Find the peak date of an incidence curve

This function can be used to find the peak of an epidemic curve stored as an incidence object.

find_peak(x, pool = TRUE)

Arguments

x

An incidence object.

pool

If TRUE (default), any groups will be pooled before finding a peak. If FALSE, separate peaks will be found for each group.

Value

The date of the (first) highest incidence in the data.

See also

estimate_peak() for bootstrap estimates of the peak time

Author

Thibaut Jombart thibautjombart@gmail.com, Zhian N. Kamvar zkamvar@gmail.com

Examples

if (require(outbreaks) && require(ggplot2)) { withAutoprint({
  i <- incidence(fluH7N9_china_2013$date_of_onset)
  i
  plot(i)

  ## one simple bootstrap
  x <- bootstrap(i)
  x
  plot(x)

  ## find 95% CI for peak time using bootstrap
  find_peak(i)


  ## show confidence interval
  plot(i) + geom_vline(xintercept = find_peak(i), col = "red", lty = 2)

})}
#> > i <- incidence(fluH7N9_china_2013$date_of_onset)
#> 10 missing observations were removed.
#> > i
#> <incidence object>
#> [126 cases from days 2013-02-19 to 2013-07-27]
#> 
#> $counts: matrix with 159 rows and 1 columns
#> $n: 126 cases in total
#> $dates: 159 dates marking the left-side of bins
#> $interval: 1 day
#> $timespan: 159 days
#> $cumulative: FALSE
#> 
#> > plot(i)

#> > x <- bootstrap(i)
#> > x
#> <incidence object>
#> [126 cases from days 2013-02-27 to 2013-05-03]
#> 
#> $counts: matrix with 66 rows and 1 columns
#> $n: 126 cases in total
#> $dates: 66 dates marking the left-side of bins
#> $interval: 1 day
#> $timespan: 66 days
#> $cumulative: FALSE
#> 
#> > plot(x)

#> > find_peak(i)
#> [1] "2013-04-03"
#> > plot(i) + geom_vline(xintercept = find_peak(i), col = "red", lty = 2)