Made S3 generic/method consistent

.Rbuildignore

@@ -14,3 +14,4 @@
 ^\.png$
 ^README_cache/
 ^codecov\.yml$
+^resources$

DESCRIPTION

@@ -21,12 +21,14 @@ License: MIT + file LICENSE
 URL: https://github.com/alwinw/epocakir
 BugReports: https://github.com/alwinw/epocakir/issues
 Depends:
-    R
+    R (>= 3.5.0)
 Imports:
     dplyr,
     tidyselect,
     tibble,
-    forcats
+    forcats,
+    ellipsis,
+    rlang
 Suggests:
     testthat,
     covr

R/aki.R

@@ -1,24 +1,46 @@
 #' Codify AKI from Serum Creatinine and/or Urine Output
 #'
-#' Some additional details
+#' Using KDIGO Clinical Practice Guideline for Acute Kidney Injury
+#' Volume 2 | Issue 1 | March 2012
 #'
-#' @param x numeric number
+#' Provided a series of Serum Creatinine readings and/or Urine Output, aki()
+#' calculates whether or not a patient has AKI. The staging (1, 2, 3) of AKI is
+#' also calculated
 #'
-#' @return
+#' @param data A data.frame with the data needed for serum creatinine (SCr)
+#'   and/or urine output (UO)
+#' @param SCr The variable name, e.g. "cr", to be used for determining
+#'   AKI based on creatinine level. A numeric vector or time series of
+#'   serum creatinine values if the data argument is unused
+#' @param UO The variable name, e.g. "urine", to be used for determining
+#'   AKI based on urine output. A numeric vector or time series of
+#'   urine output values if the data argument is unused
+#' @param bCr The variable name, e.g. "baseline_cr", to be used for determining
+#'   AKI based on urine output. A single numeric value of
+#'   baseline creatinine if the data argument is unused
+#' @param units (character) Units of SCr and UO metric (mg/dl) or SI (umol/l)
+#'   #TOFIX
+#' @param na.rm (logical) If TRUE, missing values are removed
+#' @param ... Further optional arguments that will be passed to method.
 #'
 #' @examples
+#' aki(seq(60, 200, by = 20))
+#' aki(SCr = seq(60, 200, by = 20), bCr = 50)
 #' @export
-aki <- function(x, ...) {
-  UseMethod("aki", x)
+aki <- function(...) {
+  ellipsis::check_dots_used()
+  UseMethod("aki")
 }
 
 .aki_stages <- factor(c("AKI Stage 1", "AKI Stage 2", "AKI Stage 3", "No AKI"))
 
+
 #' @rdname aki
 #' @export
-aki.numeric <- function(SCr, bCr = NULL, na.rm = FALSE) {
+aki.numeric <- function(SCr, bCr = NULL, units = "umol/l", na.rm = FALSE, ...) {
   if (is.null(bCr)) bCr <- min(SCr, na.rm = na.rm)
   aki_stages <- dplyr::case_when(
+    # Need one for SCr > X
     SCr >= 3.0 * bCr ~ .aki_stages[3],
     SCr >= 2.0 * bCr ~ .aki_stages[2],
     SCr >= 1.5 * bCr ~ .aki_stages[1],
@@ -29,13 +51,12 @@ aki.numeric <- function(SCr, bCr = NULL, na.rm = FALSE) {
 
 #' @rdname aki
 #' @export
-aki.ts <- function(ts_data) {
+aki.ts <- function(SCr, UO, units = "umol/l", ...) {
 
 }
 
-
 #' @rdname aki
 #' @export
-aki.default <- function(x) {
-  factor(x, levels = .aki_stages)
+aki.default <- function(data, SCr, bCr, units = list("SCr" = "umol/l"), na.rm = FALSE, ...) {
+  factor(data, levels = .aki_stages)
 }