Derive/Impute a Date from a Character Date

Derive a date (*DT) from a character date (--DTC). The date can be imputed (see date_imputation argument) and the date imputation flag (*DTF) can be added.

Usage

derive_vars_dt(
  dataset,
  new_vars_prefix,
  dtc,
  highest_imputation = "n",
  date_imputation = "first",
  flag_imputation = "auto",
  min_dates = NULL,
  max_dates = NULL,
  preserve = FALSE
)

Arguments

dataset

Input dataset

The variables specified by the dtc argument are expected to be in the dataset.

Permitted values: a dataset, i.e., a data.frame or tibble
Default value: none

new_vars_prefix

Prefix used for the output variable(s).

A character scalar is expected. For the date variable (*DT) is appended to the specified prefix and for the date imputation flag (*DTF), i.e., for new_vars_prefix = "AST" the variables ASTDT and ASTDTF are created.

Permitted values: a character scalar, i.e., a character vector of length one
Default value: none

dtc

The --DTC date to impute

A character date is expected in a format like yyyy-mm-dd or yyyy-mm-ddThh:mm:ss. Trailing components can be omitted and - is a valid "missing" value for any component.

Permitted values: a character date variable
Default value: none

highest_imputation

Highest imputation level

The highest_imputation argument controls which components of the --DTC value are imputed if they are missing. All components up to the specified level are imputed.

If a component at a higher level than the highest imputation level is missing, NA_character_ is returned. For example, for highest_imputation = "D" "2020" results in NA_character_ because the month is missing.

If "n" is specified no imputation is performed, i.e., if any component is missing, NA_character_ is returned.

If "Y" is specified, date_imputation must be "first" or "last" and min_dates or max_dates must be specified respectively. Otherwise, an error is thrown.

Permitted values: "Y" (year, highest level), "M" (month), "D" (day), "n" (none, lowest level)
Default value: "n"

date_imputation

The value to impute the day/month when a datepart is missing.

A character value is expected.

If highest_imputation is "M", month and day can be specified as "mm-dd": e.g. "06-15" for the 15th of June
When highest_imputation is "M" or "D", the following keywords are available: "first", "mid", "last" to impute to the first/mid/last day/month. If "mid" is specified, missing components are imputed as the middle of the possible range:
- If both month and day are missing, they are imputed as "06-30" (middle of the year).
- If only day is missing, it is imputed as "15" (middle of the month).

The year can not be specified; for imputing the year "first" or "last" together with min_dates or max_dates argument can be used (see examples).

Permitted values: "first", "mid", "last", or user-defined
Default value: "first"

flag_imputation

Whether the date imputation flag must also be derived.

If "auto" is specified and highest_imputation argument is not "n", then date imputation flag is derived.

If "date" is specified, then date imputation flag is derived.

If "none" is specified, then no date imputation flag is derived.

Please note that CDISC requirements dictate the need for a date imputation flag if any imputation is performed, so flag_imputation = "none" should only be used if the imputed variable is not part of the final ADaM dataset.

Permitted values: "auto", "date" or "none"
Default value: "auto"

min_dates

Minimum dates

A list of dates is expected. It is ensured that the imputed date is not before any of the specified dates, e.g., that the imputed adverse event start date is not before the first treatment date. Only dates which are in the range of possible dates of the dtc value are considered. The possible dates are defined by the missing parts of the dtc date (see example below). This ensures that the non-missing parts of the dtc date are not changed. A date or date-time object is expected. For example

impute_dtc_dtm(
  "2020-11",
  min_dates = list(
   ymd_hms("2020-12-06T12:12:12"),
   ymd_hms("2020-11-11T11:11:11")
  ),
  highest_imputation = "M"
)

returns "2020-11-11T11:11:11" because the possible dates for "2020-11" range from "2020-11-01T00:00:00" to "2020-11-30T23:59:59". Therefore "2020-12-06T12:12:12" is ignored. Returning "2020-12-06T12:12:12" would have changed the month although it is not missing (in the dtc date).

Permitted values: a list of dates, e.g. list(ymd_hms("2021-07-01T04:03:01"), ymd_hms("2022-05-12T13:57:23"))
Default value: NULL

max_dates

Maximum dates

A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected.

