Data on the 1918 H1N1 influenza pandemic in Baltimore.

Source: R/data.R

This data set gives:

  1. the daily incidence of onset of disease in Baltimore during the 1918 H1N1 influenza pandemic (see source and references),

  2. the discrete daily distribution of the serial interval for influenza, assuming a shifted Gamma distribution with mean 2.6 days, standard deviation 1.5 days and shift 1 day (see references).

Format

A list of two elements:

  • incidence: a vector containing 92 days of observation,

  • si_distr: a vector containing a set of 12 probabilities.

Source

Frost W. and E. Sydenstricker (1919) Influenza in Maryland: preliminary statistics of certain localities. Public Health Rep.(34): 491-504.

References

Cauchemez S. et al. (2011) Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza. Proc Natl Acad Sci U S A 108(7), 2825-2830.

Ferguson N.M. et al. (2005) Strategies for containing an emerging influenza pandemic in Southeast Asia. Nature 437(7056), 209-214.

Fraser C. et al. (2011) Influenza Transmission in Households During the 1918 Pandemic. Am J Epidemiol 174(5): 505-514.

Frost W. and E. Sydenstricker (1919) Influenza in Maryland: preliminary statistics of certain localities. Public Health Rep.(34): 491-504.

Vynnycky E. et al. (2007) Estimates of the reproduction numbers of Spanish influenza using morbidity data. Int J Epidemiol 36(4): 881-889.

White L.F. and M. Pagano (2008) Transmissibility of the influenza virus in the 1918 pandemic. PLoS One 3(1): e1498.

Examples

## load data on pandemic flu in Baltimore in 1918
data("Flu1918")

## estimate the reproduction number (method "non_parametric_si")
res <- estimate_R(Flu1918$incidence,
          method = "non_parametric_si",
          config = make_config(list(si_distr = Flu1918$si_distr)))
#> Default config will estimate R on weekly sliding windows.
#>     To change this change the t_start and t_end arguments. 
plot(res)
#> Warning: The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in
#> ggplot2 3.3.4.
#> ℹ Please use "none" instead.
#> ℹ The deprecated feature was likely used in the incidence package.
#>   Please report the issue at <https://github.com/reconhub/incidence/issues>.

## the second plot produced shows, at each each day,
## the estimate of the reproduction number
## over the 7-day window finishing on that day.