R/readPar.R

In dmattek/tca-package: Time Course Analyzer

#' Check whether a string consists only from digits
#'
#' @param x Input string
#'
#' @return True if the input string consists only from digits, False otherwise.
#' @export
#'
#' @examples
#' checkDigits('1111')
#' checkDigits('1111cccc')
checkDigits <- function(x) {
  grepl('^[-]?[0-9]+[.]?[0-9]*$' , x)
}

#' Check whether a string matches TRUE/FALSE, T/F, or T.../F...
#'
#' @param x Input string
#'
#' @return True if the input string matches the pattern, False otherwise.
#' @export
#'
#' @examples
#' checkLogical('TRUE')
#' checkLogical('xxxTxxx')
checkLogical <- function(x) {
  grepl('^TRUE$|^FALSE$|^T$|^F$' , x)
}



#' Converts string elements of a named list to apporpriate types
#'
#' Strings that consist of digits are converted to type \code{numeric}, strings with TRUE/FALSE, T/F, or T.../F... to \code{logical}.
#'
#' @param in.l Named list fo strings.
#'
#' @return Named list with elements converted to appropriate types.
#' @export
#'
#' @examples
#'  l.tst = list()
#'  l.tst$aaa = '1000'
#'  l.tst$bbb = '1000xx'
#'  l.tst$ccc = 'True'
#'  l.tst$ddd = 'xxxTrue'
#'  l.res = convertStringListToTypes(l.tst)
#'  str(l.res)

convertStringList2Types <- function(in.l) {
  # convert strings with digits to numeric
  # uses logical indexing: http://stackoverflow.com/questions/42207235/replace-list-elements-by-name-with-another-list
  loc.l = checkDigits(in.l)
  in.l[loc.l] = lapply(in.l[loc.l], as.numeric)

  # convert strings with TRUE/FALSE to logical
  loc.l = checkLogical(in.l)
  in.l[loc.l] = lapply(in.l[loc.l], as.logical)

  return(in.l)
}


#' Return a list with parameter names and their values read from xlsx or csv file
#'
#' The xlsx or csv file has to contain at least two columns:
#' 1st column with parameter names
#' 2nd column with parameter values
#'
#' @param in.fname Name of the xlsx file.
#' @param in.sheet.idx Integer with the sheet number in the xlsx to process.
#'
#' @return Named list with parameters and their values.
#' @export
#' @import readxl

readPar = function(in.fname, in.sheet.idx = 1) {

  if (length(grep('.xlsx', in.fname)) > 0) {
    require(readxl)

    df.par = as.data.frame(readxl::read_xlsx(path = in.fname,
                                             sheet = in.sheet.idx,
                                             col_names = F))
  } else if( length(grep('.csv', in.fname)) > 0 ) {
    df.par = read.csv(file = in.fname,  header = F, sep = ',', stringsAsFactors = F, strip.white = T)
  } else
    stop('LOCreadPar: file with parameters is neither a csv, nor an xlsx', call. = F)


  # convert data frame with parameters to a list
  l.par = split(df.par[, 2], df.par[, 1])

  # convert strings with digits to numeric and strings with TRUE/FALSE to logical
  l.par = LOCconvertStringList2Types(l.par)

  return(l.par)
}