Adjust or subset a line list to account for right truncation

Adjust or subset the line list <data.frame> by removing cases that have not been reported by the truncation time and setting hospitalisation admission or outcome dates that are after the truncation point to NA.

This is to replicate real-time outbreak data where recent cases or outcomes are not yet observed or reported (right truncation). It implies an assumption that symptom onsets are reported with a delay but hospitalisations are reported instantly.

Usage

truncate_linelist(
  linelist,
  truncation_day = 14,
  unit = c("days", "weeks", "months", "years"),
  direction = c("backwards", "forwards")
)

Arguments

linelist

Line list <data.frame> output from sim_linelist().

truncation_day

A single numeric specifying the number of days (default), weeks, months or years before the end of the outbreak (default) or since the start of the outbreak (see direction argument) to truncate the line list at. By default it is 14 days before the end of the outbreak.

Alternatively, truncation_day can accept a <Date> and this is used as the truncation_day and the unit and direction is ignored.

unit

A character string, either "days" (default), "weeks", "months", or "years", specifying the units of the truncation_day argument.

Years are assumed to be 365.25 days and months are assumed to be 365.25 / 12 days (same as lubridate).

direction

A character string, either "backwards" (default) or "forwards". direction = backwards defines the truncation_day as the time before the end of the outbreak. direction = forwards defines the truncation_day as the time since the start of the outbreak.

Value

A line list <data.frame>.

Details

The day on which the line list is truncated is the same for all individuals in the line list, and is specified by the truncation_day and unit arguments.

Examples

set.seed(1)
linelist <- sim_linelist()
linelist_trunc <- truncate_linelist(linelist)

# set truncation point 3 weeks before the end of outbreak
linelist_trunc <- truncate_linelist(
  linelist,
  truncation_day = 3,
  unit = "weeks"
)

# set truncation point to 2 months since the start of outbreak
linelist_trunc <- truncate_linelist(
  linelist,
  truncation_day = 2,
  unit = "months",
  direction = "forwards"
)

# set truncation point to 2023-03-01
linelist_trunc <- truncate_linelist(
  linelist,
  truncation_day = as.Date("2023-03-01")
)