R/derive_vars_extreme_event.R
derive_vars_extreme_event.RdAdd the first available record from events for each by group as new
variables, all variables of the selected observation are kept. It can be used
for selecting the extreme observation from a series of user-defined events.
derive_vars_extreme_event(
dataset,
by_vars,
events,
tmp_event_nr_var = NULL,
order,
mode,
source_datasets = NULL,
check_type = "warning",
new_vars
)Input dataset
The variables specified by the by_vars and order arguments are expected to be in the dataset.
a dataset, i.e., a data.frame or tibble
none
Grouping variables
list of variables created by exprs(), e.g., exprs(USUBJID, VISIT)
NULL
Conditions and new values defining events
A list of event() or event_joined() objects is expected. Only
observations listed in the events are considered for deriving extreme
event. If multiple records meet the filter condition, take the first
record sorted by order. The data is grouped by by_vars, i.e., summary
functions like all() or any() can be used in condition.
For event_joined() events the observations are selected by calling
filter_joined(). The condition field is passed to the filter_join argument.
none
Temporary event number variable
The specified variable is added to all source datasets and is set to the number of the event before selecting the records of the event.
It can be used in order to determine which record should be used if
records from more than one event are selected.
The variable is not included in the output dataset.
NULL
Sort order
If a particular event from events has more than one observation, within
the event and by group, the records are ordered by the specified order.
For handling of NAs in sorting variables see Sort Order.
list of expressions created by exprs(), e.g.,
exprs(ADT, desc(AVAL))
none
Selection mode (first or last)
If a particular event from events has more than one observation,
"first"/"last" is used to select the first/last record of this type of
event sorting by order.
"first", "last"
none
Source datasets
A named list of datasets is expected. The dataset_name field of event()
and event_joined() refers to the dataset provided in the list.
NULL
Check uniqueness?
If "warning" or "error" is specified, the specified message is issued
if the observations of the input dataset are not unique with respect to the
by variables and the order.
"none", "message", "warning", "error"
"warning"
Variables to add
The specified variables from the events are added to the output
dataset. Variables can be renamed by naming the element, i.e., new_vars = exprs(<new name> = <old name>).
none
The input dataset with the best or worst observation of each by group added as new variables.
For each event select the observations to consider:
If the event is of class event, the observations of the source dataset
are restricted by condition and then the first or last (mode)
observation per by group (by_vars) is selected.
If the event is of class event_joined, filter_joined() is called to
select the observations.
The variables specified by the set_values_to field of the event
are added to the selected observations.
The variable specified for tmp_event_nr_var is added and set to
the number of the event.
All selected observations are bound together.
For each group (with respect to the variables specified for the
by_vars parameter) the first or last observation (with respect to the
order specified for the order parameter and the mode specified for the
mode parameter) is selected.
The variables specified by the new_vars parameter are added to
the selected observations.
The variables are added to input dataset.
