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Generate report from data cleaning operations

Source: R/print_report.R
print_report.Rd

Generate report from data cleaning operations

Usage

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

Arguments

data

A <data.frame> or <linelist> object returned from the clean_data or the main functions of each data cleaning module.

what

A <character> with the name of the specific data cleaning report which would be displayed. The possible values are:

incorrect_date_sequence

To display rows with the incorrect date sequences

colnames

To display the column names before and after cleaning

converted_into_numeric

To display the names of the columns that that have been converted into numeric

date_standardization

To display rows in the cleaned data with date values that are outside of the specified time frame, and rows with date values that comply with multiple formats

misspelled_values

To display the detected misspelled values

removed_duplicates

To display the duplicated rows that have been removed

found_duplicates

To display the duplicated rows

constant_data

To display the constant data i.e. constant columns, empty rows and columns

missing_values_replaced_at

To display the names of the columns where the missing value strings have been replaced with NA

incorrect_subject_id

To display the missing, duplicated and invalid subject subject IDs

scanning_result

To display the output of the scan_data() function

print

A <logical> that specifies whether to to open the report in your browser in the form of a HTML file or no. Default is FALSE.

report_title

A <character> with the title that will appear on the report

output_file_name

A <character> used to specify 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

A <character> with the file format of the report. Currently only "html" is supported.

Value

A <character> containing the name and path of the saved report

Examples

if (FALSE) { # \dontrun{
  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 the report in the R temporary directory
  print_report(
    data = cleaned_data,
    report_title = "{cleanepi} data cleaning report",
    output_file_name = NULL,
    format = "html",
    print = FALSE
  )
} # }