derive_var_trtemfl: Derive Treatment-emergent Flag

In admiral: ADaM in R Asset Library

Derive Treatment-emergent Flag

Description

Derive treatment emergent analysis flag (e.g., TRTEMFL).

Usage

derive_var_trtemfl(
  dataset,
  new_var = TRTEMFL,
  start_date = ASTDTM,
  end_date = AENDTM,
  trt_start_date = TRTSDTM,
  trt_end_date = NULL,
  end_window = NULL,
  ignore_time_for_trt_end = TRUE,
  initial_intensity = NULL,
  intensity = NULL,
  group_var = NULL,
  subject_keys = get_admiral_option("subject_keys")
)

Arguments

dataset	Input dataset The variables specified by start_date, end_date, trt_start_date, trt_end_date, initial_intensity, and intensity are expected.
new_var	New variable
start_date	Event start date
end_date	Event end date
trt_start_date	Treatment start date
trt_end_date	Treatment end date
end_window	If the argument is specified (in 'days'), events starting more than the specified number of days after end of treatment, are not flagged.
ignore_time_for_trt_end	If the argument is set to TRUE, the time part is ignored for checking if the event occurred more than end_window days after end of treatment.
initial_intensity	Initial severity/intensity or toxicity initial_intensity is ignored when group_var is specified. If this argument is specified and group_var is NULL, events which start before treatment start and end after treatment start (or are ongoing) and worsened (i.e., the intensity is greater than the initial intensity), are flagged. The values of the specified variable must be comparable with the usual comparison operators. I.e., if the intensity is greater than the initial intensity initial_intensity < intensity must evaluate to TRUE.
intensity	Severity/intensity or toxicity If the argument is specified, events which start before treatment start and end after treatment start (or are ongoing) and worsened (i.e., the intensity is greater than the initial intensity), are flagged. The values of the specified variable must be comparable with the usual comparison operators. I.e., if the intensity is greater than the initial intensity initial_intensity < intensity must evaluate to TRUE.
group_var	Grouping variable If the argument is specified, it assumes that AEs are recorded as one episode of AE with multiple lines using a grouping variable. Events starting during treatment or before treatment and worsening afterward are flagged. Once an AE record in a group is flagged, all subsequent records in the treatment window are flagged regardless of severity.
subject_keys	Variables to uniquely identify a subject. This argument is only used when group_var is specified.

Details

For the derivation of the new variable the following cases are considered in this order. The first case which applies, defines the value of the variable.

• not treated: If trt_start_date is NA, it is set to NA_character_.

• event before treatment: If end_date is before trt_start_date (and end_date is not NA), it is set to NA_character_.

• no event date: If start_date is NA, it is set to "Y" as in such cases it is usually considered more conservative to assume the event was treatment-emergent.

• event started during treatment:

  • if end_window is not specified: if start_date is on or after trt_start_date, it is set to "Y",

  • if end_window is specified: if start_date is on or after trt_start_date and start_date is on or before trt_end_date + end_window days, it is set to "Y",

• event started before treatment and (possibly) worsened on treatment:

  • if initial_intensity, intensity is specified and group_var is not specified: if initial_intensity < intensity and start_date is before trt_start_date and end_date is on or after trt_start_date or end_date is NA, it is set to "Y";

  • if group_var is specified: if intensity at treatment start < intensity and start_date is after trt_start_date and end_date is on or after trt_start_date or end_date is NA, it is set to "Y";

• Otherwise it is set to NA_character_.

The behavior of derive_var_trtemfl() is aligned with the proposed treatment-emergent AE assignment in the following PHUSE White Paper. See the final example in the examples section below.

Value

The input dataset with the variable specified by new_var added

See Also

OCCDS Functions: derive_vars_atc(), derive_vars_query()

admiral documentation built on May 28, 2026, 9:08 a.m.