Derive First or Last Datetime from Multiple Sources
Source:R/derive_var_extreme_date.R
derive_var_extreme_dtm.Rd![[Deprecated]](figures/lifecycle-deprecated.svg)
The derive_var_extreme_dtm()
function has been deprecated in favor of derive_vars_extreme_event().
Add the first or last datetime from multiple sources to the dataset, e.g.,
the last known alive datetime (LSTALVDTM).
Usage
derive_var_extreme_dtm(
dataset,
new_var,
...,
source_datasets,
mode,
subject_keys = get_admiral_option("subject_keys")
)Arguments
- dataset
-
Input dataset
The variables specified by the
subject_keysargument are expected to be in the dataset.- Default value
none
- new_var
-
Name of variable to create
- Default value
none
- ...
-
Source(s) of dates. One or more
date_source()objects are expected.- Default value
none
- source_datasets
-
A named
listcontaining datasets in which to search for the first or last date- Default value
none
- mode
-
Selection mode (first or last)
If
"first"is specified, the first date for each subject is selected. If"last"is specified, the last date for each subject is selected.- Permitted values
"first","last"- Default value
none
- subject_keys
-
Variables to uniquely identify a subject
A list of expressions where the expressions are symbols as returned by
exprs()is expected.- Default value
get_admiral_option("subject_keys")
Details
The following steps are performed to create the output dataset:
For each source dataset the observations as specified by the
filterelement are selected and observations wheredateisNAare removed. Then for each patient the first or last observation (with respect todateandmode) is selected.The new variable is set to the variable or expression specified by the
dateelement. If this is a date variable (rather than datetime), then the time is imputed as"00:00:00".The variables specified by the
set_values_toelement are added.The selected observations of all source datasets are combined into a single dataset.
For each patient the first or last observation (with respect to the new variable and
mode) from the single dataset is selected and the new variable is merged to the input dataset.
See also
date_source(), derive_var_extreme_dt(),
derive_vars_merged()
Other deprecated:
date_source(),
derive_param_extreme_record(),
derive_var_dthcaus(),
derive_var_extreme_dt(),
dthcaus_source(),
get_summary_records()
Examples
library(dplyr, warn.conflicts = FALSE)
library(lubridate)
dm <- tribble(
~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU,
"PILOT01", "DM", "01-1130", 84, "YEARS",
"PILOT01", "DM", "01-1133", 81, "YEARS",
"PILOT01", "DM", "01-1211", 76, "YEARS",
"PILOT01", "DM", "09-1081", 86, "YEARS",
"PILOT01", "DM", "09-1088", 69, "YEARS"
)
ae <- tribble(
~STUDYID, ~DOMAIN, ~USUBJID, ~AESEQ, ~AESTDTC, ~AEENDTC,
"PILOT01", "AE", "01-1130", 5, "2014-05-09", "2014-05-09",
"PILOT01", "AE", "01-1130", 6, "2014-05-22", NA,
"PILOT01", "AE", "01-1130", 4, "2014-05-09", "2014-05-09",
"PILOT01", "AE", "01-1130", 8, "2014-05-22", NA,
"PILOT01", "AE", "01-1130", 7, "2014-05-22", NA,
"PILOT01", "AE", "01-1130", 2, "2014-03-09", "2014-03-09",
"PILOT01", "AE", "01-1130", 1, "2014-03-09", "2014-03-16",
"PILOT01", "AE", "01-1130", 3, "2014-03-09", "2014-03-16",
"PILOT01", "AE", "01-1133", 1, "2012-12-27", NA,
"PILOT01", "AE", "01-1133", 3, "2012-12-27", NA,
"PILOT01", "AE", "01-1133", 2, "2012-12-27", NA,
"PILOT01", "AE", "01-1133", 4, "2012-12-27", NA,
"PILOT01", "AE", "01-1211", 5, "2012-11-29", NA,
"PILOT01", "AE", "01-1211", 1, "2012-11-16", NA,
"PILOT01", "AE", "01-1211", 7, "2013-01-11", NA,
"PILOT01", "AE", "01-1211", 8, "2013-01-11", NA,
