admiral: ADaM in R Asset Library

Description Usage Arguments Details Value Author(s) Examples

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

derive_vars_dt(
  dataset,
  new_vars_prefix,
  dtc,
  date_imputation = NULL,
  flag_imputation = TRUE,
  min_dates = NULL,
  max_dates = NULL,
  preserve = FALSE
)

`dataset`	Input dataset. The date character vector (`dtc`) must be present.
`new_vars_prefix`	Prefix used for the output variable(s). A character is expected: e.g. `new_vars_prefix = "AST"`.
`dtc`	The `'--DTC'` date to impute A character date is expected in a format like `yyyy-mm-dd` or `yyyy-mm-ddThh:mm:ss`. If the year part is not recorded (missing date), no imputation is performed.
`date_imputation`	The value to impute the day/month when a datepart is missing. If `NULL`: no date imputation is performed and partial dates are returned as missing. Otherwise, a character value is expected, either as a format with month and day specified as `"mm-dd"`: e.g. `"06-15"` for the 15th of June, or as a keyword: `"FIRST"`, `"MID"`, `"LAST"` to impute to the first/mid/last day/month. Default is `NULL`.
`flag_imputation`	Whether the date imputation flag should also be derived. A logical value Default: `TRUE`
`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. For example impute_dtc( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), date_imputation = "first" ) 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).
`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.
`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: `FALSE`

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.

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

Samia Kabi

library(lubridate)

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

# Create ASTDT and ASTDTF
# no imputation for partial date
derive_vars_dt(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC
)

# Create ASTDT and ASTDTF
# Impute partial dates to first day/month
derive_vars_dt(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC,
  date_imputation = "FIRST"
)

# Impute partial dates to 6th of April
derive_vars_dt(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC,
  date_imputation = "04-06"
)

# Create AENDT and AENDTF
# Impute partial dates to last day/month
derive_vars_dt(
  mhdt,
  new_vars_prefix = "AEN",
  dtc = MHSTDTC,
  date_imputation = "LAST"
)

# Create BIRTHDT
# Impute partial dates to 15th of June. No DTF
derive_vars_dt(
  mhdt,
  new_vars_prefix = "BIRTH",
  dtc = MHSTDTC,
  date_imputation = "MID",
  flag_imputation = FALSE
)

# Impute AE start date to the first date and ensure that the imputed date
# is not before the treatment start date
adae <- tibble::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",
  date_imputation = "first",
  min_dates = vars(TRTSDTM)
)

# A user imputing dates as middle month/day, i.e. date_imputation = "MID" can
# use preserve argument to "preserve" partial dates.  For example, "2019---07",
# will be displayed as "2019-06-07" rather than 2019-06-15 with preserve = TRUE

derive_vars_dtm(
  mhdt,
  new_vars_prefix = "AST",
  dtc = MHSTDTC,
  date_imputation = "MID",
  preserve = TRUE
)