R/read_iris_csv.R

In breathtestcore: Core Functions to Read and Fit 13c Time Series from Breath Tests

#' @title Read 13C data from IRIS/Wagner Analysen in CSV Format
#'
#' @description Reads 13C data from IRIS/Wagner Analysen in CSV Format
#' The CSV files start as follows:
#' \preformatted{
#' "Name","Vorname","Test","Identifikation"
#'} 
#' This format does not have information about the substrate (acetate, octanoate),
#' the dose and body weight and height. The following defaults are used: \code{substrate = acetate, 
#' dose = 100,  weight = 75, height = 180}.
#' @param filename Name of IRIS/Wagner file in CSV format
#' @param text alternatively, text can be given as string
#' @return List of class \code{breath_test_data} with \code{file name, 
#' patient name, patient first name, test, identifikation},
#' and data frame \code{data} with \code{time} and \code{dob}
#' @examples
#' filename = btcore_file("IrisCSV.TXT")
#' cat(readLines(filename, n = 3), sep="\n")
#' #
#' iris_data = read_iris_csv(filename)
#' str(iris_data)
#' @importFrom purrr map
#' @export 
read_iris_csv = function(filename = NULL, text = NULL) {
  if (is.null(text)) {
    if (!file.exists(filename))
      stop(paste0("File ",filename," does not exist."))
    # Check if this is the right format
    to_read = filename
    header = readLines(filename, 1)
  } else {
    header = text[1]
    filename = "from text"
    # read_csv recognizes text by presence of a least one newline
    to_read = paste0(text, collapse ="\n") 
  }
  if (str_detect(header,("^\"Name\",\"Vorname\",\"Test\",\"Identifikation\"")) != 1)
    stop( paste("File",filename,
    "is not a valid IRIS CSV file. First line should be Name, Vorname,..."
    ))
  d = suppressWarnings(readr::read_csv(to_read, col_types = "cccciddddddcc",
                          locale = readr::locale(encoding = "ISO-8859-2")))
  readr::stop_for_problems(text)

  if (ncol(d) != 13)  
    stop(paste("File in IRIS CSV format", filename, 
        "has unexpected", ncol(d),"columns; expected 13 columns"))
  if (nrow(d) < 5) 
    stop(paste("File in IRIS CSV format", filename, "has only", nrow(d), "rows"))

  record_date = strptime(d$Datum[1],"%d.%m.%Y")
  patient_id = extract_id(d$Identifikation[1])
  name = d$Name[1]
  first_name = d$Vorname[1]
  initials = NA
  if (nchar(name) > 0 && nchar(first_name) > 0)
    initials =  paste0(str_sub(name,1,1),
                      str_sub(first_name,1,1))
  data = try(d[,c("Testzeit[min]","DOB [o/oo]")], silent = TRUE)
  if (inherits(data, "try-error"))
    stop("Invalid data columns in Iris data file")
  names(data) = c("time","dob")
  # remove too small values
  data = data[data$dob >= -10,]
  if (any(unlist(map(data, is.na)))) 
    stop("Invalid or missing PDR/DOB data in\n ", filename)
  breathtest_data(
    file_name = basename(filename),
    patient_id = patient_id,
    name = name,
    first_name = first_name,
    initials =  initials,
    test_no = 9999,
    dose = 100,
    study = d$Test[1],
    record_date = record_date,
    height = 180,
    weight = 75,
    device = "Iris",
    substrate = 'acetate',
    data = as.data.frame(data)
  )
}


#' @title Extracts an ID from string IRIS CSV file
#'
#' @description First tries to extract only digits, separating these by underscore 
#' when there are multiple blocks. If this give a non-valid  id, returns the 
#' whole string without spaces and periods, hoping it makes sense.
#' For internal use, but should be overridden for exotic IDs
#' @param id One item from column Identifikation, e.g. "KEK-ZH-Nr.2013-1234"
#' @examples 
#' extract_id
#' @export
extract_id = function(id){
  id1 = paste(str_match_all(id, "([\\d]+)")[[1]][,2], collapse = "_")
  if (nchar(id1) >= 5) return(id1)
  tolower(str_replace_all(id, "[\\.\\-\\W]+", "_"))
}