Smallpox1972: Data on the 1972 smallpox epidemic in Kosovo

In EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Description

This data set gives:

1. the daily incidence of onset of symptoms in Kosovo during the 1972 smallpox epidemic (see source and references),

2. the discrete daily distribution of the serial interval for smallpox, assuming a shifted Gamma distribution with mean 22.4 days, standard deviation 6.1 days and shift 1 day (see references).

Format

A list of two elements:

• incidence: a vector containing 57 days of observation,

• si_distr: a vector containing a set of 46 probabilities.

Source

Fenner F. et al. (1988) Smallpox and its Eradication. Geneva, World Health Organization.

References

Fenner F. et al. (1988) Smallpox and its Eradication. Geneva, World Health Organization.

Gani R. and S. Leach (2001) Transmission potential of smallpox in contemporary populations. Nature 414(6865): 748-751.

Riley S. and N. M. Ferguson (2006) Smallpox transmission and control: spatial dynamics in Great Britain. Proc Natl Acad Sci U S A 103(33): 12637-12642.

Examples

## load data on smallpox in Kosovo in 1972
data("Smallpox1972")

## estimate the reproduction number (method "non_parametric_si")
res <- estimate_R(Smallpox1972$incidence, method="non_parametric_si",
          config = make_config(list(
                      t_start = seq(27, 51), 
                      t_end = seq(33, 57),
                      si_distr = Smallpox1972$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.