Check patients in the DM dataset who do not have records in the AE dataset

This check looks for patients in the DM dataset who do not have records in the AE dataset, and obtains first treatment start date and earliest death date for these patients

check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)

Arguments

DM

Demographics SDTM dataset with variable USUBJID

AE

Adverse Events SDTM dataset with variable USUBJID

DS

Disposition SDTM dataset with variables USUBJID, DSSTDTC, DSDECOD

EX

Exposure SDTM dataset with variables USUBJID, EXDOSE, EXSTDTC, EXTRT

Value

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

Author

Vani Nimbal

Examples

USUBJID<- c(1:10)
DM=data.frame(USUBJID)
AE=data.frame(USUBJID)
AE$USUBJID[3]=NA
AE$USUBJID[8]=NA
AE$USUBJID[10]=NA

EX <- data.frame(
USUBJID = c(1:8, 6, 8, 10, 10, 10, 10),
EXOCCUR = rep("Y", times=14),
EXDOSE = rep(c(1,2), times=7),
EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"),
EXTRT = "GDC",
stringsAsFactors=FALSE
)

DS <- data.frame(
USUBJID = c(2,8,8),
DSDECOD = rep("DEATH", times=3),
DSSTDTC = c("2012-12-01", NA, "2013-07-01"),
stringsAsFactors=FALSE
)
check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There is/are 3 patient(s) in DM without Adverse Events reported. "
#> attr(,"data")
#>   USUBJID    EXSTDTC DSDECOD    DSSTDTC
#> 1       3 2012-01-01                   
#> 2       8 2012-01-01   DEATH 2013-07-01
#> 3      10 2012-02-04                   

EX$EXOCCUR[3]="N"

check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There is/are 3 patient(s) in DM without Adverse Events reported. "
#> attr(,"data")
#>   USUBJID    EXSTDTC DSDECOD    DSSTDTC
#> 1       3                              
#> 2       8 2012-01-01   DEATH 2013-07-01
#> 3      10 2012-02-04                   

EX$EXOCCUR=NULL

check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There is/are 3 patient(s) in DM without Adverse Events reported. "
#> attr(,"data")
#>   USUBJID    EXSTDTC DSDECOD    DSSTDTC
#> 1       3 2012-01-01                   
#> 2       8 2012-01-01   DEATH 2013-07-01
#> 3      10 2012-02-04