SARS2003: Data on the 2003 SARS epidemic in Hong Kong.

In EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Description

This data set gives:

1. the daily incidence of onset of symptoms in Hong Kong during the 2003 severe acute respiratory syndrome (SARS) epidemic (see source and references),

2. the discrete daily distribution of the serial interval for SARS, assuming a shifted Gamma distribution with mean 8.4 days, standard deviation 3.8 days and shift 1 day (see references).

Format

A list of two elements:

• incidence: a vector containing 107 days of observation,

• si_distr: a vector containing a set of 25 probabilities.

Source

Cori A. et al. (2009) Temporal variability and social heterogeneity in disease transmission: the case of SARS in Hong Kong. PLoS Comput Biol 5(8) : e1000471.

References

Cori A. et al. (2009) Temporal variability and social heterogeneity in disease transmission: the case of SARS in Hong Kong. PLoS Comput Biol 5(8): e1000471.

Lipsitch M. et al. (2003) Transmission dynamics and control of severe acute respiratory syndrome. Science 300(5627): 1966-1970.

Examples

## load data on SARS in Hong Kong in 2003
data("SARS2003")

## estimate the reproduction number (method "non_parametric_si")
res <- estimate_R(SARS2003$incidence, method="non_parametric_si",
          config = make_config(list(
                      t_start = seq(14, 101), 
                      t_end = seq(20, 107),
                      si_distr = SARS2003$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

TableGrob (3 x 1) "arrange": 3 grobs
      z     cells    name           grob
incid 1 (1-1,1-1) arrange gtable[layout]
R     2 (2-2,1-1) arrange gtable[layout]
SI    3 (3-3,1-1) arrange gtable[layout]

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