R/nmtab.R

In nonmem2rx: Converts 'NONMEM' Models to 'rxode2'

#' Read nonmem table file
#'
#'
#' @param file file name to read the results from
#' @param ... other parameters passed to `data.table::fread`
#' @return data frame of the read table
#' @export
#' @author Philip Delff, Matthew L. Fidler
#' @examples
#' nmtab(system.file("mods/cpt/runODE032.csv", package="nonmem2rx"))
nmtab <- function (file, ...)
{
  checkmate::assertFileExists(file)
  TABLE <- NULL
  NMREP <- NULL
  colnames <- readLines(file, n=2, encoding="latin1")[2]
  if (grepl(", *OMEGA\\( *1 *, *1\\)", colnames)) {
    col.names <- gsub(" ", "",strsplit(colnames, " +,")[[1]])
    dt1 <- fread(file, fill = TRUE, header = TRUE, skip = 1,
                 ...)
    dt1 <- dt1[,seq_along(col.names), with=FALSE]
    setnames(dt1, col.names)
  } else {
    dt1 <- fread(file, fill = TRUE, header = TRUE, skip = 1,
                 ...)
  }
  cnames <- colnames(dt1)
  if (length(cnames) == 0L) return(NULL)
  dt1[grep("^TABLE", as.character(get(cnames[1])), invert = FALSE,
           perl = TRUE), `:=`(TABLE, get(cnames[1]))]
  dt1[, `:=`(NMREP, cumsum(!is.na(TABLE)) + 1)]
  dt1[, `:=`(TABLE, NULL)]
  dt1 <- dt1[grep("^ *[[:alpha:]]", as.character(get(cnames[1])),
                  invert = TRUE, perl = TRUE)]
  cols.dup <- duplicated(colnames(dt1))
  if (any(cols.dup)) {
    .minfo(paste0("Cleaned duplicated column names: ",
                  paste(colnames(dt1)[cols.dup], collapse = ",")))
    dt1 <- dt1[, unique(cnames), with = FALSE]
  }
  cnames <- colnames(dt1)
  dt1[, `:=`((cnames), lapply(.SD, as.numeric))]
  dt1 <- as.data.frame(dt1)
  dt1
}