Check missing standard lab values (LBSTRESN/LBSTRESC)

This check looks for missing standardized finding (LBSTRESN/LBSTRESC) when original finding (LBORRES) is not missing

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

Arguments

LB

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

Madeleine Ma

Examples

LB <- data.frame(
 USUBJID = c("Patient 1","Patient 2","Patient 3"),
 LBTEST   = "Test A",
 LBTESTCD   = "TA",
 LBDTC   = "2017-01-01",
 LBORRES = c("5","6","7"),
 LBSTRESC = c("5","6","7"),
 LBORRESU = rep("mg",3),
 LBSTRESN  = c(5,6,NA),
 stringsAsFactors=FALSE
 )

check_lb_lbstresn_missing(LB)
#> [1] TRUE

LB$LBSTRESC[3] = ""
check_lb_lbstresn_missing(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 1 lab record(s) with result reported without standard value. "
#> attr(,"data")
#>     USUBJID LBTESTCD      LBDTC LBORRES LBORRESU LBSTRESN LBSTRESC
#> 3 Patient 3       TA 2017-01-01       7       mg       NA         

LB$LBSTRESC[1] = ""
check_lb_lbstresn_missing(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 1 lab record(s) with result reported without standard value. "
#> attr(,"data")
#>     USUBJID LBTESTCD      LBDTC LBORRES LBORRESU LBSTRESN LBSTRESC
#> 3 Patient 3       TA 2017-01-01       7       mg       NA         

LB$VISIT = "SCREENING"
check_lb_lbstresn_missing(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 1 lab record(s) with result reported without standard value. "
#> attr(,"data")
#>     USUBJID LBTESTCD      LBDTC LBORRES LBORRESU LBSTRESN LBSTRESC     VISIT
#> 3 Patient 3       TA 2017-01-01       7       mg       NA          SCREENING

LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
check_lb_lbstresn_missing(LB,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 1 lab record(s) with result reported without standard value. "
#> attr(,"data")
#>     USUBJID LBTESTCD      LBDTC LBORRES LBORRESU LBSTRESN LBSTRESC         RAVE
#> 3 Patient 3       TA 2017-01-01       7       mg       NA          FORMNAME-R:2
#>       VISIT
#> 3 SCREENING

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

LB$LBSTRESC = NULL
check_lb_lbstresn_missing(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "LB is missing the variables: LBSTRESN, LBSTRESC"