derive_var_dthcaus: Derive Death Cause

In epijim/admiral: ADaM in R Asset Library

Description

Derive death cause (DTHCAUS) and add traceability variables if required.

Usage

derive_var_dthcaus(
  dataset,
  ...,
  source_datasets,
  subject_keys = vars(STUDYID, USUBJID)
)

Arguments

dataset	Input dataset. The variables specified by subject_keys are required.
...	Objects of class "dthcaus_source" created by dthcaus_source().
source_datasets	A named list containing datasets in which to search for the death cause
subject_keys	Variables to uniquely identify a subject A list of quosures where the expressions are symbols as returned by vars() is expected.

Details

This function derives DTHCAUS along with the user-defined traceability variables, if required. If a subject has death info from multiple sources, the one from the source with the earliest death date will be used. If dates are equivalent, the first source will be kept, so the user should provide the inputs in the preferred order.

Value

The input dataset with DTHCAUS variable added.

Author(s)

Shimeng Huang, Samia Kabi, Thomas Neitmann

See Also

dthcaus_source()

Examples

adsl <- tibble::tribble(
  ~STUDYID, ~USUBJID,
  "STUDY01", "PAT01",
  "STUDY01", "PAT02"
)
ae <- tibble::tribble(
  ~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
  "STUDY01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
)
ds <- tibble::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"
)

# Derive `DTHCAUS` only
src_ae <- dthcaus_source(
  dataset_name = "ae",
  filter = AEOUT == "FATAL",
  date = AEDTHDTC,
  mode = "first",
  dthcaus = AEDECOD
)

src_ds <- dthcaus_source(
  dataset_name = "ds",
  filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
  date = DSSTDTC,
  mode = "first",
  dthcaus = DSTERM
)

derive_var_dthcaus(adsl, src_ae, src_ds, source_datasets = list(ae = ae, ds = ds))

# Derive `DTHCAUS` and add traceability variables
src_ae <- dthcaus_source(
  dataset_name = "ae",
  filter = AEOUT == "FATAL",
  date = AEDTHDTC,
  mode = "first",
  dthcaus = AEDECOD,
  traceability_vars = vars(DTHDOM = "AE", DTHSEQ = AESEQ)
)

src_ds <- dthcaus_source(
  dataset_name = "ds",
  filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
  date = DSSTDTC,
  mode = "first",
  dthcaus = DSTERM,
  traceability_vars = vars(DTHDOM = "DS", DTHSEQ = DSSEQ)
)

derive_var_dthcaus(adsl, src_ae, src_ds, source_datasets = list(ae = ae, ds = ds))

epijim/admiral documentation built on Feb. 13, 2022, 12:15 a.m.