This function can be used to estimate the peak of an epidemic curve using bootstrapped samples of the available data.
Arguments
- x
An
<incidence2>object.- n
[integer]The number of bootstrap datasets to be generated; defaults to 100.
[double]vectors will be converted viaas.integer(n).- alpha
[numeric]The type 1 error chosen for the confidence interval; defaults to 0.05.
- first_only
[bool]Should only the first peak (by date) be kept.
Defaults to
TRUE.- progress
[bool]Should a progress bar be displayed (default = TRUE)
Value
A data frame with the the following columns:
observed_date: the date of peak incidence of the original dataset.observed_count: the peak incidence of the original dataset.estimated: the median peak time of the bootstrap datasets.lower_ci/upper_ci: the confidence interval based on bootstrap datasets.bootstrap_peaks: a nested tibble containing the the peak times of the bootstrapped datasets.
Details
Input dates are resampled with replacement to form bootstrapped datasets; the peak is reported for each, resulting in a distribution of peak times. When there are ties for peak incidence, only the first date is reported.
Note that the bootstrapping approach used for estimating the peak time makes the following assumptions:
the total number of event is known (no uncertainty on total incidence)
dates with no events (zero incidence) will never be in bootstrapped datasets
the reporting is assumed to be constant over time, i.e. every case is equally likely to be reported
See also
bootstrap() for the bootstrapping underlying this approach and
find_peak() to find the peak in a single [incidence2] object.
Examples
if (requireNamespace("outbreaks", quietly = TRUE)) {
# load data and create incidence
data(fluH7N9_china_2013, package = "outbreaks")
i <- incidence(fluH7N9_china_2013, date_index = "date_of_onset")
# find 95% CI for peak time using bootstrap
estimate_peak(i)
}
#> Estimating peaks from bootstrap samples:
#>
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#>
#> # A data frame: 1 × 7
#> count_variable observed_peak observ…¹ boots…² lower_ci median upper_ci
#> <chr> <date> <int> <list> <date> <date> <date>
#> 1 date_of_onset 2013-04-03 7 <df> 2013-03-29 2013-04-06 2013-04-17
#> # … with abbreviated variable names ¹observed_count, ²bootstrap_peaks