnin = 3000, thin = 10)),
            n1 = 500, 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.
# }