Permitted values: a list of dates, e.g. list(ymd_hms("2021-07-01T04:03:01"), ymd_hms("2022-05-12T13:57:23"))
Default value: NULL

preserve

Preserve day if month is missing and day is present

For example "2019---07" would return "2019-06-07 if preserve = TRUE (and date_imputation = "MID").

Permitted values: "TRUE", "FALSE"
Default value: FALSE

Value

The input dataset with the date *DT (and the date imputation flag *DTF if requested) added.

Details

In {admiral} we don't allow users to pick any single part of the date/time to impute, we only enable to impute up to a highest level, i.e. you couldn't choose to say impute months, but not days.

The presence of a *DTF variable is checked and if it already exists in the input dataset, a warning is issued and *DTF will be overwritten.

Examples

Derive a date variable without imputation

In this example, we derive ASTDT from MHSTDTC with no imputation done for partial dates.

library(tibble)
library(lubridate)

mhdt <- tribble(
  ~MHSTDTC,
  "2019-07-18T15:25:40",
  "2019-07-18T15:25",
  "2019-07-18",
  "2019-02",
  "2019",
  "2019---07",
  ""
)

derive_vars_dt(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC
)
#> # A tibble: 7 × 2
#>   MHSTDTC               ASTDT
#>   <chr>                 <date>
#> 1 "2019-07-18T15:25:40" 2019-07-18
#> 2 "2019-07-18T15:25"    2019-07-18
#> 3 "2019-07-18"          2019-07-18
#> 4 "2019-02"             NA
#> 5 "2019"                NA
#> 6 "2019---07"           NA
#> 7 ""                    NA

Impute partial dates (`highest_imputation`)

Imputation is requested by the highest_imputation argument. Here highest_imputation = "M" for month imputation is used, i.e. the highest imputation done on a partial date is up to the month. By default, missing date components are imputed to the first day/month/year. A date imputation flag variable, ASTDTF, is automatically created. The flag variable indicates if imputation was done on the date.

derive_vars_dt(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC,
  highest_imputation = "M",
  date_imputation = "first"
)
#> # A tibble: 7 × 3
#>   MHSTDTC               ASTDT      ASTDTF
#>   <chr>                 <date>     <chr>
#> 1 "2019-07-18T15:25:40" 2019-07-18 <NA>
#> 2 "2019-07-18T15:25"    2019-07-18 <NA>
#> 3 "2019-07-18"          2019-07-18 <NA>
#> 4 "2019-02"             2019-02-01 D
#> 5 "2019"                2019-01-01 M
#> 6 "2019---07"           2019-01-01 M
#> 7 ""                    NA         <NA>

Impute to the last day/month (`date_imputation = "last"`)

In this example, we derive ADT impute partial dates to last day/month, i.e. date_imputation = "last".

qsdt <- tribble(
  ~QSDTC,
  "2019-07-18T15:25:40",
  "2019-07-18T15:25",
  "2019-07-18",
  "2019-02",
  "2019",
  "2019---07",
  ""
)

derive_vars_dt(
  qsdt,
  new_vars_prefix = "A",
  dtc = QSDTC,
  highest_imputation = "M",
  date_imputation = "last"
)
#> # A tibble: 7 × 3
#>   QSDTC                 ADT        ADTF
#>   <chr>                 <date>     <chr>
#> 1 "2019-07-18T15:25:40" 2019-07-18 <NA>
#> 2 "2019-07-18T15:25"    2019-07-18 <NA>
#> 3 "2019-07-18"          2019-07-18 <NA>
#> 4 "2019-02"             2019-02-28 D
#> 5 "2019"                2019-12-31 M
#> 6 "2019---07"           2019-12-31 M
#> 7 ""                    NA         <NA>

Impute to the middle (`date_imputaton = "mid"`) and suppress imputation flag (`flag_imputation = "none"`)

In this example, we will derive TRTSDT with date imputation flag (*DTF) suppressed. Since date_imputation = "mid", partial date imputation will be set to June 30th for missing month and 15th for missing day only. The flag_imputation = "none" call ensures no date imputation flag is created. In practice, as per CDISC requirements this option can only be selected if the imputed variable is not part of the final ADaM dataset.


