print_report: Generate report from data cleaning operations

In cleanepi: Clean and Standardize Epidemiological Data

Generate report from data cleaning operations

Description

Generate report from data cleaning operations

Usage

print_report(
  data,
  report_title = "{cleanepi} data cleaning report",
  output_file_name = NULL,
  format = "html",
  print = TRUE
)

Arguments

data	A data.frame or linelist object returned from the clean_data() or the main functions of each data cleaning module.
report_title	The title to appear on the report
output_file_name	A string specifying the name of the report file, excluding any file extension. If no file name is supplied, one will be automatically generated with the format cleanepi_report_YYMMDD_HHMMSS.
format	The file format of the report. Currently only "html" is supported.
print	A logical that specifies whether to print the generated HTML file or no.

Value

A string containing the name and path of the saved report

Examples

data <- readRDS(system.file("extdata", "test_df.RDS", package = "cleanepi"))
test_dictionary <- readRDS(system.file("extdata", "test_dictionary.RDS",
                                       package = "cleanepi"))

# scan through the data
scan_res <- scan_data(data)

# Perform data cleaning
cleaned_data <- data |>
 standardize_column_names(keep = NULL, rename = c("DOB" = "dateOfBirth")) |>
 replace_missing_values(target_columns = NULL, na_strings = "-99") |>
 remove_constants(cutoff = 1.0) |>
 remove_duplicates(target_columns = NULL) |>
 standardize_dates(target_columns  = NULL,
                   error_tolerance = 0.4,
                   format          = NULL,
                   timeframe     = as.Date(c("1973-05-29", "2023-05-29"))) |>
 check_subject_ids(target_columns = "study_id",
                   prefix         = "PS",
                   suffix         = "P2",
                   range          = c(1L, 100L),
                   nchar          = 7L) |>
 convert_to_numeric(target_columns = "sex", lang = "en") |>
 clean_using_dictionary(dictionary = test_dictionary)

# add the data scanning result to the report
cleaned_data <- add_to_report(x     = cleaned_data,
                              key   = "scanning_result",
                              value = scan_res)

# save a report in the current directory using the previously-created objects
print_report(
  data             = cleaned_data,
  report_title     = "{cleanepi} data cleaning report",
  output_file_name = NULL,
  format           = "html",
  print            = TRUE
)

cleanepi documentation built on June 22, 2024, 9:48 a.m.