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

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

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

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

Value

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

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
)

# no case
check_dd_ae_aeout_aedthdtc(AE)
#> [1] TRUE

# 2 cases
AE[3, "AEDTHDTC"] <- NA
AE[1, "AEOUT"] <- NA
check_dd_ae_aeout_aedthdtc(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 1 patients with a discrepant AE outcome and death date. "
#> attr(,"data")
#>   USUBJID AEDECOD AESTDTC AEDTHDTC AEOUT
#> 3       3       3       3     <NA> FATAL
check_dd_ae_aeout_aedthdtc(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 1 patients with a discrepant AE outcome and death date. "
#> attr(,"data")
#>   USUBJID AEDECOD AESTDTC AEDTHDTC AEOUT          RAVE
#> 3       3       3       3     <NA> FATAL FORMNAME-R:19

# check for non existence of vars
AE$AEDTHDTC <- NULL
AE$USUBJID <- NULL
check_dd_ae_aeout_aedthdtc(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE is missing the variables: USUBJID, AEDTHDTC"