exdt <- tribble(
  ~EXSTDTC,
  "2019-07-18T15:25:40",
  "2019-07-18T15:25",
  "2019-07-18",
  "2019-02",
  "2019",
  "2019---07",
  ""
)
derive_vars_dt(
  exdt,
  new_vars_prefix = "TRTS",
  dtc = EXSTDTC,
  highest_imputation = "M",
  date_imputation = "mid",
  flag_imputation = "none"
)
#> # A tibble: 7 × 2
#>   EXSTDTC               TRTSDT
#>   <chr>                 <date>
#> 1 "2019-07-18T15:25:40" 2019-07-18
#> 2 "2019-07-18T15:25"    2019-07-18
#> 3 "2019-07-18"          2019-07-18
#> 4 "2019-02"             2019-02-15
#> 5 "2019"                2019-06-30
#> 6 "2019---07"           2019-06-30
#> 7 ""                    NA

Impute to a specific date (`date_imputation = "04-06"`)

In this example, we derive ASTDT with specific date imputation, i.e. date_imputation = "04-06". Note that day portion, "-06", is used in the imputation of the record with "2019-02".

derive_vars_dt(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC,
  highest_imputation = "M",
  date_imputation = "04-06"
)
#> # A tibble: 7 × 3
#>   MHSTDTC               ASTDT      ASTDTF
#>   <chr>                 <date>     <chr>
#> 1 "2019-07-18T15:25:40" 2019-07-18 <NA>
#> 2 "2019-07-18T15:25"    2019-07-18 <NA>
#> 3 "2019-07-18"          2019-07-18 <NA>
#> 4 "2019-02"             2019-02-06 D
#> 5 "2019"                2019-04-06 M
#> 6 "2019---07"           2019-04-06 M
#> 7 ""                    NA         <NA>

Avoid imputation before a user-defined date (`min_dates`)

In this example, we derive ASTDT where AESTDTC is all partial dates in need of imputation. Using min_dates = exprs(TRTSDTM), we are telling the function to not allow imputation dates to be before the treatment start date via min_dates argument. Note that the second record does not get imputed as it is before TRTSDTM.

adae <- tribble(
  ~AESTDTC, ~TRTSDTM,
  "2020-12", ymd_hms("2020-12-06T12:12:12"),
  "2020-11", ymd_hms("2020-12-06T12:12:12")
)

derive_vars_dt(
  adae,
  dtc = AESTDTC,
  new_vars_prefix = "AST",
  highest_imputation = "M",
  min_dates = exprs(TRTSDTM)
)
#> # A tibble: 2 × 4
#>   AESTDTC TRTSDTM             ASTDT      ASTDTF
#>   <chr>   <dttm>              <date>     <chr>
#> 1 2020-12 2020-12-06 12:12:12 2020-12-06 D
#> 2 2020-11 2020-12-06 12:12:12 2020-11-01 D

Preserve lower components if higher ones were imputed (`preserve`)

The preserve argument can be used to "preserve" information from the partial dates. For example, "2019---07", will be displayed as "2019-06-07" rather than "2019-06-30" with preserve = TRUE and date_imputation = "mid" .

derive_vars_dt(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC,
  highest_imputation = "M",
  date_imputation = "mid",
  preserve = TRUE
)
#> # A tibble: 7 × 3
#>   MHSTDTC               ASTDT      ASTDTF
#>   <chr>                 <date>     <chr>
#> 1 "2019-07-18T15:25:40" 2019-07-18 <NA>
#> 2 "2019-07-18T15:25"    2019-07-18 <NA>
#> 3 "2019-07-18"          2019-07-18 <NA>
#> 4 "2019-02"             2019-02-15 D
#> 5 "2019"                2019-06-30 M
#> 6 "2019---07"           2019-06-07 M
#> 7 ""                    NA         <NA>

Further examples

Further example usages of this function can be found in the Date and Time Imputation vignette.

Usage

Arguments

Value

Details

See also

Examples

Derive a date variable without imputation

Impute partial dates (highest_imputation)

Impute to the last day/month (date_imputation = "last")

Impute to the middle (date_imputaton = "mid") and suppress imputation flag (flag_imputation = "none")

Impute to a specific date (date_imputation = "04-06")

Avoid imputation before a user-defined date (min_dates)

Preserve lower components if higher ones were imputed (preserve)