R/tte_sources.R

In Roche-GSK/admiral: ADaM in R Asset Library

#' Pre-Defined Time-to-Event Source Objects
#'
#' These pre-defined `tte_source` objects can be used as input to [derive_param_tte()].
#'
#' @details
#' To see the definition of the various objects simply print the object in the
#' R console, e.g. `print(death_event)`. For details of how to use these objects
#' please refer to [derive_param_tte()].
#'
#' @seealso [derive_param_tte()], [tte_source()], [event_source()], [censor_source()]
#'
#' @format NULL
#'
#' @export
#'
#' @family source_specifications
#' @keywords source_specifications
#'
#' @rdname tte_source_objects
#'
#' @examples
#' # This shows the definition of all pre-defined `tte_source` objects that ship
#' # with {admiral}
#' for (obj in list_tte_source_objects()$object) {
#'   cat(obj, "\n")
#'   print(get(obj))
#'   cat("\n")
#' }
death_event <- event_source(
  dataset_name = "adsl",
  filter = DTHFL == "Y",
  date = DTHDT,
  set_values_to = exprs(
    EVNTDESC = "DEATH",
    SRCDOM = "ADSL",
    SRCVAR = "DTHDT"
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
lastalive_censor <- censor_source(
  dataset_name = "adsl",
  date = LSTALVDT,
  set_values_to = exprs(
    EVNTDESC = "ALIVE",
    SRCDOM = "ADSL",
    SRCVAR = "LSTALVDT"
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_ser_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & AESER == "Y",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "SERIOUS ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_gr1_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & ATOXGR == "1",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "GRADE 1 ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_gr2_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & ATOXGR == "2",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "GRADE 2 ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_gr3_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & ATOXGR == "3",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "GRADE 3 ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_gr4_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & ATOXGR == "4",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "GRADE 4 ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_gr5_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & ATOXGR == "5",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "GRADE 5 ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_gr35_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & ATOXGR %in% c("3", "4", "5"),
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "GRADE 3-5 ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_sev_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & AESEV == "SEVERE",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "SEVERE ADVERSE EVENT",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)

#' @keywords source_specifications
#' @rdname tte_source_objects
#' @format NULL
#' @export
ae_wd_event <- event_source(
  dataset_name = "adae",
  filter = TRTEMFL == "Y" & AEACN == "DRUG WITHDRAWN",
  date = ASTDT,
  set_values_to = exprs(
    EVNTDESC = "ADVERSE EVENT LEADING TO DRUG WITHDRAWAL",
    SRCDOM = "ADAE",
    SRCVAR = "ASTDT",
    SRCSEQ = AESEQ
  )
)