Diagnostic autoplot for a tbl_now — autoplot.tbl

Produces a multi-panel diagnostic overview of a tbl_now using ggplot2::ggplot() and patchwork. Two families of panels are available — one describing the case counts and one describing the reporting delay — and you choose which to draw with the panels argument.

Case-count panels

"delay_distribution" — a (case-count weighted) histogram of the reporting delay (.delay).
"epidemic" — the latest reported case counts per event_date, with a dashed vertical line marking where the data become incomplete (less than level of the delay distribution has arrived). Holidays from the attached temporal_effects() spec are marked with dots.
"calendar_weekday", "calendar_week", "calendar_month" — boxplots of the normalized case effect (each event date's cases divided by the overall mean, so 1 is average) by day of week, epidemiological week, or month.
"seasonality" — a periodogram of the incidence series whose dominant peak suggests a Fourier season length for temporal_effects().

Reporting-delay panels (to inspect delay effects)

"delay_weekday", "delay_week", "delay_month" — boxplots of the normalized mean reporting delay (each event date's mean delay divided by the overall mean delay, so 1 is average) by day of week, epidemiological week, or month; these reveal whether the delay itself has a calendar pattern. Normalizing keeps them on the same scale as the case-count calendar panels and makes them comparable across strata.
"delay_seasonality" — a periodogram of the mean-delay series, whose peak marks a cycle in the reporting delay (e.g. a weekly reporting rhythm).

The calendar/delay panels shown depend on the event unit: daily data offers day-of-week and week-of-year panels, weekly data week-of-year, monthly data month-of-year. The delay panels are computed on the complete portion of the series (event dates on or before the incompleteness line) so the recent reporting truncation does not bias them.

Usage

# S3 method for class 'tbl_now'
autoplot(
  object,
  ...,
  panels = "all",
  by_strata = FALSE,
  strata = NULL,
  level = 0.95,
  palette = .tbl_now_palette(),
  delay_distribution_xlim = NULL,
  event_date_xlim = NULL,
  calendar_effect_xlim = NULL,
  seasonality_xlim = NULL
)

Arguments

object: A tbl_now object.
...: Unused; present for compatibility with ggplot2::autoplot().
panels: Which panels to draw. Either a vector of the concrete keys listed above, or one of the aliases "all" (default; every applicable panel), "calendar" (the case-count calendar panels) or "delay_calendar" (the reporting-delay calendar panels). Selecting a single panel returns that panel as a plain ggplot2 object instead of a patchwork.
by_strata: Logical (default FALSE). When TRUE, every panel is split by stratum: the calendar / delay boxplots become dodged boxes (one per stratum, side by side), the epidemic process and both periodograms become one coloured line per stratum (no area fill), and the delay distribution becomes dodged bars (one per stratum). The boxplots are then normalized per stratum (1 = that stratum's own average) so the calendar pattern is comparable across strata. Colours use a viridis scale. In this mode the holiday dots are omitted from the epidemic panel.
strata: Character vector of column names to group by when by_strata = TRUE. NULL (default) uses the object's strata (see get_strata()); pass a subset (e.g. strata = "gender") to group by only some of them. Ignored when by_strata = FALSE.
level: Completeness level used for the incompleteness line in the "epidemic" panel (and to trim the delay panels). The line is drawn at now - q, where q is the level quantile of the delay distribution. With the default 0.95, the line marks where at least 5 percent of delays are yet to arrive.
palette: A named character vector of colours. Defaults to the package palette.
delay_distribution_xlim, event_date_xlim, calendar_effect_xlim, seasonality_xlim: Optional length-2 vectors giving the x-axis limits for the corresponding panel (delay-distribution histogram, epidemic process, calendar-effect boxplots, incidence periodogram). NULL (default) lets each panel pick its own range. For event_date_xlim pass Dates; the others take numeric limits.

Value

A patchwork object combining the selected panels, or — when a single panel is selected — that panel as a ggplot2 object.

Examples

data(denguedat)
# A recent window keeps the example fast.
recent <- denguedat[denguedat$onset_week >= as.Date("2010-01-01"), ]
dengue <- tbl_now(recent,
  event_date = "onset_week",
  report_date = "report_week", strata = "gender", verbose = FALSE
)
autoplot(dengue)


# \donttest{
# Only the reporting-delay calendar effect
autoplot(dengue, panels = "delay_calendar")


# A single panel (returned as a plain ggplot)
autoplot(dengue, panels = "delay_week")


# Split every panel by stratum
autoplot(dengue, by_strata = TRUE)


# Zoom the delay panel to delays of 0-10 weeks
autoplot(dengue, delay_distribution_xlim = c(0, 10))

# }