mers_2014_15: Data on Middle East Respiratory Syndrome (MERS) in Saudi...

Description Format Source References Examples

Description

This data set gives:

  1. the daily incidence of onset of symptoms of laboratory confirmed human infections with MERS-CoV in Saudi Arabia between the beginning of July 2014 and the end of December 2015, and

  2. estimates of the mean and standard deviation of the serial interval for MERS.

Format

A list of two elements:

Source

The incidence data was extracted from the EMPRES I system from FAO (Global Animal Disease Information System - Food and Agriculture Organization of the United Nations, 2017). Note incidence on the first day was originally made of one local case and zero imported cases; this has been modified to zero local cases and one imported case in the dataset shown here so the reproduction number can be estimated from the start using the function estimate_R(). The serial interval parameters were those estimated by Cauchemez et al. (2016).

References

Global Animal Disease Information System - Food and Agriculture Organization of the United Nations, 2017

Cauchemez S, Nouvellet P, Cori A, Jombart T, Garske T, Clapham H, Moore S, Linden Mills H, Salje H, Collins C, et al. 2016. Unraveling the drivers of MERS-CoV transmission. Proc Natl Acad Sci 113: 9081-9086.

Examples

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## load data
data("mers_2014_15")

## estimate the reproduction number (method "parametric_si")
bimonthly_R <- estimate_R(mers_2014_15$incidence[,c("local", "imported")],
                          method = "parametric_si",
                          config = make_config(
                          mean_si = mers_2014_15$si$mean_si,
                          std_si = mers_2014_15$si$std_si,
                          t_start = 2:(nrow(mers_2014_15$incidence)-8*7),
                          t_end = (2:(nrow(mers_2014_15$incidence)-8*7)) + 8*7))

plot(bimonthly_R, legend = FALSE, add_imported_cases = TRUE,
                          options_I = list(col = c("local" = "black", 
                             "imported" = "red"),
                             interval = 7, # show weekly incidence
                             ylab = "Weekly incidence"),
                          options_R = list(ylab = "Bimonthly R")) 
# The first plot shows the weekly incidence, 
# with imported cases shown in red and local cases in black

annecori/EpiEstim documentation built on May 4, 2021, 9:41 a.m.