Detect an abrupt change point in the reporting-delay distribution

Usage

test_delay_changepoint(
  x,
  ...,
  stat = c("median", "spread", "mean", "iqr"),
  by_strata = FALSE,
  strata = NULL,
  mature_only = TRUE,
  level = 0.95,
  alpha = 0.05
)

Arguments

x: A tbl_now object.
...: Passed to the underlying modifiedmk function (e.g. nsim for "block-bootstrap").
stat: Which delay summaries to test: any of "median", "mean", "iqr" (q75 - q25) and "spread" (q90 - q10). Defaults to median + spread, i.e. one location and one dispersion statistic.
by_strata: Logical (default FALSE). When TRUE, the test is run separately per stratum.
strata: Character vector of columns to group on when by_strata = TRUE. NULL (default) uses the object's strata.
mature_only: Logical (default TRUE). Drop event dates after the level incompleteness cutoff before testing.
level: Completeness level for the maturity cutoff (default 0.95).
alpha: Significance level for the drift verdict column (default 0.05).

Value

A tibble with one row per stat x stratum: strata, stat, n (series length), changepoint (the event date of the estimated change, NA when none is found), statistic (Pettitt's K), p_value, before / after (the mean of the statistic on each side of the change), shift (after - before) and a logical changepoint_detected (p_value < alpha).

Details

Complements test_delay_drift(). Where that tests for a gradual monotonic trend, this tests for a single abrupt shift (e.g. a reporting-system change on some date) in the per-period delay summaries, using Pettitt's nonparametric change-point test. As with test_delay_drift() it works on both a location statistic (median / mean) and a dispersion statistic (IQR / 10-90 spread), on mature data only, and — being rank-based — it is robust to the skew and serial dependence of a delay series.

Examples

data(denguedat)
dengue <- tbl_now(denguedat,
  event_date = "onset_week", report_date = "report_week", verbose = FALSE
)
test_delay_changepoint(dengue)
#> Warning: ! `test_delay_changepoint()` is experimental: results are not guaranteed and
#>   the interface may change.
#> ℹ Treat a detected change as a potential change point, not a confirmed one.
#> This warning is displayed once every 8 hours.
#> # A tibble: 4 × 10
#>   strata stat       n changepoint statistic  p_value before after  shift
#>   <chr>  <chr>  <int> <date>          <dbl>    <dbl>  <dbl> <dbl>  <dbl>
#> 1 all    median  1090 1998-01-19      38402 2.17e- 3   1.53  1.39 -0.136
#> 2 all    spread  1090 1997-09-01      93409 5.77e-18   2.55  1.91 -0.639
#> 3 all    mean    1090 1998-01-19      75959 5.04e-12   1.86  1.72 -0.145
#> 4 all    iqr     1090 1998-11-16      45245 1.53e- 4   1.19  1    -0.194
#> # ℹ 1 more variable: changepoint_detected <lgl>