check_package_parameters: Validate Package Parameters

In piavat/PRE2DUP-R: Package for PRE2DUP-R method

Validate Package Parameters

Description

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.

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.

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.

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
)
package_parameters

piavat/PRE2DUP-R documentation built on June 11, 2025, 11:42 a.m.