Check if, whenever a patient experiences an AE leading to study discontinuation, they also have a DS record indicating this.

This code checks that when a patient has an AE with AEACNOTx = "SUBJECT DISCONTINUED FROM STUDY" (x = "H", "1", "2", ...) then there should also be a record in DS where DS.DSSCAT = "STUDY COMPLETION/EARLY DISCONTINUATION" and DS.DSDECOD != "COMPLETED".

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

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AEDECOD, AEACNOTx

DS

Disposition SDTM dataset with variables USUBJID, DSCAT, DSSCAT, DSDECOD

preproc

An optional company specific preprocessing script

...

Other arguments passed to methods

Value

boolean value if check returns 0 obs, otherwise return subset dataframe.

Author

Edoardo Mancini

Examples

AE <- data.frame(
    STUDYID  = "1001",
    USUBJID  = c("1","2","3","4","5","1"),
    AESTDTC  = rep('2020-05-05', 6),
    AEDECOD  = c("HEADACHE", "HEART ATTACK","CHILLS", "PNEUMONIA", "ARTHRITIS", "FATIGUE"),
    AEACNOTH = c("NONE", "SUBJECT DISCONTINUED FROM STUDY", "MULTIPLE", "NONE",
                 "SUBJECT DISCONTINUED FROM STUDY", "SUBJECT DISCONTINUED FROM STUDY"),
    AEACNOT1 = c("", "", "PROCEDURE/SURGERY", "", "", ""),
    AEACNOT2 = c("", "", "SUBJECT DISCONTINUED FROM STUDY", "", "", ""),
    AESPID = "FORMNAME-R:13/L:13XXXX",
    stringsAsFactors = FALSE
)

DS <- data.frame(
    USUBJID = c("1","5"),
    DSCAT   = c("DISPOSITION EVENT", "DISPOSITION EVENT"),
    DSSCAT  = c("STUDY COMPLETION/EARLY DISCONTINUATION", "STUDY COMPLETION/EARLY DISCONTINUATION"),
    DSDECOD = c("ADVERSE EVENT", "ADVERSE EVENT" ),
    stringsAsFactors = FALSE
)

check_ae_aeacnoth_ds_disctx(AE, DS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 patient(s) with AEs leading to Study Discontinuation but no corresponding record in DS. "
#> attr(,"data")
#>   USUBJID      AEDECOD    AESTDTC                        AEACNOTH
#> 1       2 HEART ATTACK 2020-05-05 SUBJECT DISCONTINUED FROM STUDY
#> 2       3       CHILLS 2020-05-05                        MULTIPLE
#>            AEACNOT1                        AEACNOT2 DSCAT DSSCAT DSDECOD
#> 1                                                    <NA>   <NA>    <NA>
#> 2 PROCEDURE/SURGERY SUBJECT DISCONTINUED FROM STUDY  <NA>   <NA>    <NA>
check_ae_aeacnoth_ds_disctx(AE, DS, preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 patient(s) with AEs leading to Study Discontinuation but no corresponding record in DS. "
#> attr(,"data")
#>   USUBJID      AEDECOD    AESTDTC                        AEACNOTH
#> 1       2 HEART ATTACK 2020-05-05 SUBJECT DISCONTINUED FROM STUDY
#> 2       3       CHILLS 2020-05-05                        MULTIPLE
#>            AEACNOT1                        AEACNOT2          RAVE DSCAT DSSCAT
#> 1                                                   FORMNAME-R:13  <NA>   <NA>
#> 2 PROCEDURE/SURGERY SUBJECT DISCONTINUED FROM STUDY FORMNAME-R:13  <NA>   <NA>
#>   DSDECOD
#> 1    <NA>
#> 2    <NA>