derive_var_trtemfl: Derive Treatment-emergent Flag
In Roche-GSK/admiral: ADaM in R Asset Library
View source: R/derive_var_trtemfl.R
derive_var_trtemfl R Documentation
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.
- Default value
none
new_var
New variable
- Default value
TRTEMFL
start_date
Event start date
- Permitted values
A symbol referring to a date or datetime variable of
the input dataset
- Default value
ASTDTM
end_date
Event end date
- Permitted values
A symbol referring to a date or datetime variable of
the input dataset
- Default value
AENDTM
trt_start_date
Treatment start date
- Permitted values
A symbol referring to a date or datetime variable of
the input dataset
- Default value
TRTSDTM
trt_end_date
Treatment end date
- Permitted values
A symbol referring to a date or datetime variable of
the input dataset or NULL
- Default value
NULL
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.
- Permitted values
A non-negative integer or NULL
- Default value
NULL
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.
- Permitted values
TRUE, FALSE
- Default value
TRUE
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.
- Permitted values
A symbol referring to a variable of the input dataset
or NULL
- Default value
NULL
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.
- Permitted values
A symbol referring to a variable of the input dataset
or NULL
- Default value
NULL
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.
- Permitted values
A symbol referring to a variable of the input dataset
or NULL
- Default value
NULL
subject_keys
Variables to uniquely identify a subject.
A list of symbols created using exprs() is expected. This argument is only
used when group_var is specified.
- Default value
get_admiral_option("subject_keys")
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 previous intensity < 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 Example 3 in the examples section.
Value
The input dataset with the variable specified by new_var added
See Also
OCCDS Functions:
derive_vars_atc(),
derive_vars_query(),
get_terms_from_db()
Examples
library(tibble)
library(dplyr, warn.conflicts = FALSE)
library(lubridate)
# Note: Examples 1 and 2 exhaustively showcase all arguments of
# derive_var_trtemfl(). Example 3 presents 13 more cases (some new, some similar
# to Examples 1 and 2) which are aligned one-to-one with the scenarios
# in the PHUSE White Paper on Treatment-Emergent AEs linked above.
# Example 1a: Derive TRTEMFL without considering treatment end and worsening
adae <- tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR,
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1",
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3",
# starting before treatment and ending during treatment
"1", "2021-12-30T20:00", "2022-01-14T11:00", "1", "3",
"1", "2021-12-31T20:15", "2022-01-01T01:23", "1", "1",
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "3", "4",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2",
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2",
# missing dates
"1", "", "", "3", "4",
"1", "2021-12-30T09:00", "", "3", "4",
"1", "2021-12-30T11:00", "", "3", "3",
"1", "", "2022-01-04T09:00", "3", "4",
"1", "", "2021-12-24T19:00", "3", "4",
"1", "", "2022-06-04T09:00", "3", "4",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2",
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2",
"2", "2021-12-06T18:00", "", "1", "2"
) %>%
mutate(
ASTDTM = ymd_hm(ASTDTM),
AENDTM = ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms(""))
)
derive_var_trtemfl(adae) %>% select(ASTDTM, AENDTM, TRTSDTM, TRTEMFL)
# Example 1b: Derive TRTEM2FL taking treatment end and worsening into account
derive_var_trtemfl(
adae,
new_var = TRTEM2FL,
trt_end_date = TRTEDTM,
end_window = 10,
initial_intensity = AEITOXGR,
intensity = AETOXGR
) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, TRTEM2FL)
# Example 2: Derive TRTEMFL taking treatment end and worsening into account
# within a grouping variable
adae2 <- tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~AEGRPID,
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1",
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", "1",
# starting before treatment and ending during treatment
"1", "2021-12-30T20:15", "2022-01-14T01:23", "3", "3", "2",
"1", "2022-01-05T20:00", "2022-06-01T11:00", "3", "1", "2",
"1", "2022-01-10T20:15", "2022-01-11T01:23", "3", "2", "2",
"1", "2022-01-13T20:15", "2022-03-01T01:23", "3", "1", "2",
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "4", "4", "3",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "4",
"1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "4",
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "4",
# missing dates
"1", "", "", "3", "4", "5",
"1", "2021-12-30T09:00", "", "3", "4", "5",
"1", "2021-12-30T11:00", "", "3", "3", "5",
"1", "", "2022-01-04T09:00", "3", "4", "5",
"1", "", "2021-12-24T19:00", "3", "4", "5",
