Visualise whether the reporting-delay distribution drifts over time

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.

Usage

plot_delay_drift(
  x,
  ...,
  window = NULL,
  step = NULL,
  min_n = 1,
  by_strata = FALSE,
  strata = NULL,
  changepoint = FALSE,
  level = 0.95,
  plotly = FALSE,
  axis = c("report", "revision"),
  linewidth = 1,
  grid_linewidth = 0.5,
  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 diagnose_changepoint().

level

Completeness level for the immature-region shading (default 0.95; see autoplot()).

plotly

If TRUE, return an interactive plotly widget instead of a static plot. Default FALSE.

axis

Which time axis the delay is measured to: "report" (default) or "revision". Report-axis delays are measured from event to report; revision-axis delays are measured from report to revision, the same quantity as .revision_delay. Needs a revision process (see add_revision_date()); cases still "pending" are left out.

linewidth

Multiplier on the width of the mean and median delay lines. Default 1 (drawn at 0.6 and 0.8, so the median stays the heavier of the two at any setting).

grid_linewidth

Line width of the dashed maturity line and of the changepoint marker – the reference lines the package draws itself, not ggplot2's panel grid. Default 0.5.

palette

A named colour palette (see tbl_now_palette()).

Value

A ggplot2 object.

Details

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 diagnose_drift() for a formal test.

See also

diagnose_drift() for the formal trend test behind this picture, and diagnose_changepoint() for an abrupt shift rather than a gradual one; plot_delay_distribution() for the delay pooled over the whole period; autoplot() and diagnostic_plot() for the galleries this belongs to.

Examples

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