Flag reports with an implausibly long delay as censored

Marks every report whose reporting delay exceeds max_delay (in event units) as censored: the recorded delay becomes an upper bound rather than an exact value. This is the natural response to a "delay too long" outlier: instead of letting, say, a 300-day delay drag the delay distribution, you tell the model only that the case arrived by that delay.

The delay is read from the tbl_now's generated .delay column (the report date minus the event date, in the data's event units). The is_censored column is updated (or created) and merged with any existing censoring flags (already-censored reports stay censored).

Usage

censor_delays_above(data, max_delay, quiet = FALSE)

Arguments

data

A tbl_now object.

max_delay

Numeric. Reports with delay strictly greater than this (in the data's event units) are flagged as censored.

quiet

If TRUE, suppress the informational message.

Value

The tbl_now with its is_censored column updated (created if absent).

See also

add_is_censored(), change_is_censored(), remove_is_censored()

Examples

df <- data.frame(
  onset = as.Date("2020-01-01") + c(0, 0, 1, 2),
  reported = as.Date("2020-01-01") + c(1, 5, 2, 300)
)
tn <- tbl_now(df,
  event_date = onset, report_date = reported,
  data_type = "linelist", verbose = FALSE
)

# the 300-day report becomes censored (an upper bound on its delay)
tn <- censor_delays_above(tn, max_delay = 60)
#> ℹ Marked 1 report with delay > 60 days as censored.
#> • This delay is now an upper bound (is_censored).