"1", "", "2022-06-04T09:00", "3", "4", "5",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2", "1",
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2",
"2", "2021-12-06T18:00", "", "1", "2", "3"
) %>%
mutate(
STUDYID = "ABC12345",
ASTDTM = ymd_hm(ASTDTM),
AENDTM = ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms(""))
)
derive_var_trtemfl(
adae2,
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 10,
intensity = AETOXGR,
group_var = AEGRPID
) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, AEGRPID, TRTEMFL)
# Example 3: PHUSE-white-paper scenarios
adae3 <- tribble(
~USUBJID, ~TRTSDTM, ~TRTEDTM, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR,
# Patient 1: Pre-treatment AE
"1", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
# Patient 2: On-treatment AE
"2", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "2",
# Patient 3: Pre-treatment AE, then on-treatment AE at same intensity
"3", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
"3", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "2",
# Patient 4: Pre-treatment AE, then on-treatment AE at wors. intensity
"4", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
"4", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "3",
# Patient 5: Pre-treatment AE, then on-treatment AE at impr. intensity
"5", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
"5", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "1",
# Patient 6: AE starting pre-treatment, continuing on-treatment, then 2nd AE at same intensity
"6", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
"6", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "2",
# Patient 7: AE starting pre-treatment, continuing on-treatment, then 2nd AE at wors. intensity
"7", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
"7", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "3",
# Patient 8: AE starting pre-treatment, continuing on-treatment, then 2nd AE at impr. intensity
"8", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
"8", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "1",
# Patient 9: AE starting pre-treatment, continuing on-treatment, and no change in intensity
"9", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
# Patient 10: AE starting pre-treatment, continuing on-treatment, and wors. intensity
"10", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "4",
# Patient 11: AE starting pre-treatment, continuing on-treatment, and impr. intensity
"11", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "1",
# Patient 12: AE starting pre-treatment, worsening, then improving
"12", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "3", "2",
# Patient 13: AE starting pre-treatment, improving, then worsening
"13", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "1", "2",
) %>%
mutate(
ASTDTM = ymd(ASTDTM),
AENDTM = ymd(AENDTM),
TRTSDTM = ymd(TRTSDTM),
TRTEDTM = ymd(TRTEDTM),
)
derive_var_trtemfl(
adae3,
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 0,
initial_intensity = AEITOXGR,
intensity = AETOXGR,
subject_keys = exprs(USUBJID)
) %>%
select(USUBJID, TRTSDTM, TRTEDTM, ASTDTM, AENDTM, AEITOXGR, AETOXGR, TRTEMFL)
Roche-GSK/admiral documentation built on April 14, 2025, 12:36 p.m.
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View source: R/derive_var_trtemfl.R
| derive_var_trtemfl | R Documentation |
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
|
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
|
initial_intensity |
Initial severity/intensity or toxicity
If this argument is specified and 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
|
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
|
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. A list of symbols created using
|
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_dateisNA, it is set toNA_character_. -
event before treatment: If
end_dateis beforetrt_start_date(andend_dateis notNA), it is set toNA_character_. -
no event date: If
start_dateisNA, 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_windowis not specified: ifstart_dateis on or aftertrt_start_date, it is set to"Y",if
end_windowis specified: ifstart_dateis on or aftertrt_start_dateandstart_dateis on or beforetrt_end_date+end_windowdays, it is set to"Y",
-
event started before treatment and (possibly) worsened on treatment:
if
initial_intensity,intensityis specified andgroup_varis not specified: ifinitial_intensity < intensityandstart_dateis beforetrt_start_dateandend_dateis on or aftertrt_start_dateorend_dateisNA, it is set to"Y";if
group_varis specified: if previousintensity<intensityandstart_dateis aftertrt_start_dateandend_dateis on or aftertrt_start_dateorend_dateisNA, 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 Example 3 in the examples section.
Value
The input dataset with the variable specified by new_var added
See Also
OCCDS Functions:
derive_vars_atc(),
derive_vars_query(),
get_terms_from_db()
Examples
library(tibble)
library(dplyr, warn.conflicts = FALSE)
library(lubridate)
