derive_var_dthcaus: Derive Death Cause

In admiral: ADaM in R Asset Library

Derive Death Cause

Description

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

Usage

derive_var_dthcaus(
  dataset,
  ...,
  source_datasets,
  subject_keys = get_admiral_option("subject_keys")
)

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 expressions where the expressions are symbols as returned by exprs() 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.

See Also

dthcaus_source()

ADSL Functions that returns variable appended to dataset: derive_var_age_years(), derive_var_extreme_dtm(), derive_var_extreme_dt(), derive_vars_aage(), derive_vars_period()

Examples

library(tibble)
library(dplyr, warn.conflicts = FALSE)

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"
)

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 `DTHCAUS` only - for on-study deaths only
src_ae <- dthcaus_source(
  dataset_name = "ae",
  filter = AEOUT == "FATAL",
  date = convert_dtc_to_dt(AEDTHDTC),
  mode = "first",
  dthcaus = AEDECOD
)

src_ds <- dthcaus_source(
  dataset_name = "ds",
  filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
  date = convert_dtc_to_dt(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 - for on-study deaths only
src_ae <- dthcaus_source(
  dataset_name = "ae",
  filter = AEOUT == "FATAL",
  date = convert_dtc_to_dt(AEDTHDTC),
  mode = "first",
  dthcaus = AEDECOD,
  set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ)
)

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

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

# Derive `DTHCAUS` as above - now including post-study deaths with different `DTHCAUS` value
src_ae <- dthcaus_source(
  dataset_name = "ae",
  filter = AEOUT == "FATAL",
  date = convert_dtc_to_dt(AEDTHDTC),
  mode = "first",
  dthcaus = AEDECOD,
  set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ)
)

ds <- mutate(
  ds,
  DSSTDT = convert_dtc_to_dt(DSSTDTC)
)

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

src_ds_post <- dthcaus_source(
  dataset_name = "ds",
  filter = DSDECOD == "DEATH" & DSTERM == "POST STUDY REPORTING OF DEATH",
  date = DSSTDT,
  mode = "first",
  dthcaus = "POST STUDY: UNKNOWN CAUSE",
  set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ)
)

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

admiral documentation built on Oct. 19, 2023, 1:08 a.m.