Check for missing values in the MISPEC variable

Source: R/check_mi_mispec.R

This check looks for missing values in the MISPEC variable, which is required. This will be flagged in P21. This may reflect a mapping issue.

check_mi_mispec(MI)

Arguments

MI

Microscopic Findings with variables USUBJID, MISPEC, MITESTCD, MIDTC

Value

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

Author

Stella Banjo (HackR 2021)

Examples


MI <- data.frame(
  USUBJID = c("1","2", "3"),
  DOMAIN = "MI",
  MISEQ = c(1, 2, 1),
  MISPEC = c("","BLOCK SLIDE",NA),
  MITESTCD = "TESTCD1",
  MIDTC = "2020-01-01",
stringAsFactors = FALSE
)

 check_mi_mispec(MI)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 record(s) with required variable MISPEC not populated. "
#> attr(,"data")
#>   USUBJID MITESTCD MISPEC      MIDTC
#> 1       1  TESTCD1        2020-01-01
#> 2       3  TESTCD1   <NA> 2020-01-01

## No errors, MISPEC values present
MI2 <- data.frame(
 USUBJID = c("1","2", "3"),
 DOMAIN = "MI",
 MISEQ = 1,
 MISPEC = c("SLIDE", "TUMOR TISSUE", "BLOCK SLIDE"),
 MITESTCD = "TESTCD1",
 MIDTC = "",
 stringsAsFactors = FALSE
)

 check_mi_mispec(MI2)
#> [1] TRUE