R/keepGood.R

In CentreForHydrology/CRHMr: Pre- and post- processing for CRHM

#' Keeps rows where there are some obs values
#'
#' @description Removes rows where all values are missing, keeps the remainder.
#' @param obs Required. A \pkg{CRHMr} obs dataframe.
#' @param quiet Optional. Suppresses display of messages, except for errors. If you
#' are calling this function in an \R script, you will usually leave \code{quiet=TRUE}
#' (i.e. the default). If you are working interactively, you will probably want to set
#' \code{quiet=FALSE}.
#' @param logfile Optional. Name of the file to be used for logging the action. Normally not used.
#' @return If successful, returns the dataframe containing all rows with any non-missing
#' alues. If unsuccessful (including if there are only missing values in the original data),
#' returns an error.
#' @author Kevin Shook
#' @seealso  \code{\link{trimObs}}
#' @examples
#' BadLake.good <- keepGood(BadLake7376)
#' @export

keepGood <- function(obs, quiet = TRUE, logfile = "") {
  # trims off rows where all obs are missing
  minval <- -99999
  if (nrow(obs) == 0) {
    stop("No obs values")
  }

  # check to see if all data are missing
  if (all(is.na(obs[, -1]))) {
    stop("No data present in data frame")
  }

  obsName <- deparse(substitute(obs))
  vals <- abs(data.frame(obs[, -1]))
  ncols <- ncol(obs) - 1

  # get smallest possible value
  mintotal <- ncols * minval

  # set missing values to minval

  vals[is.na(vals)] <- minval
  totals <- rowSums(vals)
  kept <- obs[totals > mintotal, ]

  # output info to screen and write to log file

  if (!quiet) {
    obs.info <- CRHM_summary(kept)
    print(obs.info)
  }

  comment <- paste("keepGood dataframe:", obsName, sep = "")
  result <- logAction(comment, logfile)
  if (result) {
    return(kept)
  } else {
    return(result)
  }
}