psHarmonize (version 0.3.6)

create_long_dataset: Create long dataset.

Description

This function is usually not called by the user. Instead it is usually called by harmonization() function.

Usage

create_long_dataset(
  vars_interest,
  subdomain,
  previous_dataset,
  error_log,
  na_string,
  verbose = TRUE
)

Value

Returns a list with the harmonized long dataset, and error log.

Arguments

vars_interest

Variable currently being harmonized

subdomain

Category of variable

previous_dataset

Dataframe created so far

error_log

Error log

na_string

Character string of final recode value to be set to NA.

verbose

(TRUE/FALSE) Should the function print the current progress to the console?

Details

The function takes the harmonization sheet, and input dataframe, and creates a dataframe with the harmonized variable.

Examples

# Example sheet
test_sheet <- harmonization_sheet_example[harmonization_sheet_example$study == 'Cohort A',]

# Example dataset
test_data <- cohort_a

# create error log
test_error_log <- test_sheet[,c('item','study','visit','possible_range')]

test_error_log$completed_status <- NA_character_
test_error_log$completed_reason <- NA_character_
test_error_log$range_set_to_na <- NA_integer_
test_error_log$range_out_of_range_warning <- NA

long_dataset <- create_long_dataset(vars_interest = test_sheet,
                                    subdomain = 'age',
                                    previous_dataset = test_data,
                                    error_log = test_error_log,
                                    na_string = 'NA',
                                    verbose = TRUE)