Check LBORRES/LBSTRESC populated with number beginning with character '>' or '<', which will yield missing AVAL in ADaM and records will be omitted in analyses such as Hy's Law

This check looks for missing numeric standardized finding (LBSTRESN) when original finding (LBORRES) and character standardized finding (LBSTRESC) are not missing and LBORRES/LBSTRESC populated with number beginning with character '>' or '<'

check_lb_lbstresc_char(LB)

Arguments

LB

Lab SDTM dataset with variables USUBJID, LBTEST, LBDTC, LBORRES, LBORRESU, LBSTRESN, LBSTRESC

Value

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

Author

Vira Vrakina

Examples

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

check_lb_lbstresc_char(LB)
#> [1] TRUE

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

check_lb_lbstresc_char(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "LBSTRESN missing but LBORRES/LBSTRESC populated with number beginning with character > or < for 1 record(s). "
#> attr(,"data")
#>     USUBJID LBTEST      LBDTC LBORRES LBORRESU LBSTRESN LBSTRESC
#> 3 Patient 3 Test A 2017-01-01      <7       mg       NA       <7

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

check_lb_lbstresc_char(LB)
#> [1] FALSE
#> attr(,"msg")
#> [1] "LBSTRESN missing but LBORRES/LBSTRESC populated with number beginning with character > or < for 1 record(s). "
#> attr(,"data")
#>     USUBJID LBTEST      LBDTC LBORRES LBORRESU LBSTRESN LBSTRESC
#> 3 Patient 3 Test A 2017-01-01      <7       mg       NA       <7