Diagnostic plots of the reporting process

Lays out a gallery of complementary views of a tbl_now's reporting process, all aimed at spotting reporting artefacts – especially batch reporting. Each view is also available on its own (see See also); diagnostic_plot() picks the ones named in panels and combines them with patchwork. Selecting a single panel returns it as a plain plot. Every view is facetted by stratum when the tbl_now declares strata.

Usage

diagnostic_plot(
  x,
  panels = "all",
  by = c("report", "event"),
  max_delay = NULL,
  ...,
  plotly = FALSE,
  axis = c("report", "revision"),
  size = 1,
  linewidth = 1,
  grid_linewidth = 0.3,
  palette = .tbl_now_palette()
)

Arguments

x

A tbl_now() object.

panels

Which panels, "all" (default) or any subset of "reporting", "triangle", "profiles", "delay_drift" and "transport".

by

For the "profiles" panel, one mark per "report" date (default) or per "event" date.

max_delay

Largest delay on the delay-based panels. NULL (default) caps at the delay covering 99% of reported mass.

...

Batch controls (lookback, period, alpha) routed to the "transport" panel.

plotly

If TRUE, return an interactive plotly widget (the panels stacked) instead of a static patchwork. Default FALSE.

axis

Which time axis the delay is measured on: "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.

size

Multiplier on point and label sizes, forwarded to every panel that draws them ("triangle", "transport"). Default 1.

linewidth

Multiplier on data line widths, forwarded to every panel that draws them ("profiles", "delay_drift"). Default 1.

grid_linewidth

Line width of the reference grids the package draws itself – not ggplot2's panel grid. Forwarded to "triangle", "transport" and "delay_drift". Default 0.3.

palette

A named colour palette (see tbl_now_palette()).

Value

A patchwork object, or a single plot when one panel is selected (or a plotly widget when plotly = TRUE).

See also

Every panel is also a function of its own: plot_reporting_process() and plot_epidemic_process() (when reports arrived, versus when cases happened), plot_reporting_triangle() (the full event-by-delay grid), plot_delay_profiles() (each date's delay curve), plot_delay_drift() (whether delays are getting longer), plot_transport_discriminant().

Examples

data(denguedat)
# The two and a half years around the 1996 and 1997 backlog dumps: enough
# for the transport panel to have something to flag, quick enough to draw.
window <- denguedat[
  denguedat$onset_week >= as.Date("1995-06-01") &
    denguedat$onset_week <= as.Date("1998-01-01"),
]
dn <- tbl_now(window, onset_week, report_week, verbose = FALSE)
diagnostic_plot(dn, panels = c("triangle", "transport"))
#> Warning: ! `transport_discriminant()` is experimental: results are not guaranteed and
#>   the interface may change.
#> ℹ Treat a flagged report date as a potential batch, not a confirmed one.
#> This warning is displayed once every 8 hours.