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Validate Package Parameters

check_package_parameters.Rd

This function checks the structure and content of a given package parameter file (data.frame or data.table) for use in pre2dup workflows. The validation covers required columns, uniqueness, data types, value ranges, and logical consistency. The function stops execution and prints error messages if critical errors are found.

Usage

check_package_parameters(
  dt,
  pack_atc = NULL,
  pack_id = NULL,
  pack_ddd_low = NULL,
  pack_ddd_usual = NULL,
  pack_dur_min = NULL,
  pack_dur_usual = NULL,
  pack_dur_max = NULL,
  print_all = FALSE,
  return_data = FALSE
)

Arguments

dt

data.frame or data.table containing the package parameters to validate.

pack_atc

Character. Name of the column containing the Anatomical Therapeutic Chemical (ATC) Classification code.

pack_id

Character. Name of the column containing the package identifier (e.g., vnr code).

pack_ddd_low

Character. Name of the column with the minimum daily DDD value.

pack_ddd_usual

Character. Name of the column with the usual daily DDD value.

pack_dur_min

Character. Name of the column with the minimum package duration (in days).

pack_dur_usual

Character. Name of the column with the usual package duration (in days).

pack_dur_max

Character. Name of the column with the maximum package duration (in days).

print_all

Logical. If TRUE, all warnings are printed. If FALSE, only the first 5 problematic rows are printed.

return_data

Logical. If TRUE and no errors are detected, returns a data.table with the validated columns and proper types. If FALSE, only a message is printed.

Value

If return_data = TRUE, returns a data.table containing only the validated columns, with converted types. If errors are detected, the function stops and prints error messages.

Details

The following checks are performed:

  • Existence and naming of required columns

  • Uniqueness of package identifiers (no duplicates)

  • Validity of ATC codes (no missing or invalid values, correct type)

  • Validity of package IDs (should be numeric, no missing values)

  • Validity of DDD and duration values (no negative or missing values, logical value ranges)

  • Correct order of minimum, usual, and maximum durations

  • Correct order of minimum and usual DDD values

If any errors are found, the function stops execution and prints all error messages.

Examples

ATC <- c("N05AA01", rep("N05AH03", 3), "N05AX13")
vnr <- c(141473, 80307, 145698, 457780 , 412581)
lower_ddd = c(0.167, 0.500, 0.500, 0.375, 0.714)
usual_ddd <- c(0.33, 1.00, 1.00, 0.75, 1.00)
minimum_duration <- c(33, 9.3, 9.3, 33.3, 14)
usual_duration <- c(100, 28, 28, 100, 30)
maximum_duration <- c(200, 56, 56, 200, 42)
df_pack_params <- data.frame(ATC, vnr, lower_ddd, usual_ddd,
  minimum_duration, usual_duration, maximum_duration)

package_parameters <- check_package_parameters(
  dt = df_pack_params,
  pack_atc = "ATC",
  pack_id = "vnr",
  pack_ddd_low = "lower_ddd",
  pack_ddd_usual = "usual_ddd",
  pack_dur_min = "minimum_duration",
  pack_dur_usual = "usual_duration",
  pack_dur_max = "maximum_duration",
  return_data = TRUE
)
#> Checks passed for 'df_pack_params'
package_parameters
#>        ATC    vnr lower_ddd usual_ddd minimum_duration usual_duration
#>     <char>  <int>     <num>     <num>            <num>          <num>
#> 1: N05AA01 141473     0.167      0.33             33.0            100
#> 2: N05AH03  80307     0.500      1.00              9.3             28
#> 3: N05AH03 145698     0.500      1.00              9.3             28
#> 4: N05AH03 457780     0.375      0.75             33.3            100
#> 5: N05AX13 412581     0.714      1.00             14.0             30
#>    maximum_duration
#>               <num>
#> 1:              200
#> 2:               56
#> 3:               56
#> 4:              200
#> 5:               42