sdtmchecks (version 1.0.0)

check_dd_ae_aeout_aedthdtc: Check if there is a death date and AEOUT='FATAL' agreement

Description

This check looks for AE death dates if AEOUT='FATAL' and for the reverse, i.e if there is an AE death date, then AEOUT should have the value "FATAL".

Usage

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

Value

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

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AEDTHDTC, AEDECOD, AESTDTC and AEOUT

preproc

An optional company specific preprocessing script

...

Other arguments passed to methods

Author

Joel Laxamana

Examples

AE <- data.frame(
 USUBJID = 1:3,
 AEDTHDTC = c("2020-01-01","2020-01-02","2020-01-03"),
 AEDECOD = 1:3,
 AESTDTC = 1:3,
 AEOUT = rep("FATAL", 3),
 AESPID = "FORMNAME-R:19/L:19XXXX",
 stringsAsFactors = FALSE
)

# pass
check_dd_ae_aeout_aedthdtc(AE)

# fail - 1 case (AEDTHDTC not populated but AEOUT == FATAL)
AE1 <- AE
AE1[3, "AEDTHDTC"] <- NA
check_dd_ae_aeout_aedthdtc(AE1)
check_dd_ae_aeout_aedthdtc(AE1,preproc=roche_derive_rave_row)

# pass -- even though AEDTHDTC populated 
AE2 <- AE
AE2[1, "AEOUT"] <- NA
check_dd_ae_aeout_aedthdtc(AE2)
check_dd_ae_aeout_aedthdtc(AE2,preproc=roche_derive_rave_row)

# 2 cases 
AE[3, "AEDTHDTC"] <- NA
AE[1, "AEOUT"] <- NA
check_dd_ae_aeout_aedthdtc(AE)
check_dd_ae_aeout_aedthdtc(AE,preproc=roche_derive_rave_row)

# 2 cases 
AE[1, "AEOUT"] <- 'NOT RECOVERED/NOT RESOLVED'
check_dd_ae_aeout_aedthdtc(AE)
check_dd_ae_aeout_aedthdtc(AE,preproc=roche_derive_rave_row)

# non-critical variable missing
AE$AESPID <- NULL
check_dd_ae_aeout_aedthdtc(AE)
check_dd_ae_aeout_aedthdtc(AE,preproc=roche_derive_rave_row)

# critical variables are missing
AE$AEDTHDTC <- NULL
AE$USUBJID <- NULL
check_dd_ae_aeout_aedthdtc(AE)
check_dd_ae_aeout_aedthdtc(AE,preproc=roche_derive_rave_row)