Check for missing CMDECOD values

This check looks for missing CMDECOD values

check_cm_cmdecod(CM, preproc = identity, ...)

Arguments

CM

Concomitant Medications SDTM dataset with variables USUBJID, CMTRT, CMDECOD

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

Lei Zhao, Stella Banjo (HackR 2021)

Examples

CM <- data.frame(
 USUBJID = 1:5,
 DOMAIN = rep("CM", 5),
 CMTRT = rep("DRUG TERM", 5),
 CMDECOD = rep("CODED DRUG TERM", 5),
 CMSTDTC = 1:5,
 CMENDTC = 1:5,
 CMCAT = "CONCOMITANT MEDICATIONS",
 CMSPID = c("FORMNAME-R:13/L:13XXXX",
             "FORMNAME-R:16/L:16XXXX",
             "FORMNAME-R:2/L:2XXXX",
             "FORMNAME-R:19/L:19XXXX",
             "FORMNAME-R:5/L:5XXXX"),
 stringsAsFactors=FALSE
)

check_cm_cmdecod(CM)
#> [1] TRUE

CM$CMDECOD[1] = NA
CM$CMDECOD[2] = "NA"
CM$CMDECOD[3:5] = ""
check_cm_cmdecod(CM)
#> [1] FALSE
#> attr(,"msg")
#> [1] "CM has 5 record(s) with missing CMDECOD. "
#> attr(,"data")
#>   USUBJID CMSTDTC     CMTRT CMDECOD
#> 1       1       1 DRUG TERM    <NA>
#> 2       2       2 DRUG TERM      NA
#> 3       3       3 DRUG TERM        
#> 4       4       4 DRUG TERM        
#> 5       5       5 DRUG TERM        
check_cm_cmdecod(CM,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "CM has 5 record(s) with missing CMDECOD. "
#> attr(,"data")
#>   USUBJID CMSTDTC     CMTRT CMDECOD          RAVE
#> 1       1       1 DRUG TERM    <NA> FORMNAME-R:13
#> 2       2       2 DRUG TERM      NA FORMNAME-R:16
#> 3       3       3 DRUG TERM          FORMNAME-R:2
#> 4       4       4 DRUG TERM         FORMNAME-R:19
#> 5       5       5 DRUG TERM          FORMNAME-R:5

CM$CMDECOD <- NULL
check_cm_cmdecod(CM)
#> [1] FALSE
#> attr(,"msg")
#> [1] "CM is missing the variable: CMDECOD"