"PILOT01", "AE", "01-1211", 4, "2012-11-22", NA,
"PILOT01", "AE", "01-1211", 2, "2012-11-21", "2012-11-21",
"PILOT01", "AE", "01-1211", 3, "2012-11-21", NA,
"PILOT01", "AE", "01-1211", 6, "2012-12-09", NA,
"PILOT01", "AE", "01-1211", 9, "2013-01-14", "2013-01-14",
"PILOT01", "AE", "09-1081", 2, "2014-05-01", NA,
"PILOT01", "AE", "09-1081", 1, "2014-04-07", NA,
"PILOT01", "AE", "09-1088", 1, "2014-05-08", NA,
"PILOT01", "AE", "09-1088", 2, "2014-08-02", NA
)
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, "2013-04-29T10:13",
"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"
)
adsl <- tribble(
~STUDYID, ~USUBJID, ~TRTEDTM,
"PILOT01", "01-1130", "2014-08-16 23:59:59",
"PILOT01", "01-1133", "2013-04-28 23:59:59",
"PILOT01", "01-1211", "2013-01-12 23:59:59",
"PILOT01", "09-1081", "2014-04-27 23:59:59",
"PILOT01", "09-1088", "2014-10-09 23:59:59"
) %>%
mutate(
TRTEDTM = as_datetime(TRTEDTM)
)
# derive last known alive datetime (LSTALVDTM)
ae_start <- date_source(
dataset_name = "ae",
date = convert_dtc_to_dtm(AESTDTC, highest_imputation = "M"),
)
ae_end <- date_source(
dataset_name = "ae",
date = convert_dtc_to_dtm(AEENDTC, highest_imputation = "M"),
)
ae_ext <- ae %>%
derive_vars_dtm(
dtc = AESTDTC,
new_vars_prefix = "AEST",
highest_imputation = "M"
) %>%
derive_vars_dtm(
dtc = AEENDTC,
new_vars_prefix = "AEEN",
highest_imputation = "M"
)
lb_date <- date_source(
dataset_name = "lb",
date = convert_dtc_to_dtm(LBDTC),
)
lb_ext <- derive_vars_dtm(
lb,
dtc = LBDTC,
new_vars_prefix = "LB"
)
adsl_date <- date_source(
dataset_name = "adsl",
date = TRTEDTM
)
dm %>%
derive_var_extreme_dtm(
new_var = LSTALVDTM,
ae_start, ae_end, lb_date, adsl_date,
source_datasets = list(
adsl = adsl,
ae = ae_ext,
lb = lb_ext
),
mode = "last"
) %>%
select(USUBJID, LSTALVDTM)
#> `derive_var_extreme_dtm()` was deprecated in admiral 1.2.0.
#> ℹ Please use `derive_vars_extreme_event()` instead.
#> ✖ This message will turn into a warning at the beginning of 2026.
#> ℹ See admiral's deprecation guidance:
#> https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
#> # A tibble: 5 × 2
#> USUBJID LSTALVDTM
#> <chr> <dttm>
#> 1 01-1130 2014-08-16 23:59:59
#> 2 01-1133 2013-04-29 10:13:00
#> 3 01-1211 2013-01-14 00:00:00
#> 4 09-1081 2014-05-10 11:15:00
#> 5 09-1088 2014-10-09 23:59:59
# derive last alive datetime and traceability variables
ae_start <- date_source(
dataset_name = "ae",
date = convert_dtc_to_dtm(AESTDTC, highest_imputation = "M"),
set_values_to = exprs(
LALVDOM = "AE",
LALVSEQ = AESEQ,
LALVVAR = "AESTDTC"
)
)
ae_end <- date_source(
dataset_name = "ae",
date = convert_dtc_to_dtm(AEENDTC, highest_imputation = "M"),
set_values_to = exprs(
LALVDOM = "AE",
LALVSEQ = AESEQ,
LALVVAR = "AEENDTC"
)
)
lb_date <- date_source(
dataset_name = "lb",
date = convert_dtc_to_dtm(LBDTC),
set_values_to = exprs(
LALVDOM = "LB",
LALVSEQ = LBSEQ,
LALVVAR = "LBDTC"
)
)
adsl_date <- date_source(
dataset_name = "adsl",
date = TRTEDTM,
set_values_to = exprs(
LALVDOM = "ADSL",
LALVSEQ = NA_integer_,
LALVVAR = "TRTEDTM"
)
)
dm %>%
derive_var_extreme_dtm(
new_var = LSTALVDTM,
ae_start, ae_end, lb_date, adsl_date,
source_datasets = list(
adsl = adsl,
ae = ae_ext,
lb = lb_ext
),
mode = "last"
) %>%
select(USUBJID, LSTALVDTM, LALVDOM, LALVSEQ, LALVVAR)
#> # A tibble: 5 × 5
#> USUBJID LSTALVDTM LALVDOM LALVSEQ LALVVAR
#> <chr> <dttm> <chr> <dbl> <chr>
#> 1 01-1130 2014-08-16 23:59:59 ADSL NA TRTEDTM
#> 2 01-1133 2013-04-29 10:13:00 LB 304 LBDTC
#> 3 01-1211 2013-01-14 00:00:00 AE 9 AEENDTC
#> 4 09-1081 2014-05-10 11:15:00 LB 219 LBDTC
#> 5 09-1088 2014-10-09 23:59:59 ADSL NA TRTEDTM