Check if death in AE then there should be a study discon form

Source: R/check_ae_death_ds_discon.R

This checks that if death is indicated in AE via AEDTHDTC/AESDTH/AEOUT (as well as grade 5 AE if AETOXGR exists) then there should be a study discontinuation record indicated by DS.DSSCAT

check_ae_death_ds_discon(AE, DS, preproc = identity, ...)

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AEDTHDTC, AESDTH, AEOUT

DS

Disposition SDTM dataset with variables USUBJID, DSCAT, DSSCAT

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

Examples


AE <- data.frame(
 STUDYID = rep(1,6),
 USUBJID = 1:6,
 AEDTHDTC = c(NA,"2020-01-01",NA,NA,NA,NA),
 AESDTH = c(NA,NA,"Y",NA,NA,NA),
 AEOUT = c(NA,NA,NA,"FATAL",NA,NA),
 AETOXGR = c(NA,NA,NA,NA,"5",NA),
 AESPID="FORMNAME-R:2/L:2XXXX"
)

DS <- data.frame(
 STUDYID = 1,
 USUBJID = 1:3,
 DSCAT="DISPOSITION EVENT",
 DSSCAT=c("STUDY DISCON",
 "STUDY DISCON",
 "STUDY COMPLETION/EARLY DISCONTINUATION")
)

check_ae_death_ds_discon(AE,DS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 patient(s) where AE data indicates death but no study discontinuation record in DS. "
#> attr(,"data")
#>   USUBJID DSSCAT DSCAT AEDTHDTC AETOXGR AESDTH AEOUT
#> 1       4   <NA>  <NA>     <NA>    <NA>   <NA> FATAL
#> 2       5   <NA>  <NA>     <NA>       5   <NA>  <NA>
check_ae_death_ds_discon(AE,DS,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 patient(s) where AE data indicates death but no study discontinuation record in DS. "
#> attr(,"data")
#>   USUBJID DSSCAT DSCAT AEDTHDTC AETOXGR AESDTH AEOUT         RAVE
#> 1       4   <NA>  <NA>     <NA>    <NA>   <NA> FATAL FORMNAME-R:2
#> 2       5   <NA>  <NA>     <NA>       5   <NA>  <NA> FORMNAME-R:2

DS$DSSCAT = NULL

check_ae_death_ds_discon(AE,DS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "DS is missing the variable: DSSCAT"