missings.R

####################################################################
#' Calculate and Visualize Missingness
#'
#' This function lets the user calculate the percentage of NAs or
#' missingness in a data.frame. It also plots the results if needed.
#'
#' @family Exploratory
#' @family Missing Values
#' @param df Dataframe. Dataframe to study
#' @param plot Boolean. Do you wish to plot results?
#' @param full Boolean. Return all variables (or only with missings)?
#' @param subtitle Character. Subtitle to show in plot
#' @param summary Boolean. Show numerical summary text?
#' @return data.frame with each variable, number of missing values and percentage.
#' If \code{plot=TRUE}, a plot with the same information reflected.
#' @examples
#' Sys.unsetenv("LARES_FONT") # Temporal
#'
#' # Dummy data
#' df <- data.frame(
#'   A = c(1:5),
#'   B = c(NA, NA, 1, 1, 1),
#'   C = rep(NA, 5),
#'   D = c(NA, LETTERS[1:4])
#' )
#'
#' # Missing values summary
#' missingness(df)
#'
#' # Visual results
#'
#' missingness(df, plot = TRUE)
#'
#' # Show all variables (including those with no missing values)
#' missingness(df, plot = TRUE, full = TRUE)
#' @export
missingness <- function(df, plot = FALSE, full = FALSE,
                        subtitle = NA, summary = TRUE) {
  if (sum(is.na(df)) == 0) {
    if (summary) message("No missing values found!")
    invisible(return(NULL))
  }

  m <- df %>%
    ungroup() %>%
    summarize_all(.funs = ~ sum(is.na(.))) %>%
    gather() %>%
    arrange(desc(.data$value)) %>%
    filter(.data$value > 0) %>%
    mutate(missing = round(100 * .data$value / nrow(df), 2))
  colnames(m) <- c("variable", "missing", "missingness")

  if (plot) {
    obs <- nrow(df) * ncol(df)
    miss <- sum(m$missing)
    missp <- 100 * miss / obs
    note <- sprintf(
      "%s cols x %s rows | Values: %s | Missing: %s (%s)",
      formatNum(ncol(df), 0),
      formatNum(nrow(df), 0),
      formatNum(obs, 0),
      formatNum(miss, 0),
      formatNum(missp, 1, pos = "%")
    )


    p <- is.na(df) %>%
      data.frame() %>%
      tidyr::gather() %>%
      {
        if (!full) {
          filter(., .data$key %in% m$variable)
        } else {
          .
        }
      } %>%
      mutate(type = ifelse(.data$key %in% m$variable, "with", "without")) %>%
      group_by(.data$key) %>%
      mutate(row_num = row_number()) %>%
      mutate(perc = round(100 * sum(.data$value) / nrow(df), 2)) %>%
      mutate(label = ifelse(.data$type == "with", paste0(.data$key, " | ", .data$perc, "%"), .data$key)) %>%
      arrange(.data$value) %>%
      ggplot(aes(x = reorder(.data$label, .data$perc), y = .data$row_num, fill = .data$value)) +
      geom_raster() +
      coord_flip() +
      {
        if (full) {
          facet_grid(.data$type ~ ., space = "free", scales = "free")
        }
      } +
      {
        if (summary) {
          scale_y_comma(note, expand = c(0, 0))
        } else {
          scale_y_comma(NULL, expand = c(0, 0))
        }
      } +
      scale_fill_grey(name = NULL, labels = c("Present", "Missing"), expand = c(0, 0)) +
      labs(title = "Missing values", x = "", subtitle = if (!is.na(subtitle)) subtitle) +
      theme_lares(legend = "top") +
      theme(axis.text.y = element_text(size = 8))

    return(p)
  }
  return(m)
}


####################################################################
#' Impute Missing Values (using MICE)
#'
#' This function uses the MICE methodology to impute missing values.
#'
#' @family Data Wrangling
#' @family Machine Learning
#' @family Missing Values
#' @param df Dataframe. Dataframe to transform.
#' @param m Integer. Number of multiple imputations.
#' @param iters Integer. Number of iterations.
#' @param seed Integer. Set a seed for reproducibility.
#' @param quiet Boolean. Keep quiet? (or print replacements).
#' @return data.frame with imputed values.
#' @export
impute <- function(df, m = 5, iters = 5, seed = 0, quiet = FALSE) {
  try_require("mice")
  on.exit(set.seed(seed))
  aux <- mice(df, seed = seed, m = m, maxit = iters, printFlag = !quiet)
  ret <- complete(aux)
  return(ret)
}