harmonization: Harmonization Function

In psHarmonize: Creates a Harmonized Dataset Based on a Set of Instructions

Harmonization Function

Description

This is the main function in the psHarmonize package. Takes a harmonization sheet as input, and returns a harmonization object (list with S3 class of 'psHarmonize'). Requires source data.frames to be in the global environment.

Usage

harmonization(
  harmonization_sheet,
  long_dataset = TRUE,
  wide_dataset = TRUE,
  error_log = TRUE,
  source_variables = TRUE,
  na_string = "NA",
  verbose = TRUE
)

Arguments

harmonization_sheet	Harmonization sheet input. Set of coding instructions
long_dataset	(TRUE/FALSE) Should the function return a long dataset?
wide_dataset	(TRUE/FALSE) Should the function return a wide dataset?
error_log	(TRUE/FALSE) Should the function return an error log?
source_variables	(TRUE/FALSE) Should the output datasets contain the original non modified values?
na_string	Character string of final recode value to be set to missing. Default is 'NA'. For example, if you use code_type of 'recode', and some of your final values are 'NA', they will be set to missing.
verbose	(TRUE/FALSE) Should the harmonization() function print the current progress to the console?

Details

Note: psHarmonize evaluates and runs code entered in the harmonization sheet. Make sure to only use harmonization sheets from authors you trust.

Value

List of return objects with S3 class of 'psHarmonize'. Can be used as input for report function create_summary_report() and create_error_log_report().

Examples

# Running harmonization function with example harmonization sheet
harmonization_obj <- harmonization(harmonization_sheet = harmonization_sheet_example)

# Extracting harmonized long dataset (each row is a visit)
long_dataset <- harmonization_obj$long_dataset

# Extracting harmonized wide dataset (each row is a person)
# Visits are expressed in multiple columns
wide_dataset <- harmonization_obj$wide_dataset

psHarmonize documentation built on April 4, 2025, 1:50 a.m.