# Note: Examples 1 and 2 exhaustively showcase all arguments of
# derive_var_trtemfl(). Example 3 presents 13 more cases (some new, some similar
# to Examples 1 and 2) which are aligned one-to-one with the scenarios
# in the PHUSE White Paper on Treatment-Emergent AEs linked above.
# Example 1a: Derive TRTEMFL without considering treatment end and worsening
adae <- tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR,
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1",
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3",
# starting before treatment and ending during treatment
"1", "2021-12-30T20:00", "2022-01-14T11:00", "1", "3",
"1", "2021-12-31T20:15", "2022-01-01T01:23", "1", "1",
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "3", "4",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2",
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2",
# missing dates
"1", "", "", "3", "4",
"1", "2021-12-30T09:00", "", "3", "4",
"1", "2021-12-30T11:00", "", "3", "3",
"1", "", "2022-01-04T09:00", "3", "4",
"1", "", "2021-12-24T19:00", "3", "4",
"1", "", "2022-06-04T09:00", "3", "4",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2",
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2",
"2", "2021-12-06T18:00", "", "1", "2"
) %>%
mutate(
ASTDTM = ymd_hm(ASTDTM),
AENDTM = ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms(""))
)
derive_var_trtemfl(adae) %>% select(ASTDTM, AENDTM, TRTSDTM, TRTEMFL)
# Example 1b: Derive TRTEM2FL taking treatment end and worsening into account
derive_var_trtemfl(
adae,
new_var = TRTEM2FL,
trt_end_date = TRTEDTM,
end_window = 10,
initial_intensity = AEITOXGR,
intensity = AETOXGR
) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, TRTEM2FL)
# Example 2: Derive TRTEMFL taking treatment end and worsening into account
# within a grouping variable
adae2 <- tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~AEGRPID,
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1",
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", "1",
# starting before treatment and ending during treatment
"1", "2021-12-30T20:15", "2022-01-14T01:23", "3", "3", "2",
"1", "2022-01-05T20:00", "2022-06-01T11:00", "3", "1", "2",
"1", "2022-01-10T20:15", "2022-01-11T01:23", "3", "2", "2",
"1", "2022-01-13T20:15", "2022-03-01T01:23", "3", "1", "2",
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "4", "4", "3",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "4",
"1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "4",
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "4",
# missing dates
"1", "", "", "3", "4", "5",
"1", "2021-12-30T09:00", "", "3", "4", "5",
"1", "2021-12-30T11:00", "", "3", "3", "5",
"1", "", "2022-01-04T09:00", "3", "4", "5",
"1", "", "2021-12-24T19:00", "3", "4", "5",
"1", "", "2022-06-04T09:00", "3", "4", "5",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2", "1",
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2",
"2", "2021-12-06T18:00", "", "1", "2", "3"
) %>%
mutate(
STUDYID = "ABC12345",
ASTDTM = ymd_hm(ASTDTM),
AENDTM = ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms(""))
)
derive_var_trtemfl(
adae2,
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 10,
intensity = AETOXGR,
group_var = AEGRPID
) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, AEGRPID, TRTEMFL)
# Example 3: PHUSE-white-paper scenarios
adae3 <- tribble(
~USUBJID, ~TRTSDTM, ~TRTEDTM, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR,
# Patient 1: Pre-treatment AE
"1", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
# Patient 2: On-treatment AE
"2", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "2",
# Patient 3: Pre-treatment AE, then on-treatment AE at same intensity
"3", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
"3", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "2",
# Patient 4: Pre-treatment AE, then on-treatment AE at wors. intensity
"4", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
"4", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "3",
# Patient 5: Pre-treatment AE, then on-treatment AE at impr. intensity
"5", "2021-01-01", "2021-12-31", "2020-12-20", "2020-12-21", "2", "2",
"5", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "1",
# Patient 6: AE starting pre-treatment, continuing on-treatment, then 2nd AE at same intensity
"6", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
"6", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "2",
# Patient 7: AE starting pre-treatment, continuing on-treatment, then 2nd AE at wors. intensity
"7", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
"7", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "3",
# Patient 8: AE starting pre-treatment, continuing on-treatment, then 2nd AE at impr. intensity
"8", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
"8", "2021-01-01", "2021-12-31", "2021-12-20", "2021-12-21", "2", "1",
# Patient 9: AE starting pre-treatment, continuing on-treatment, and no change in intensity
"9", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "2",
# Patient 10: AE starting pre-treatment, continuing on-treatment, and wors. intensity
"10", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "4",
# Patient 11: AE starting pre-treatment, continuing on-treatment, and impr. intensity
"11", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "2", "1",
# Patient 12: AE starting pre-treatment, worsening, then improving
"12", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "3", "2",
# Patient 13: AE starting pre-treatment, improving, then worsening
"13", "2021-01-01", "2021-12-31", "2020-12-23", "2021-01-21", "1", "2",
) %>%
mutate(
ASTDTM = ymd(ASTDTM),
AENDTM = ymd(AENDTM),
TRTSDTM = ymd(TRTSDTM),
TRTEDTM = ymd(TRTEDTM),
)
derive_var_trtemfl(
adae3,
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 0,
initial_intensity = AEITOXGR,
intensity = AETOXGR,
subject_keys = exprs(USUBJID)
) %>%
select(USUBJID, TRTSDTM, TRTEDTM, ASTDTM, AENDTM, AEITOXGR, AETOXGR, TRTEMFL)
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