R/read_nmtab.R

In guiastrennec/modelviz: Generation of QMD for NONMEM outputs

#' NONMEM output table import function
#'
#' @description Quickly import NONMEM output tables into R.
#' When both \code{skip} and \code{header} are \code{NULL},
#' \code{read_nmtab} will automatically detect the optimal
#' settings to import the tables. When more than one files are
#' provided for a same NONMEM run, they will be combined into
#' a single \code{data.frame}.
#'
#' @param file full file name
#' @param skip number of lines to skip before reading data
#' @param header logical value indicating whether the file contains the names
#' of the variables as its first line
#' @param rm_duplicates logical value indicating whether duplicated columns should be removed
#' @param nonmem_tab logical value indicading to the function whether the file is a
#' table or a nonmem additional output file.
#'
#' @seealso \code{\link{parse_nonmem_model}}, \code{\link{import_qmd_info}}
#' @return A \code{data.frame}
#' @examples
#' \dontrun{
#' data <- read_nmtab(file = '../models/pk/sdtab101')
#' }
#' @export
read_nmtab <- function(file = NULL,
                       skip = NULL,
                       header = NULL,
                       rm_duplicates = FALSE,
                       nonmem_tab = TRUE) {

  # Check inputs
  if(is.null(file)) {
    stop('Argument \"file\" required.')
  }

  if(!any(file.exists(file))) {
    stop('No file not found.')
  } else {
    file <- file[file.exists(file)]
  }

  if(nonmem_tab) {
    # If auto mode required
    if(is.null(skip) & is.null(header)) {
      test    <- readLines(file[1], n = 3)
      skip    <- ifelse(grepl('TABLE NO', test[1]), 1, 0)
      header  <- ifelse(grepl('[a-zA-Z]', test[2]), TRUE, FALSE)
    }

    # Import data
    tab_file <- do.call('cbind', lapply(file, readr::read_table,
                                        skip = skip, col_names = header))

    tab_file <- as.data.frame(apply(tab_file, MARGIN = 2, FUN = as.numeric))

    # Drop rows with NA (in simtab)
    tab_file <- stats::na.omit(tab_file)

    # Correct bug in the headers
    if (header) {
      colnames(tab_file)[grepl('\n',colnames(tab_file))] <-
        gsub('\n.+', '', colnames(tab_file)[grepl('\n', colnames(tab_file))])
    }

  } else {
    # Search for final results only
    skip     <- max(grep('TABLE NO', readLines(file[1])))

    # Import all files
    tab_file <- do.call('cbind', lapply(file, utils::read.table, skip = skip,
                           header = FALSE, fill = TRUE, as.is = TRUE))
    colnames(tab_file) <- tab_file[1, ]
    tab_file <- suppressWarnings(as.data.frame(apply(tab_file[-1, ], 2, as.numeric)))
  }

  if(rm_duplicates) {
    tab_file <- tab_file[, !duplicated(colnames(tab_file))]
  }

  return(tab_file)

} # End read_nmtab