Check AEs with AESDTH of "Y" but No AEDTHDTC Value

Source: R/check_ae_aesdth_aedthdtc.R

This check looks for AE entries with AESDTH of "Y" but no AEDTHDTC (death date) value

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

Arguments

AE

Adverse Event SDTM dataset with variables USUBJID, AEDTHDTC, AESDTH, AETERM, AEDECOD and AESTDTC

preproc

An optional company specific preprocessing script

...

Other arguments passed to methods

Value

Boolean value for whether the check passed or failed, with 'msg' attribute if the check failed

Author

Shumei Chi

Examples



AE <- data.frame(
USUBJID = c(1:7), 
AEDECOD = c(letters[1:5], "", NA), 
AETERM = letters[1:7],
AESDTH = c(NA, rep("", 4), "Y", "Y"),
AEDTHDTC = c(1:5, "2020", "2020-01-02"),
AESTDTC = c(1:7),
AESPID = "FORMNAME-R:5/L:5XXXX",
stringsAsFactors=FALSE)

# expect pass
check_ae_aesdth_aedthdtc(AE)
#> [1] TRUE
check_ae_aesdth_aedthdtc(AE,preproc=roche_derive_rave_row)
#> [1] TRUE

# expect fail 
AE1 <- AE
AE1$AEDTHDTC[3] <- NA
AE1$AESDTH[3] <- "Y"

check_ae_aesdth_aedthdtc(AE1)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 1 record(s) with AESDTH equal to 'Y' where AEDTHDTC does not have a value. "
#> attr(,"data")
#>   USUBJID AETERM AEDECOD AESTDTC AESDTH AEDTHDTC
#> 1       3      c       c       3      Y     <NA>
check_ae_aesdth_aedthdtc(AE1,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 1 record(s) with AESDTH equal to 'Y' where AEDTHDTC does not have a value. "
#> attr(,"data")
#>   USUBJID AETERM AEDECOD AESTDTC AESDTH AEDTHDTC         RAVE
#> 1       3      c       c       3      Y     <NA> FORMNAME-R:5

# expect fail 
AE2 <- AE1
AE2$AEDTHDTC[4] <- ""
AE2$AESDTH[4] <- "Y"

check_ae_aesdth_aedthdtc(AE2)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 record(s) with AESDTH equal to 'Y' where AEDTHDTC does not have a value. "
#> attr(,"data")
#>   USUBJID AETERM AEDECOD AESTDTC AESDTH AEDTHDTC
#> 1       3      c       c       3      Y     <NA>
#> 2       4      d       d       4      Y         
check_ae_aesdth_aedthdtc(AE2,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 record(s) with AESDTH equal to 'Y' where AEDTHDTC does not have a value. "
#> attr(,"data")
#>   USUBJID AETERM AEDECOD AESTDTC AESDTH AEDTHDTC         RAVE
#> 1       3      c       c       3      Y     <NA> FORMNAME-R:5
#> 2       4      d       d       4      Y          FORMNAME-R:5

# non-required variable missing
AE2$AESPID <- NULL
check_ae_aesdth_aedthdtc(AE2)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 record(s) with AESDTH equal to 'Y' where AEDTHDTC does not have a value. "
#> attr(,"data")
#>   USUBJID AETERM AEDECOD AESTDTC AESDTH AEDTHDTC
#> 1       3      c       c       3      Y     <NA>
#> 2       4      d       d       4      Y         
check_ae_aesdth_aedthdtc(AE2,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 record(s) with AESDTH equal to 'Y' where AEDTHDTC does not have a value. "
#> attr(,"data")
#>   USUBJID AETERM AEDECOD AESTDTC AESDTH AEDTHDTC
#> 1       3      c       c       3      Y     <NA>
#> 2       4      d       d       4      Y         

# required variable missing 
AE2$AESDTH <- NULL
check_ae_aesdth_aedthdtc(AE2)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE is missing the variable: AESDTH"
check_ae_aesdth_aedthdtc(AE2,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE is missing the variable: AESDTH"