R/reviewInvalidRecords.R

In redcapAPI: Interface to 'REDCap'

#' @name reviewInvalidRecords
#' @title Review Invalid Records Following Field Validation
#' 
#' @description This function retrieves a summary of data elements that 
#'   failed validation during field validation and casting. 
#'   
#' @param data `data.frame`. The result of a function that performed
#'   field validation. 
#' @param quiet `logical(1)`. When `TRUE`, a message will be printed
#'   if the `invalid` attribute is not found on `data`. Otherwise, 
#'   the message is suppressed. 
#'   
#' @details 
#'   When discussing field validation and invalid data, it is helpful to 
#'   establish the following terminology: 
#'   
#'   A _Records data frame_ is a data frame returned by a function 
#'   where the fields (columns) in the data frame have been cast for
#'   subsequent analysis. 
#'   
#'   Some casting function also perform field validation and return an
#'   _Invalid data frame_, which is a listing of data elements that 
#'   have failed validation. The Invalid data frame is attached as an 
#'   attribute to the Records data frame. If no data elements fail the 
#'   validation, the Invalid data frame will have zero rows. If at least 
#'   one data element fails validation, a warning is printed to notify 
#'   the user so that the user may review the Invalid data frame and 
#'   mitigate the failed validations. 
#'   
#'   The Invalid data frame has an additional class (`c("invalid", "data.frame")`)
#'   and comes with a print method. The `print.invalid` method displays the
#'   content of the Invalid data frame neatly in both the console
#'   and within reports utilizing markdown.
#'   
#' @return
#' If `data` has the `"invalid"` attribute, an object with class 
#' `c("invalid", "data.frame")` is returned. (`NULL` will be returned if 
#' `data` does not have the attribute).
#' 
#' The colums in the Invalid data frame are 
#' |              |                                                                                               |
#' |--------------|-----------------------------------------------------------------------------------------------|
#' | `row`        | The row number from the Records data frame for which validation failed.                       |
#' | `record_id`  | The record ID for the failed validation.                                                      |
#' | `field_name` | The field name (column) of the failed validation.                                             |
#' | `field_type` | The field type of the failed validation.                                                      |
#' | `value`      | The original value that failed validation. It will be replaced with `NA` in the Records data. |
#' 
#' The Invalid data frame has additional attributes
#' 
#' * `time` - The date/time at which the validation was performed. 
#' * `version` - The REDCap version number (as retrieved by `exportVersion`). 
#' * `project` - The title of the REDCap project (as retrieved by `exportProjectInformation`).
#' 
#' @seealso
#' [exportRecordsTyped()], \cr
#' [exportReportsTyped()], \cr
#' [castForImport()], \cr
#' [guessCast()]
#' 
#' @examples
#' \dontrun{
#' unlockREDCap(connections = c(rcon = "project_alias"), 
#'              url = "your_redcap_url", 
#'              keyring = "API_KEYs", 
#'              envir = globalenv())
#'              
#' # Review the Invalid data frame after export
#' Records <- exportRecordsTyped(rcon)
#' reviewInvalidRecords(Records)
#' 
#' 
#' 
#' # Review Invalid data frame before import
#' RecordsForIMport <- castForImport(rcon)
#' reviewInvalidRecords(Records)
#' 
#' 
#' 
#' # Access the Invalid data frame the attributes
#' Records <- exportRecordsTyped(rcon)
#' attr(Records, "invalid")
#' attributes(Records)$invalid
#' }
#' 
#' @export

reviewInvalidRecords <- function(data, quiet = TRUE){
  coll <- checkmate::makeAssertCollection()
  
  checkmate::assert_data_frame(x = data, 
                               add = coll)
  
  checkmate::assert_logical(x = quiet, 
                            len = 1, 
                            any.missing = FALSE, 
                            add = coll)
  
  checkmate::reportAssertions(coll)
  
  Invalid <- attr(data, "invalid")
  
  if (is.null(Invalid) && !quiet){
    message(sprintf("`%s` does not have an 'invalid' attribute.", 
                    as.character(substitute(data))))
  }
  Invalid
}