R/check_ae_fatal.R
check_ae_fatal.RdThis 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.
check_ae_fatal(AE, preproc = identity, ...)Adverse Events SDTM dataset with variables USUBJID, AEDECOD, AESTDTC, AEDTHDTC, AEOUT, AESDTH
An optional company specific preprocessing script
Other arguments passed to methods
boolean value if check failed or passed with 'msg' attribute if the test failed
# 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)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 4 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AETOXGR
#> 1 2 01JAN2017 AE2 FATAL <NA> Y 5
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N 5
#> 3 4 01JAN2017 AE4 FATAL 03FEB2017 Y <NA>
#> 4 5 01JAN2017 AE5 FATAL <NA> <NA> <NA>
check_ae_fatal(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 4 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AETOXGR RAVE
#> 1 2 01JAN2017 AE2 FATAL <NA> Y 5 FORMNAME-R:12
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N 5 FORMNAME-R:12
#> 3 4 01JAN2017 AE4 FATAL 03FEB2017 Y <NA> FORMNAME-R:12
#> 4 5 01JAN2017 AE5 FATAL <NA> <NA> <NA> FORMNAME-R:12
AE$AETOXGR <- NULL
check_ae_fatal(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH
#> 1 2 01JAN2017 AE2 FATAL <NA> Y
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N
#> 3 5 01JAN2017 AE5 FATAL <NA> <NA>
AE$AEDECOD <- NULL
check_ae_fatal(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE is missing the variable: AEDECOD"
# 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)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV
#> 1 2 01JAN2017 AE2 FATAL 02FEB2017 Y MILD
#> 2 3 01JAN2017 AE3 FATAL 03FEB2017 N SEVERE
#> 3 5 01JAN2017 AE5 FATAL <NA> <NA> <NA>
check_ae_fatal(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV RAVE
#> 1 2 01JAN2017 AE2 FATAL 02FEB2017 Y MILD FORMNAME-R:12
#> 2 3 01JAN2017 AE3 FATAL 03FEB2017 N SEVERE FORMNAME-R:12
#> 3 5 01JAN2017 AE5 FATAL <NA> <NA> <NA> FORMNAME-R:12
AE$AESEV <- NULL
check_ae_fatal(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH
#> 1 3 01JAN2017 AE3 FATAL 03FEB2017 N
#> 2 5 01JAN2017 AE5 FATAL <NA> <NA>
# 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)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 5 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV AETOXGR
#> 1 2 01JAN2017 AE2 FATAL <NA> Y MILD 5
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N SEVERE 5
#> 3 4 01JAN2017 AE4 FATAL 03FEB2017 Y <NA> <NA>
#> 4 5 01JAN2017 AE5 FATAL <NA> <NA> <NA> <NA>
#> 5 6 01JAN2017 AE6 FATAL 04FEB2017 Y MILD 1
check_ae_fatal(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 5 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV AETOXGR RAVE
#> 1 2 01JAN2017 AE2 FATAL <NA> Y MILD 5 FORMNAME-R:12
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N SEVERE 5 FORMNAME-R:12
#> 3 4 01JAN2017 AE4 FATAL 03FEB2017 Y <NA> <NA> FORMNAME-R:12
#> 4 5 01JAN2017 AE5 FATAL <NA> <NA> <NA> <NA> FORMNAME-R:12
#> 5 6 01JAN2017 AE6 FATAL 04FEB2017 Y MILD 1 FORMNAME-R:12
# 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)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH
#> 1 2 01JAN2017 AE2 FATAL <NA> Y
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N
#> 3 5 01JAN2017 AE5 FATAL <NA> <NA>
# 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)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 4 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV AETOXGR
#> 1 2 01JAN2017 AE2 FATAL <NA> Y NA 5
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N NA 5
#> 3 4 01JAN2017 AE4 FATAL 03FEB2017 Y NA <NA>
#> 4 5 01JAN2017 AE5 FATAL <NA> <NA> NA <NA>
check_ae_fatal(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 4 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV AETOXGR RAVE
#> 1 2 01JAN2017 AE2 FATAL <NA> Y NA 5 FORMNAME-R:12
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N NA 5 FORMNAME-R:12
#> 3 4 01JAN2017 AE4 FATAL 03FEB2017 Y NA <NA> FORMNAME-R:12
#> 4 5 01JAN2017 AE5 FATAL <NA> <NA> NA <NA> FORMNAME-R:12
# 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)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV AETOXGR
#> 1 2 01JAN2017 AE2 FATAL <NA> Y NA NA
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N NA NA
#> 3 5 01JAN2017 AE5 FATAL <NA> <NA> NA NA
check_ae_fatal(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 patient(s) with AE death variable inconsistencies when outcome marked FATAL. "
#> attr(,"data")
#> USUBJID AESTDTC AEDECOD AEOUT AEDTHDTC AESDTH AESEV AETOXGR RAVE
#> 1 2 01JAN2017 AE2 FATAL <NA> Y NA NA FORMNAME-R:12
#> 2 3 01JAN2017 AE3 FATAL 02FEB2017 N NA NA FORMNAME-R:12
#> 3 5 01JAN2017 AE5 FATAL <NA> <NA> NA NA FORMNAME-R:12