R/labels.R

In kfre: Kidney Failure Risk Equation (KFRE) Tools

#' Label CKD stages or ESRD outcomes.
#'
#' @param df Data frame with an eGFR column.
#' @param col Column name with ESRD event indicator, 0 or 1.
#' @param years Integer horizon, 2 or 5.
#' @param duration_col Column name with follow up time in days.
#' @param prefix Optional prefix for the derived outcome column.
#' @param create_years_col Logical, add a `<years>_year_outcome` column.
#' @return The modified data frame with added label columns.
#' @export
#' @examples
#' df <- data.frame(
#'   eGFR = c(90, 45, 25, 10),
#'   esrd = c(0, 0, 1, 0),
#'   followup_days = c(365, 800, 500, 1200)
#' )
#' class_esrd_outcome(
#'   df,
#'   col = "esrd",
#'   years = 2,
#'   duration_col = "followup_days"
#' )
#' 
class_esrd_outcome <- function(df, col, years, duration_col, prefix = NULL,
                               create_years_col = TRUE) {
  years_col <- duration_col
  if (isTRUE(create_years_col)) {
    years_col <- "ESRD_duration_years"
    df[[years_col]] <- df[[duration_col]] / 365.25
  }
  cname <- if (is.null(prefix)) {
    sprintf("%s_year_outcome", years)
  } else {
    sprintf("%s_%s_year_outcome", prefix, years)
  }
  if (cname %in% names(df)) df[[cname]] <- NULL
  df[[cname]] <- ifelse(df[[col]] == 1 & df[[years_col]] <= years, 1, 0)
  df
}
#' Label CKD stages or ESRD outcomes.
#'
#' @param df Data frame input.
#' @param egfr_col Column name for eGFR, mL/min/1.73 m^2.
#' @param stage_col Output column name for detailed CKD stages.
#' @param combined_stage_col Output column for combined stages 3 to 5.
#' @return The modified data frame with added label columns.
#' @export
#' @examples
#' df <- data.frame(eGFR = c(92, 58, 42, 28, 12))
#' class_ckd_stages(df, egfr_col = "eGFR")
class_ckd_stages <- function(df, egfr_col = "eGFR", stage_col = NULL,
                             combined_stage_col = NULL) {
  if (!is.null(stage_col)) {
    x <- df[[egfr_col]]
    df[[stage_col]] <- ifelse(x >= 90, "CKD Stage 1",
      ifelse(x >= 60, "CKD Stage 2",
        ifelse(x >= 45, "CKD Stage 3a",
          ifelse(x >= 30, "CKD Stage 3b",
            ifelse(x >= 15, "CKD Stage 4", "CKD Stage 5")
          )
        )
      )
    )
    df[[stage_col]][is.na(x)] <- "Not Classified"
  }
  if (!is.null(combined_stage_col)) {
    x <- df[[egfr_col]]
    df[[combined_stage_col]] <- ifelse(x < 60,
      "CKD Stage 3 - 5",
      "Not Classified"
    )
  }
  df
}