Check for missing lab units (LBSTRESU)

This check identifies records where original lab values (LBORRES) exist but standard lab units (LBSTRESU) are not populated, excluding qualitative results (LBMETHOD) and excluding records when LBTESTCD in ("PH" "SPGRAV")

check_lb_lbstresu(LB, preproc = identity, ...)

Arguments

LB

Lab SDTM dataset with variables USUBJID, LBSTRESC, LBSTRESN, LBORRES, LBSTRESU, LBTESTCD, LBDTC, LBMETHOD (optional), LBSPID (optional), and VISIT (optional)

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

Iris Zhao

Examples

LB <- data.frame(
USUBJID = 1:10,
LBSTRESC = "5",
LBSTRESN = 1:10,
LBORRES = "5",
LBSTRESU = "g/L",
LBTESTCD = "ALB",
LBDTC = 1:10,
stringsAsFactors=FALSE
)

check_lb_lbstresu(LB)
#> [1] TRUE

LB$LBSTRESU[1]=""
check_lb_lbstresu(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 1 record(s) with missing lab units and non-missing test results. "
#> attr(,"data")
#>   USUBJID LBTESTCD LBORRES LBSTRESU LBSTRESC LBDTC
#> 1       1      ALB       5                 5     1

LB$LBSTRESU[2]="NA"
check_lb_lbstresu(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 unique patient(s) with 2 record(s) with missing lab units and non-missing test results. "
#> attr(,"data")
#>   USUBJID LBTESTCD LBORRES LBSTRESU LBSTRESC LBDTC
#> 1       1      ALB       5                 5     1
#> 2       2      ALB       5       NA        5     2

LB$LBSTRESU[3]=NA
check_lb_lbstresu(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "3 unique patient(s) with 3 record(s) with missing lab units and non-missing test results. "
#> attr(,"data")
#>   USUBJID LBTESTCD LBORRES LBSTRESU LBSTRESC LBDTC
#> 1       1      ALB       5                 5     1
#> 2       2      ALB       5       NA        5     2
#> 3       3      ALB       5     <NA>        5     3

LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
check_lb_lbstresu(LB,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "3 unique patient(s) with 3 record(s) with missing lab units and non-missing test results. "
#> attr(,"data")
#>   USUBJID LBTESTCD LBORRES LBSTRESU LBSTRESC LBDTC         RAVE
#> 1       1      ALB       5                 5     1 FORMNAME-R:2
#> 2       2      ALB       5       NA        5     2 FORMNAME-R:2
#> 3       3      ALB       5     <NA>        5     3 FORMNAME-R:2

LB$VISIT= "SCREENING"
check_lb_lbstresu(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "3 unique patient(s) with 3 record(s) with missing lab units and non-missing test results. "
#> attr(,"data")
#>   USUBJID LBTESTCD LBORRES LBSTRESU LBSTRESC LBDTC     VISIT
#> 1       1      ALB       5                 5     1 SCREENING
#> 2       2      ALB       5       NA        5     2 SCREENING
#> 3       3      ALB       5     <NA>        5     3 SCREENING

LB$LBSTRESU=NULL
check_lb_lbstresu(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "LB is missing the variable: LBSTRESU"