derive_disposition_status: Derive a Disposition Status at a Specific Timepoint

In epijim/admiral: ADaM in R Asset Library

Description

Deprecated, please use derive_var_disposition_status() instead.

Derive a disposition status from the the relevant records in the disposition domain.

Usage

derive_disposition_status(
  dataset,
  dataset_ds,
  new_var,
  status_var,
  format_new_var = format_eoxxstt_default,
  filter_ds,
  subject_keys = vars(STUDYID, USUBJID)
)

Arguments

dataset	Input dataset.
dataset_ds	Dataset containing the disposition information (e.g.: ds). It must contain: STUDYID, USUBJID, The variable(s) specified in the status_var The variables used in filter_ds.
new_var	Name of the disposition status variable. A variable name is expected (e.g. EOSSTT).
status_var	The variable used to derive the disposition status. A variable name is expected (e.g. DSDECOD).
format_new_var	The format used to derive the status. Default: format_eoxxstt_default() defined as: format_eoxxstt_default <- function(x) { case_when( x == "COMPLETED" ~ "COMPLETED", x != "COMPLETED" & !is.na(x) ~ "DISCONTINUED", TRUE ~ "ONGOING" ) } where x is the status_var.
filter_ds	Filter condition for the disposition data. one observation per patient. An error is issued otherwise. Permitted Values: logical expression.
subject_keys	Variables to uniquely identify a subject A list of quosures where the expressions are symbols as returned by vars() is expected.

Value

The input dataset with the disposition status (new_var) added. new_var is derived based on the values given in status_var and according to the format defined by format_new_var (e.g. when the default format is used, the function will derive new_var as: "COMPLETED" if status_var == "COMPLETED", "DISCONTINUED" if status_var is not "COMPLETED" nor NA, "ONGOING" otherwise).

Author(s)

Samia Kabi

Examples

library(dplyr, warn.conflicts = FALSE)
library(admiral.test)
data("dm")
data("ds")

# Default derivation: EOSSTT =
#- COMPLETED when status_var = COMPLETED
#- DISCONTINUED when status_var is not COMPLETED nor NA
#- ONGOING otherwise

dm %>%
  derive_disposition_status(
    dataset_ds = ds,
    new_var = EOSSTT,
    status_var = DSDECOD,
    filter_ds = DSCAT == "DISPOSITION EVENT"
  ) %>%
  select(STUDYID, USUBJID, EOSSTT)

# Specific derivation: EOSSTT =
#- COMPLETED when status_var = COMPLETED
#- DISCONTINUED DUE TO AE when status_var = ADVERSE EVENT
#- DISCONTINUED NOT DUE TO AE when status_var != ADVERSE EVENT nor COMPLETED nor missing
#- ONGOING otherwise

format_eoxxstt1 <- function(x) {
  case_when(
    x == "COMPLETED" ~ "COMPLETED",
    x == "ADVERSE EVENT" ~ "DISCONTINUED DUE TO AE",
    !(x %in% c("ADVERSE EVENT", "COMPLETED")) & !is.na(x) ~ "DISCONTINUED NOT DUE TO AE",
    TRUE ~ "ONGOING"
  )
}

dm %>%
  derive_disposition_status(
    dataset_ds = ds,
    new_var = EOSSTT,
    status_var = DSDECOD,
    format_new_var = format_eoxxstt1,
    filter_ds = DSCAT == "DISPOSITION EVENT"
  ) %>%
  select(STUDYID, USUBJID, EOSSTT)

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