R/Missing_Values.R

In KO112/KO: Kevin O'Brien's Personal Package

# Allow convenient use of functions from other packages
#' @include Pipes.R
#' @include Error_Handling.R
NULL


#' Find the percent of missing values
#' 
#' Count the percent of missing values in a vector.
#' Counts the percent of NA values for non-character vectors,
#'   and the number of NA or "" values for characters.
#' 
#' @param vec Vector to count missing values in.
#' 
#' @return Numeric scalar containing the percent of missing values.
#' @export
#' 
#' @examples
#' percent_missing(c(NA))
#' percent_missing(c(1, 2, 3, 4, 5))
#' percent_missing(c(1, 2, NA, 4, 5))
#' 
percent_missing <- function(vec) {
  # if (is.numeric(vec) | is.logical(vec) | lubridate::is.Date(vec) | is.factor(vec)) {
  #   numMissing <- sum(is.na(vec))
  # } else if (is.character(vec)) {
  #   numMissing <- sum(vec == "", na.rm = TRUE) + sum(is.na(vec))
  # } else {
  #   message("Unknown vector data type: ", class(vec))
  #   numMissing <- sum(is.na(vec))
  # }
  return(num_missing(vec) / length(vec))
}


#' Find the number of missing values
#' 
#' Count the number of missing values in a vector.
#' Counts the number of NA values for non-character vectors,
#'   and the number of NA or "" values for characters.
#' 
#' @param vec Vector to count missing values in.
#' 
#' @return Numeric scalar containing the number of missing values.
#' @export
#' 
#' @examples
#' num_missing(c(NA))
#' num_missing(c(1, 2, 3, 4, 5))
#' num_missing(c(1, 2, NA, 4, 5))
#' 
num_missing <- function(vec) {
  if (is.numeric(vec) | is.logical(vec) | lubridate::is.Date(vec) | is.factor(vec)) {
    numMissing <- sum(is.na(vec))
  } else if (is.character(vec)) {
    numMissing <- sum(is.na(vec)) + sum(vec == "", na.rm = TRUE)
  } else {
    message("Unknown vector data type: ", class(vec))
    numMissing <- sum(is.na(vec))
  }
  return(numMissing)
}


#' Replace missing values in a vector
#' 
#' Replace missing values in a vector with either the mode, median,
#'   or mean of the vector, removing NA values in the calculation.
#' 
#' @param vec Vector in which to replace missing values.
#' @param method The method to use to determine the imputed value.
#' @param with The value to impute missing values with (if specified, method will be ignored).
#' @param return_imputed Whether or not to return the value that missing elements were imputed with.
#' 
#' @return Vector with missing values replaced as desired,
#'   or a list of that and the replacement (imputed) value.
#' @export
#' 
#' @examples
#' replace_missing(c(1, 1, 1, 2, NA))
#' replace_missing(c(1, 1, 1, 2, NA), method = "mode") # Same as above
#' replace_missing(c(1, NA, 1, 2), method = "median")
#' replace_missing(c(1, NA, 1, 2), method = "mean")
#' replace_missing(c(1, NA, 1, 2), method = "mean", return_imputed = TRUE)
#' replace_missing(c(1, NA, 1, 2), with = 5)
#' replace_missing(c(1, NA, 1, 2), method = "mean", with = 5)
#' 
replace_missing <- function(vec, method = "mode", with, return_imputed = FALSE) {

  # Find the value to replace missing values with based on the desired method,
  #   ensuring that we have a numeric vector for median and mean
  if (!missing(with)) {
    if (!missing(method)) warning(paste0("Both the 'method' and 'with' fields were specified ",
                                         "inside the 'replace_missing' function. ",
                                         "The 'method' field will be ignored."))
    imputedVal <- with
  } else if (method == "median") {
    stop_if(!is.numeric(vec), "Can only calculate median for numeric vector.")
    imputedVal <- stats::median(vec, na.rm = TRUE)
  } else if (method == "mean") {
    stop_if(!is.numeric(vec), "Can only calculate mean for numeric vector.")
    imputedVal <- mean(vec, na.rm = TRUE)
  } else {
    if (method != "mode") message("Invalid method chosen to replace missing values. Mode will be used.")
    imputedVal <- table(vec, useNA = "no") %>% sort() %>% utils::tail(1) %>% names()
  }

  # Convert the imputed value to the appropriate type
  if (lubridate::is.Date(vec)) {
    imputedVal <- lubridate::as_date(imputedVal)
  } else if (is.factor(vec)) {
    imputedVal <- as.character(imputedVal)
  } else {
    imputedVal <- as.vector(imputedVal, mode = class(vec))
  }

  # Replace NA/missing values with the imputed value, and return the vector
  if (is.numeric(vec) | is.factor(vec) | is.logical(vec) | lubridate::is.Date(vec)) {
    vec[is.na(vec)] <- imputedVal
  } else if (is.character(vec)) {
    vec[(vec == "") | is.na(vec)] <- imputedVal
  } else {
    message("Unknown vector data type: ", class(vec))
    vec[is.na(vec)] <- imputedVal
  }

  # Return the vector, and the imputed value as well if desired
  if (return_imputed) return(list(Vec = vec, ImputedVal = imputedVal))
  return(vec)

}