Check Control Terminology for a Dataset — check_ct

This function checks that all columns in the dataset only contains the control terminology as defined by the metacore specification.

Usage

check_ct_data(
  data,
  metacore,
  na_acceptable = NULL,
  omit_vars = NULL,
  verbose = "message"
)

Arguments

data: Dataset to check
metacore: metacore object that contains the specifications for the dataset of interest. If any variable has different codelists for different datasets the metacore object will need to be subsetted using select_dataset from the metacore package.
na_acceptable: logical value or character vector, set to NULL by default. NULL sets the acceptability of missing values based on if the core for the variable is "Required" in the metacore object. If set to TRUE then will pass check if values are in the control terminology or are missing. If set to FALSE then NA will not be acceptable. If set to a character vector then only the specified variables may contain NA values.
omit_vars: character vector indicating which variables should be skipped when doing the controlled terminology checks. Internally, omit_vars is evaluated before na_acceptable.
verbose: character string controlling the verbosity of the output. Possible values are "message" (for general information and success messages) and "warn" (for warnings). Partial matching is allowed. Important: "silent" is explicitly not a valid option for verbose in this function. The primary purpose of check_ct_data is to identify and warn the user about non-compliant or problematic control terminology. Allowing the suppression of these warnings would bypass the function's intent and could lead to unnoticed data quality issues. If verbose = "silent" is provided, it will be coerced to "message" with a warning.

Value

Given data if all columns pass. It will issue a warning otherwise.

Examples

library(haven)
library(metacore)
library(magrittr)
load(metacore_example("pilot_ADaM.rda"))
spec <- metacore %>% select_dataset("ADSL", quiet = TRUE)
#> Warning: The `quiet` argument of `select_dataset()` is deprecated as of metacore 0.3.0.
#> ℹ Please use the `verbose` argument instead.
data <- read_xpt(metatools_example("adsl.xpt"))

check_ct_data(data, spec, omit_vars = c("AGEGR2", "AGEGR2N"))
#> ✔ All controlled terminology checks passed
#> # A tibble: 254 × 51
#>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN
#>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl>
#>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0
#>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0
#>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81
#>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54
#>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81
#>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0
#>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54
#>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54
#>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54
#> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0
#> # ℹ 244 more rows
#> # ℹ 41 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>,
#> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>,
#> #   AGEGR2 <chr>, AGEGR2N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>,
#> #   SEX <chr>, ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>,
#> #   COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>,
#> #   DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, …
if (FALSE) { # \dontrun{
# These examples produce errors:
check_ct_data(data, spec, na_acceptable = FALSE)
check_ct_data(data, spec, na_acceptable = FALSE, omit_vars = "DISCONFL")
check_ct_data(data, spec, na_acceptable = c("DSRAEFL", "DCSREAS"), omit_vars = "DISCONFL")
} # }