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Check Control Terminology for a Single Column

Source: R/checks.R
check_ct_col.Rd

This function checks the column in the dataset only contains the control terminology as defined by the metacore specification

Usage

check_ct_col(
  data,
  metacore,
  var,
  na_acceptable = NULL,
  verbose = "message",
  .internal = FALSE
)

Arguments

data

Data to check

metacore

A metacore object to get the codelist from. If the variable has different codelists for different datasets the metacore object will need to be subsetted using select_dataset from the metacore package.

var

Name of variable to check

na_acceptable

Logical value, set to NULL by default, so the acceptability of missing values is 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 FALSEthen NA will not be 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.

.internal

Logical value indicating whether the function is being called internally by another package function. If TRUE, the function suppresses user-facing messages and instead returns a logical indicator of whether any controlled terminology violations were detected. This argument is intended for internal use only and should not be set by end users.

Value

Given data if column only contains control terms. If not, will error given the values which should not be in the column

Examples

library(metacore)
library(haven)
library(magrittr)
load(metacore_example("pilot_ADaM.rda"))
spec <- metacore %>% select_dataset("ADSL")
#> Warning: 'ds_vars' has incorrect column names. It should be: dataset, variable, key_seq,
#> order, mandatory, core, supp_flag
#> Warning: Other checks were not performed, because column names were incorrect
#> ✔ ADSL dataset successfully selected
data <- read_xpt(metatools_example("adsl.xpt"))
check_ct_col(data, spec, TRT01PN)
#> # 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>, …
check_ct_col(data, spec, "TRT01PN")
#> # 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>, …