check_ae_fatal: Check for death variable consistency when AEOUT=="FATAL"

In sdtmchecks: Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets

Check for death variable consistency when AEOUT=="FATAL"

Description

This check looks for consistency in AESDTH, AEDTHDTC, and AETOXGR (if applicable) when AEOUT is 'FATAL'. Note, this check expects AE grade/severity variables to be populated for either all records or none. In a case where both AETOXGR and AESEV exist and some records are supposed to have AETOXGR populated while others have AESEV (ie the two variables are mutually exclusive) then this check will likely return false positives.

Usage

check_ae_fatal(AE, preproc = identity, ...)

Arguments

AE	Adverse Events SDTM dataset with variables USUBJID, AEDECOD, AESTDTC, AEDTHDTC, AEOUT, AESDTH
preproc	An optional company specific preprocessing script
...	Other arguments passed to methods

Value

boolean value if check failed or passed with 'msg' attribute if the test failed

Author(s)

Aldrich Salva

Examples

# AETOXGR, no AESEV

AE <- data.frame(
 USUBJID = 1:5,
 AESTDTC = "01JAN2017",
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5"),
 AEOUT = "FATAL",
 AEDTHDTC = c("01FEB2017",NA,"02FEB2017","03FEB2017",NA),
 AESDTH = c("Y","Y","N","Y",NA),
 AETOXGR = c("5","5","5",NA,NA),
 AESPID = "FORMNAME-R:12/L:2XXXX",
 stringsAsFactors = FALSE
)

check_ae_fatal(AE)
check_ae_fatal(AE,preproc=roche_derive_rave_row)

AE$AETOXGR <- NULL
check_ae_fatal(AE)

AE$AEDECOD <- NULL
check_ae_fatal(AE)


# AESEV, no AETOXGR

 AE <- data.frame(
 USUBJID = 1:5,
 AESTDTC = "01JAN2017",
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5"),
 AEOUT = "FATAL",
 AEDTHDTC = c("01FEB2017","02FEB2017","03FEB2017","04FEB2017",NA),
 AESDTH = c("Y","Y","N","Y",NA),
 AESEV = c("SEVERE","MILD","SEVERE",NA,NA),
 AESPID = "FORMNAME-R:12/L:2XXXX",
 stringsAsFactors = FALSE
)

check_ae_fatal(AE)
check_ae_fatal(AE,preproc=roche_derive_rave_row)

AE$AESEV <- NULL
check_ae_fatal(AE)

# Both AESEV and AETOXGR have non-missing values

AE <- data.frame(
 USUBJID = 1:7,
 AESTDTC = "01JAN2017",
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5","AE6","AE7"),
 AEOUT = "FATAL",
 AEDTHDTC = c("01FEB2017",NA,"02FEB2017","03FEB2017",NA,"04FEB2017","05FEB2017"),
 AESDTH = c("Y","Y","N","Y",NA,"Y","Y"),
 AESEV = c("SEVERE","MILD","SEVERE",NA,NA,"MILD","SEVERE"),
 AETOXGR = c("5","5","5",NA,NA,"1","5"),
 AESPID = "FORMNAME-R:12/L:2XXXX",
 stringsAsFactors = FALSE
)

check_ae_fatal(AE)
check_ae_fatal(AE,preproc=roche_derive_rave_row)


# Neither AESEV or AETOXGR

AE <- data.frame(
 USUBJID = 1:5,
 AESTDTC = "01JAN2017",
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5"),
 AEOUT = "FATAL",
 AEDTHDTC = c("01FEB2017",NA,"02FEB2017","03FEB2017",NA),
 AESDTH = c("Y","Y","N","Y",NA),
 AESPID = "FORMNAME-R:12/L:2XXXX",
 stringsAsFactors = FALSE
)

check_ae_fatal(AE)

# AETOXGR exists but unmapped AESEV

 AE <- data.frame(
 USUBJID = 1:5,
 AESTDTC = "01JAN2017",
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5"),
 AEOUT = "FATAL",
 AEDTHDTC = c("01FEB2017",NA,"02FEB2017","03FEB2017",NA),
 AESDTH = c("Y","Y","N","Y",NA),
 AESEV = rep(NA,5),
 AETOXGR = c("5","5","5",NA,NA),
 AESPID = "FORMNAME-R:12/L:2XXXX",
 stringsAsFactors = FALSE
)

check_ae_fatal(AE)
check_ae_fatal(AE,preproc=roche_derive_rave_row)

# AETOXGR and AESEV exist, by both are unmapped

 AE <- data.frame(
 USUBJID = 1:5,
 AESTDTC = "01JAN2017",
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5"),
 AEOUT = "FATAL",
 AEDTHDTC = c("01FEB2017",NA,"02FEB2017","03FEB2017",NA),
 AESDTH = c("Y","Y","N","Y",NA),
 AESEV = NA,
 AETOXGR = NA,
 AESPID = "FORMNAME-R:12/L:2XXXX",
 stringsAsFactors = FALSE
)

check_ae_fatal(AE)
check_ae_fatal(AE,preproc=roche_derive_rave_row)

sdtmchecks documentation built on Sept. 11, 2024, 9:34 p.m.