Measles1861: Data on the 1861 measles epidemic in Hagelloch, Germany.

In EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Description

This data set gives:

1. the daily incidence of onset of symptoms in Hallegoch (Germany) during the 1861 measles epidemic (see source and references),

2. the discrete daily distribution of the serial interval for measles, assuming a shifted Gamma distribution with mean 14.9 days, standard deviation 3.9 days and shift 1 day (see references).

Format

A list of two elements:

• incidence: a vector containing 48 days of observation,

• si_distr: a vector containing a set of 38 probabilities.

Source

Groendyke C. et al. (2011) Bayesian Inference for Contact Networks Given Epidemic Data. Scandinavian Journal of Statistics 38(3): 600-616.

References

Groendyke C. et al. (2011) Bayesian Inference for Contact Networks Given Epidemic Data. Scandinavian Journal of Statistics 38(3): 600-616.

Examples

## load data on measles in Hallegoch in 1861
data("Measles1861")

## estimate the reproduction number (method "non_parametric_si")
res <- estimate_R(Measles1861$incidence, method="non_parametric_si",
          config = make_config(list(
                t_start = seq(17, 42), 
                t_end = seq(23, 48),
                si_distr = Measles1861$si_distr)))
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.

Example output

EpiEstim documentation built on Jan. 7, 2021, 5:10 p.m.