Skip to contents

Package Required Field Check

Source: R/pkg_field_check.R
pkg_field_check.Rd

This function checks for additional fields required by this package including variable type (TYPE), minimum value (MIN), and maximum value (MAX).

Usage

pkg_field_check(DD.dict, DS.data, verbose = TRUE)

Arguments

DD.dict

Data dictionary.

DS.data

Data set.

verbose

When TRUE, the function prints the Message out, as well as a list of the fields not found in the data dictionary.

Value

Tibble, returned invisibly, containing: (1) Time (Time stamp); (2) Name (Name of the function); (3) Status (Passed/Failed); (4) Message (A copy of the message the function printed out); (5) Information (Named vector of TRUE/FALSE values alerting user if checks passed (TRUE) or failed (FALSE) for TYPE, MIN, and MAX).

Details

Even though MIN, MAX, and TYPE are not required by dbGaP, our package was created to use these variables in a series of other checks and awareness functions (e.g., render_report, values_check, etc.). If this function fails, the add_missing_fields function can be used.

See also

add_missing_fields

Examples

# Example 1: Fail check
data(ExampleD)
pkg_field_check(DD.dict.D, DS.data.D)
#> $Message
#> [1] "ERROR: not all package-level required fields are present in the data dictionary. Consider using the add_missing_fields function to auto fill these fields."
#> 
#> $Missing
#> [1] "TYPE" "MIN"  "MAX" 
#> 
# Use the add_missing_fields function to add in data
DD.dict.updated <- add_missing_fields(DD.dict.D, DS.data.D)
#> $Message
#> [1] "CORRECTED ERROR: not all package-level required fields were present in the data dictionary. The missing fields have now been added! TYPE was inferred from the data, and MIN/MAX have been added as empty fields."
#> 
#> $Missing
#> [1] "TYPE" "MIN"  "MAX" 
#> 
# Be sure to call in the new version of the dictionary (DD.dict.updated)
pkg_field_check(DD.dict.updated, DS.data.D) 
#> $Message
#> [1] "Passed: package-level required fields TYPE, MIN, and MAX present in the data dictionary."
#> 

# Example 2: Pass check
data(ExampleA)
pkg_field_check(DD.dict.A, DS.data.A)
#> $Message
#> [1] "Passed: package-level required fields TYPE, MIN, and MAX present in the data dictionary."
#> 
print(pkg_field_check(DD.dict.A, DS.data.A, verbose=FALSE))
#> # A tibble: 1 × 5
#>   Time                Function        Status Message                 Information
#>   <dttm>              <chr>           <chr>  <chr>                   <named lis>
#> 1 2023-09-27 11:01:20 pkg_field_check Passed Passed: package-level … <lgl [3]>