Visualise whether the reporting-delay distribution drifts over time

Usage

plot_delay_drift(
  x,
  ...,
  window = NULL,
  step = NULL,
  min_n = 1,
  by_strata = FALSE,
  strata = NULL,
  changepoint = FALSE,
  level = 0.95,
  palette = .tbl_now_palette()
)

Arguments

x: A tbl_now object.
...: Unused.
window: Rolling-window width, in event-time periods. NULL (default) uses 7 periods regardless of the time unit — that is, 7 days for daily data and 7 weeks for weekly data.
step: Step between window centres, in periods. NULL (default) uses max(1, window / 4).
min_n: Minimum total case count for a window to be drawn (default 1).
by_strata: Logical (default FALSE). When TRUE, one fan is drawn per stratum (faceted).
strata: Character vector of columns to group on when by_strata = TRUE. NULL (default) uses the object's strata.
changepoint: Logical (default FALSE). When TRUE, mark the estimated abrupt change point of the median delay (Pettitt's test, on mature data) with a vertical line, when one is detected (p < 0.05). See test_delay_changepoint().
level: Completeness level for the immature-region shading (default 0.95; see autoplot()).
palette: A named colour palette (defaults to the package palette).

Value

A ggplot2 object.

Details

Draws a rolling fan chart of the count-weighted reporting-delay distribution indexed by event date: a solid line for the rolling median, a dashed line for the rolling mean, and two shaded bands (the 25-75% and 10-90% quantile ranges). Reading it left to right answers "do delays drift?" — a rising/falling centre line is location drift, widening/narrowing bands are spread drift.

Because recent event dates have not had time to be fully reported, their delay summaries are downward-biased (only short delays are observable yet). That immature region — event dates after the level incompleteness cutoff — is shaded grey and should not be read as drift. Pair the plot with test_delay_drift() for a formal test.

Examples

data(denguedat)
dengue <- tbl_now(denguedat,
  event_date = "onset_week", report_date = "report_week", verbose = FALSE
)
plot_delay_drift(dengue)