Check for AE outcome (AEOUT) of 'FATAL' with non-missing resolution date that is not equal to the death date

This check looks for AEs with outcome of 'FATAL' but AE resolution date is not equal to AE death date. Note that these datapoints are not collected the same way for all trials - some trials leave AEENDTC missing if it was unresolved at death date. Confirm within your team before querying this issue.

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

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AETERM, AEDTHDTC, AEENDTC, 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

Sara Bodach, Stella Banjo(HackR 2021)

Examples

AE <- data.frame(
    USUBJID = 1:10,
    DOMAIN = "AE",
    AEDTHDTC = c(NA, "NA", rep("2015-03-12",4), NA, NA, "2020-01-01", ""),
    AEENDTC = c(NA, "NA", rep("2015-03-12",4), NA, "2020-01-01", NA, ""),
    AEOUT = c("", "", "","FATAL","RECOVERED/RESOLVED", rep("FATAL",5)),
    AETERM = 1:10,
    AESPID = "FORMNAME-R:13/L:13XXXX",
    stringsAsFactors = FALSE
)

check_ae_aeout_aeendtc_aedthdtc(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "3 AE(s) with AEOUT = 'FATAL' but AEDTHDTC and AEENDTC inconsistent. "
#> attr(,"data")
#>   USUBJID AETERM AEENDTC   AEDTHDTC AEOUT                          NOTE
#> 1       7      7    <NA>       <NA> FATAL **QUERY ONLY IF TEAM AGREES**
#> 2       9      9    <NA> 2020-01-01 FATAL **QUERY ONLY IF TEAM AGREES**
#> 3      10     10                    FATAL **QUERY ONLY IF TEAM AGREES**
check_ae_aeout_aeendtc_aedthdtc(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "3 AE(s) with AEOUT = 'FATAL' but AEDTHDTC and AEENDTC inconsistent. "
#> attr(,"data")
#>   USUBJID AETERM AEENDTC   AEDTHDTC AEOUT          RAVE
#> 1       7      7    <NA>       <NA> FATAL FORMNAME-R:13
#> 2       9      9    <NA> 2020-01-01 FATAL FORMNAME-R:13
#> 3      10     10                    FATAL FORMNAME-R:13
#>                            NOTE
#> 1 **QUERY ONLY IF TEAM AGREES**
#> 2 **QUERY ONLY IF TEAM AGREES**
#> 3 **QUERY ONLY IF TEAM AGREES**

AE$AESPID <- NULL
check_ae_aeout_aeendtc_aedthdtc(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "3 AE(s) with AEOUT = 'FATAL' but AEDTHDTC and AEENDTC inconsistent. "
#> attr(,"data")
#>   USUBJID AETERM AEENDTC   AEDTHDTC AEOUT                          NOTE
#> 1       7      7    <NA>       <NA> FATAL **QUERY ONLY IF TEAM AGREES**
#> 2       9      9    <NA> 2020-01-01 FATAL **QUERY ONLY IF TEAM AGREES**
#> 3      10     10                    FATAL **QUERY ONLY IF TEAM AGREES**

AE$AEDTHDTC <- NULL
AE$AEOUT <- NULL
check_ae_aeout_aeendtc_aedthdtc(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE is missing the variables: AEDTHDTC, AEOUT"