Plot the reporting triangle as an age-period-cohort hexamap

Draws the reporting triangle as a hexagonal age-period-cohort map, using the projection of Jalal and Burke (2020). Event date, report date and reporting delay are the cohort, period and age of the map (report = event + delay), and each (event, delay) cell is one hexagon coloured by its report count. Because a batch is a single report date, it appears as a clean vertical stripe; the fast-reporting bulk sits along the short-delay bottom edge.

Usage

plot_reporting_hexamap(
  x,
  max_delay = NULL,
  complete = FALSE,
  iso = NULL,
  iso_minor = NULL,
  format = "%d/%b/%y",
  max_cells = 12000L,
  trans = "sqrt",
  palette = .tbl_now_palette()
)

Arguments

x

A tbl_now() object.

max_delay

Largest delay (in report units) to draw. NULL (default) shows the observed range, auto-capped to respect max_cells.

complete

If TRUE, fill the whole observable triangle with zeros so the grey background shows every observable cell. Default FALSE (observed cells only). Coerces linelist input to counts via to_count().

iso, iso_minor

Major and minor grid spacings (in report units). NULL picks sensible defaults from the data.

format

Date format for the event/report tick labels (see strftime()). Default "%d/%b/%y".

max_cells

Safety cap on the number of hexagons. Default 12000.

trans

Fill transform for the count scale. Default "sqrt".

palette

A named colour palette. Defaults to the package palette.

Value

A ggplot2 object.

Details

The three axes are read off three families of iso-lines: report date (period) runs vertically, delay (age) up the right-hand spine, and event date (cohort) up the left. A major/minor triangular grid is drawn so any hexagon can be traced back to its event date, report date and delay.

The number of hexagons is #\{observed (event, delay) cells\}, which grows with the delay range. To stay responsive the delay axis is capped so at most max_cells hexagons are drawn (raise max_cells, or set max_delay, to change this). complete = TRUE first fills the whole observable triangle with explicit zeros (via complete_zeroes()) so the empty cells are shown in grey.

References

Jalal, H. and Burke, D. S. (2020). Hexamaps for Age-Period-Cohort Data Visualization. Epidemiology 31, e47-e49.

See also

plot_reporting_triangle(), diagnostic_plot().

Examples

data(denguedat)
dn <- tbl_now(denguedat, onset_week, report_week, verbose = FALSE)
plot_reporting_hexamap(dn)