Merge pull request #6 from alwinw/dev/aki-calc

Added aki.units() method

.Rbuildignore

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

DESCRIPTION

@@ -21,12 +21,16 @@ 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,
+    units,
+    lubridate
 Suggests:
     testthat,
     covr

NAMESPACE

@@ -3,4 +3,5 @@
 S3method(aki,default)
 S3method(aki,numeric)
 S3method(aki,ts)
+S3method(aki,units)
 export(aki)

R/aki.R

@@ -1,24 +1,67 @@
+.sCr2metric <- function(SCr) {
+  if (grepl("mol", units::deparse_unit(SCr))) {
+    return(units::set_units(SCr * units::set_units(113.120, "g/mol"), "mg/dl"))
+  } else {
+    return(units::set_units(SCr, "mg/dl"))
+  }
+}
+
 #' 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, consider changing to a list
+#' @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, ...) {
+  SCr <- units::as_units(SCr, units)
+  if (is.null(bCr)) {
+    bCr <- min(SCr, na.rm = na.rm) # Must be run after as_units(SCr, ...)
+  }
+  else {
+    bCr <- units::as_units(bCr, units)
+  }
+  aki_stages <- aki.units(SCr = SCr, bCr = bCr, na.rm = na.rm)
+  return(aki_stages)
+}
+
+#' @rdname aki
+#' @export
+aki.units <- function(SCr, bCr = NULL, na.rm = FALSE, ...) {
   if (is.null(bCr)) bCr <- min(SCr, na.rm = na.rm)
   aki_stages <- dplyr::case_when(
+    .sCr2metric(SCr) >= units::set_units(4.0, mg / dl) ~ .aki_stages[3],
     SCr >= 3.0 * bCr ~ .aki_stages[3],
     SCr >= 2.0 * bCr ~ .aki_stages[2],
     SCr >= 1.5 * bCr ~ .aki_stages[1],
@@ -27,15 +70,15 @@ aki.numeric <- function(SCr, bCr = NULL, na.rm = FALSE) {
   return(aki_stages)
 }
 
+
 #' @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)
 }

R/utils.R

@@ -0,0 +1 @@
+# set_units(set_units(1:5, mg/dl) * set_units(2, mol/g), mol/l)

tests/testthat/test-aki.R

@@ -1,3 +1,17 @@
+test_that(".sCr2metric() conversion 88.4 umol/l to 1mg/dl is correct", {
+  expect_lte(
+    abs(.sCr2metric(units::set_units(88.4, "umol/l")) - units::set_units(1, "mg/dl")),
+    units::set_units(1e-4, "mg/dl")
+  )
+})
+
+test_that(".sCr2metric() conversion 353.6 umol/l to 4mg/dl is correct", {
+  expect_lte(
+    abs(.sCr2metric(units::set_units(353.6, "umol/l")) - units::set_units(4, "mg/dl")),
+    units::set_units(1e-4, "mg/dl")
+  )
+})
+
 test_that("aki() for numeric vector of SCr with no baseline", {
   SCr <- seq(60, 200, by = 20)
   aki_stages <- forcats::fct_c(
@@ -27,3 +41,55 @@ test_that("aki() for numeric vector of SCr with baseline", {
   )
   expect_equal(aki(SCr, bCr = 50), aki_stages)
 })
+
+test_that("aki() for vector of SCr in mg/dl with no baseline", {
+  SCr <- units::set_units(seq(1.5, 4.5, by = 0.5), "mg/dl")
+  aki_stages <- forcats::fct_c(
+    .aki_stages[length(.aki_stages)],
+    .aki_stages[length(.aki_stages)],
+    .aki_stages[1],
+    .aki_stages[2],
+    .aki_stages[2],
+    .aki_stages[3],
+    .aki_stages[3]
+  )
+  expect_equal(aki(SCr), aki_stages)
+})
+
+test_that("aki() for vector of SCr in mg/dl with baseline", {
+  SCr <- units::set_units(seq(2.0, 4.5, by = 0.5), "mg/dl")
+  bCr <- units::set_units(1.5, "mg/dl")
+  aki_stages <- forcats::fct_c(
+    .aki_stages[length(.aki_stages)],
+    .aki_stages[1],
+    .aki_stages[2],
+    .aki_stages[2],
+    .aki_stages[3],
+    .aki_stages[3]
+  )
+  expect_equal(aki(SCr, bCr), aki_stages)
+})
+
+data <- data.frame(
+  pt_id = c(rep("pt1", 11), rep("pt2", 13)),
+  dttm = c(
+    seq(
+      lubridate::as_datetime("2020-10-18 09:00:00", tz = "Australia/Melbourne"),
+      lubridate::as_datetime("2020-10-20 09:00:00", tz = "Australia/Melbourne"),
+      length.out = 11
+    ),
+    seq(
+      lubridate::as_datetime("2020-10-18 10:00:00", tz = "Australia/Melbourne"),
+      lubridate::as_datetime("2020-10-29 10:00:00", tz = "Australia/Melbourne"),
+      length.out = 13
+    )
+  ),
+  SCr = c(
+    units::set_units(seq(2.0, 4.5, by = 0.25), "mg/dl"),
+    units::set_units(seq(3.0, 4.2, by = 0.10), "mg/dl")
+  ),
+  bCr = c(
+    rep(units::set_units(1.8, "mg/dl"), 11),
+    rep(units::set_units(3.0, "mg/dl"), 13)
+  )
+)