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Add short outbreaks to the end of simulated daily counts

Source: R/simulation_data_baseline.R
simulate_spike_outbreak_data.Rd

Adds n_sp_outbreak short outbreaks to the output of simulate_baseline_data(), after Noufaily et al. (2019). Each starts on a random day in the last 344 days, 49 weeks, of the data.

Usage

simulate_spike_outbreak_data(data, n_sp_outbreak = 1, m)

Arguments

data

The output of simulate_baseline_data().

n_sp_outbreak

The number of outbreaks.

m

The size factor of an outbreak: the mean size is 10 * m * sd.

Value

A copy of data with the cases added to n, and these columns:

  • sd and weight,

  • sp_outbreak: 2 on an outbreak day and 0 on other days,

  • sp_outbreak_n: the cases, which are added to n,

  • sp_outbreak_n_rw: the weighted cases, which n does not use.

Details

The size and the spread are as in simulate_seasonal_outbreak_data(), over about half as many days, and with no day-of-week weight on n. The size draw also calls set.seed().

References

Noufaily A, Enki DG, Farrington P, Garthwaite P, Andrews N, Charlett A. An improved algorithm for outbreak detection in multiple surveillance systems. Statistics in Medicine. 2013.

See also

vignette("csalert", package = "csalert"), which runs it.

Other data simulation functions: add_holiday_effect(), simulate_baseline_data(), simulate_seasonal_outbreak_data()

Examples

library(data.table)
set.seed(4)
baseline <- simulate_baseline_data(
  start_date = as.Date("2018-01-01"),
  end_date = as.Date("2019-12-31"),
  seasonal_pattern_n = 1,
  weekly_pattern_n = 1,
  alpha = 3,
  beta = 0,
  gamma_1 = 0.8,
  gamma_2 = 0.6,
  gamma_3 = 0.8,
  gamma_4 = 0.4,
  phi = 4,
  shift_1 = 29
)
d <- simulate_spike_outbreak_data(
  baseline,
  n_sp_outbreak = 1,
  m = 2
)
print(d[, .(date, n, sp_outbreak, sp_outbreak_n)])
#>            date     n sp_outbreak sp_outbreak_n
#>          <Date> <num>       <num>         <num>
#>   1: 2018-01-01    64           0             0
#>   2: 2018-01-02    32           0             0
#>   3: 2018-01-03    19           0             0
#>   4: 2018-01-04    37           0             0
#>   5: 2018-01-05    72           0             0
#>  ---                                           
#> 726: 2019-12-27    68           0             0
#> 727: 2019-12-28   109           0             0
#> 728: 2019-12-29   139           0             0
#> 729: 2019-12-30    60           0             0
#> 730: 2019-12-31    41           0             0