Check for missing AETOXGR and/or AESEV values

This check looks for missing AETOXGR and/or AESEV values and returns a data frame. If both variables exist it returns records where both are missing.

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

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AESTDTC, AEDECOD, AETERM, and AETOXGR (or AESEV)

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

Will Harris, Stella Banjo (HackR 2021)

Examples

# test with sample data


AE <- data.frame(
 USUBJID = 1:3,
 DOMAIN = c(rep("AE", 3)),
 AESEQ = 1:3,
 AESTDTC = 1:3,
 AETERM = c("FLU COUGH", "HEADACHE", "FEVER"),
 AEDECOD = c("", "Headache", "Fever"),
 AETOXGR = 1:3,
 AESEV = 1:3,
 AESPID = "FORMNAME-R:16/L:16XXXX",
 stringsAsFactors = FALSE
)

check_ae_aetoxgr(AE)
#> [1] TRUE

AE$AETOXGR[1] <- NA
check_ae_aetoxgr(AE)
#> [1] TRUE

AE$AESEV[1] <- NA
check_ae_aetoxgr(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has records where both AESEV and AETOXGR have missing values. "
#> attr(,"data")
#>   USUBJID    AETERM AESTDTC AEDECOD AETOXGR AESEV          RAVE
#> 1       1 FLU COUGH       1              NA    NA FORMNAME-R:16

AE$AETOXGR <- NULL
check_ae_aetoxgr(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 1 record(s) with missing AESEV"
#> attr(,"data")
#>   USUBJID AESTDTC    AETERM AEDECOD AESEV          RAVE
#> 1       1       1 FLU COUGH            NA FORMNAME-R:16

AE$AESPID <- NULL
check_ae_aetoxgr(AE,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 1 record(s) with missing AESEV"
#> attr(,"data")
#>   USUBJID AESTDTC    AETERM AEDECOD AESEV
#> 1       1       1 FLU COUGH            NA

AE$AESEV <- NULL
check_ae_aetoxgr(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE is missing both the AETOXGR and AESEV variable."

AE$AEDECOD <- NULL
check_ae_aetoxgr(AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE is missing the variable: AEDECOD"