R/post-get-HSPF-sup-file.R

In kbrannan/bacteriaSourceModels: Models for estimation of bacteria loads from several sources

#' get reads in HSPF-sup-file and returns a long-format data.frame with accum and sqolim info
#'
#' @param chr.file.sup is the file name for the HSPF-sup-file (includes path if necessary)
#' @export

post.get.HSPF.sup.file <- function(chr.file.sup) {
  options(stringsAsFactors = FALSE)

  chr.sup <- scan(file = chr.file.sup,
                  what = "character",
                  sep = "\n", quiet = TRUE)
  lng.accum.st <- grep("MON-ACCUM", chr.sup)
  lng.sqolim.st <- grep("MON-SQOLIM", chr.sup)
  lng.accum.blk <- c(lng.accum.st, lng.sqolim.st - 1)
  lng.sqolim.blk <- c(lng.sqolim.st, length(chr.sup))
  chr.sup.accum <- chr.sup[lng.accum.blk[1]:lng.accum.blk[2]]
  chr.sup.sqolim <- chr.sup[lng.sqolim.blk[1]:lng.sqolim.blk[2]]
  make.mon.df <- function(chr.table, chr.pre = "") {

    chr.sup.line <- gsub("(( ){1,}12)|[^0-9]","",
                         chr.table[seq(from = 1,
                                       to = length(chr.table),
                                       by = 2)])
    df.table <- as.data.frame(
      cbind(
        strftime(as.POSIXct(paste0("1967-",1:12,"-1")), format = "%b"),
        do.call(cbind,
                strsplit(chr.table[
                  seq(from = 2, to = length(chr.table), by = 2)],
                  split = "( ){1,}"))[-1,]))

    names(df.table) <- c("month", paste0(chr.pre, "supln",chr.sup.line))
    return(df.table)
  }
  df.accum <- make.mon.df(chr.sup.accum, "accum")
  df.sqolim <- make.mon.df(chr.sup.sqolim, "sqolim")
  make.long <- function(df.cur) {
    df.sup <- data.frame(character(0), character(0))
    for(ii in 2:length(names(df.cur))) {
      df.sup <- rbind(df.sup,
                      cbind(paste0(names(df.cur)[ii], df.cur$month),
                            df.cur[, ii]))
    }
    df.sup <- data.frame(df.sup)
    names(df.sup) <- c("varname", "value")
    return(df.sup)
  }
  df.sup <- rbind(make.long(df.accum), make.long(df.sqolim))
}