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

# \donttest{
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)
#> Warning: Detected incorrect subject ids at lines: 3, 5, 7
#> Use the correct_subject_ids() function to adjust them.

# 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
)
#> Generating html report in /tmp/Rtmpf5yHpu
#> [1] "/tmp/Rtmpf5yHpu/cleanepi_report__2024-09-02Mont_123757.html"
# }