event(), event_joined(), derive_extreme_event()
ADSL Functions that returns variable appended to dataset:
derive_var_age_years(),
derive_vars_aage(),
derive_vars_period()
library(tibble)
library(dplyr)
library(lubridate)
adsl <- tribble(
~STUDYID, ~USUBJID, ~TRTEDT, ~DTHDT,
"PILOT01", "01-1130", ymd("2014-08-16"), ymd("2014-09-13"),
"PILOT01", "01-1133", ymd("2013-04-28"), ymd(""),
"PILOT01", "01-1211", ymd("2013-01-12"), ymd(""),
"PILOT01", "09-1081", ymd("2014-04-27"), ymd(""),
"PILOT01", "09-1088", ymd("2014-10-09"), ymd("2014-11-01"),
)
lb <- tribble(
~STUDYID, ~DOMAIN, ~USUBJID, ~LBSEQ, ~LBDTC,
"PILOT01", "LB", "01-1130", 219, "2014-06-07T13:20",
"PILOT01", "LB", "01-1130", 322, "2014-08-16T13:10",
"PILOT01", "LB", "01-1133", 268, "2013-04-18T15:30",
"PILOT01", "LB", "01-1133", 304, "2013-05-01T10:13",
"PILOT01", "LB", "01-1211", 8, "2012-10-30T14:26",
"PILOT01", "LB", "01-1211", 162, "2013-01-08T12:13",
"PILOT01", "LB", "09-1081", 47, "2014-02-01T10:55",
"PILOT01", "LB", "09-1081", 219, "2014-05-10T11:15",
"PILOT01", "LB", "09-1088", 283, "2014-09-27T12:13",
"PILOT01", "LB", "09-1088", 322, "2014-10-09T13:25"
) %>%
mutate(
ADT = convert_dtc_to_dt(LBDTC)
)
derive_vars_extreme_event(
adsl,
by_vars = exprs(STUDYID, USUBJID),
events = list(
event(
dataset_name = "adsl",
condition = !is.na(DTHDT),
set_values_to = exprs(LSTALVDT = DTHDT, DTHFL = "Y")
),
event(
dataset_name = "lb",
condition = !is.na(ADT),
order = exprs(ADT),
mode = "last",
set_values_to = exprs(LSTALVDT = ADT, DTHFL = "N")
),
event(
dataset_name = "adsl",
condition = !is.na(TRTEDT),
order = exprs(TRTEDT),
mode = "last",
set_values_to = exprs(LSTALVDT = TRTEDT, DTHFL = "N")
)
),
source_datasets = list(adsl = adsl, lb = lb),
tmp_event_nr_var = event_nr,
order = exprs(LSTALVDT, event_nr),
mode = "last",
new_vars = exprs(LSTALVDT, DTHFL)
)
#> # A tibble: 5 × 6
#> STUDYID USUBJID TRTEDT DTHDT LSTALVDT DTHFL
#> <chr> <chr> <date> <date> <date> <chr>
#> 1 PILOT01 01-1130 2014-08-16 2014-09-13 2014-09-13 Y
#> 2 PILOT01 01-1133 2013-04-28 NA 2013-05-01 N
#> 3 PILOT01 01-1211 2013-01-12 NA 2013-01-12 N
#> 4 PILOT01 09-1081 2014-04-27 NA 2014-05-10 N
#> 5 PILOT01 09-1088 2014-10-09 2014-11-01 2014-11-01 Y
# Derive DTHCAUS from AE and DS domain data
adsl <- tribble(
~STUDYID, ~USUBJID,
"STUDY01", "PAT01",
"STUDY01", "PAT02",
"STUDY01", "PAT03"
)
ae <- tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"STUDY01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04",
"STUDY01", "PAT01", 13, "CARDIAC ARREST", "FATAL", "2021-04-03",
)
ds <- tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"STUDY01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"STUDY01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"STUDY01", "PAT02", 3, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01",
"STUDY01", "PAT03", 1, "DEATH", "POST STUDY REPORTING OF DEATH", "2022-03-03"
)
derive_vars_extreme_event(
adsl,
by_vars = exprs(STUDYID, USUBJID),
events = list(
event(
dataset_name = "ae",
condition = AEOUT == "FATAL",
set_values_to = exprs(DTHCAUS = AEDECOD, DTHDT = convert_dtc_to_dt(AEDTHDTC)),
order = exprs(DTHDT)
),
event(
dataset_name = "ds",
condition = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
set_values_to = exprs(DTHCAUS = DSTERM, DTHDT = convert_dtc_to_dt(DSSTDTC)),
order = exprs(DTHDT)
)
),
source_datasets = list(ae = ae, ds = ds),
tmp_event_nr_var = event_nr,
order = exprs(DTHDT, event_nr),
mode = "first",
new_vars = exprs(DTHCAUS, DTHDT)
)
#> # A tibble: 3 × 4
#> STUDYID USUBJID DTHCAUS DTHDT
#> <chr> <chr> <chr> <date>
#> 1 STUDY01 PAT01 CARDIAC ARREST 2021-04-03
#> 2 STUDY01 PAT02 DEATH DUE TO PROGRESSION OF DISEASE 2022-02-01
#> 3 STUDY01 PAT03 NA NA