Reuse aki.units

alwinw · Oct 25, 2020 · cf8ced2 · cf8ced2
1 parent 8b9c568
commit cf8ced2
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Showing 2 changed files with 42 additions and 42 deletions.
diff --git a/R/aki.R b/R/aki.R
@@ -81,28 +81,23 @@ aki.default <- function(data,
                         aki = "aki",
                         units = list("SCr" = "umol/l"), na.rm = FALSE, ...) {
   # TODO check if aki is an existing company
-  # Check SCr or bCr are given1
+  # Check SCr or bCr are given!
   # Calc bCr if not given
   # TODO consider fuctionalising aki.bCr, etc
 
   data %>%
-    dplyr::mutate("{aki}.test" := !!as.name(SCr) * 2) %>%
     dplyr::mutate(
-      "{aki}.bCr" := dplyr::case_when(
-        .sCr2metric(!!as.name(SCr)) >= units::set_units(4.0, "mg/dl") ~ .aki_stages[3],
-        !!as.name(SCr) >= 3.0 * !!as.name(bCr) ~ .aki_stages[3],
-        !!as.name(SCr) >= 2.0 * !!as.name(bCr) ~ .aki_stages[2],
-        !!as.name(SCr) >= 1.5 * !!as.name(bCr) ~ .aki_stages[1],
-        TRUE ~ .aki_stages[length(.aki_stages)]
-      )
+      "{aki}.bCr" := aki.units(!!as.name(SCr), !!as.name(bCr))
+    ) %>%
+    dplyr::mutate(
+      "{aki}.cr_ch" := !!as.name(SCr) * 2
     )
 }
 
 
 #' @importFrom rlang .data
 #' @importFrom rlang `:=`
 .generate_cr_ch <- function(data, SCr, dttm, pt_id = NULL) {
-  # TODO break into 48hr increments to reduce combn
   # TODO Consider saving current grouping settings e.g. dplyr::group_data()
   # Ref: https://tidyeval.tidyverse.org/dplyr.html
   data_gr <- data[, c(SCr, dttm)]
@@ -118,7 +113,8 @@ aki.default <- function(data,
     unique() %>%
     dplyr::mutate(
       admin = cumsum(
-        (dttm - dplyr::lag(dttm, default = lubridate::as_date(0))) >= lubridate::duration(hours = 48)
+        (dttm - dplyr::lag(dttm, default = lubridate::as_date(0))) >=
+          lubridate::duration(hours = 48)
       )
     ) %>%
     dplyr::group_by(.data$admin, .add = TRUE)

diff --git a/tests/testthat/test-aki.R b/tests/testthat/test-aki.R
@@ -56,39 +56,43 @@ test_that("aki() for vector of SCr in mg/dl with baseline", {
   expect_equal(aki(SCr, bCr), aki_stages)
 })
 
-pt_id <- "pt_id_"
-dttm <- "dttm_"
-SCr <- "SCr_"
-bCr <- "bCr_"
-aki <- "aki"
-data_ <- data.frame(
-  pt_id_ = c(rep("pt1", 11 + 7), 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
+# Test for .generate_cr_ch
+
+test_that("aki() for dataframe of SCr and bCr only", {
+  pt_id <- "pt_id_"
+  dttm <- "dttm_"
+  SCr <- "SCr_"
+  bCr <- "bCr_"
+  aki <- "aki"
+  data_ <- data.frame(
+    pt_id_ = c(rep("pt1", 11 + 7), 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("2020-10-23 09:00:00", tz = "Australia/Melbourne"),
+        lubridate::as_datetime("2020-10-25 09:00:00", tz = "Australia/Melbourne"),
+        length.out = 7
+      ),
+      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
+      )
     ),
-    seq(
-      lubridate::as_datetime("2020-10-23 09:00:00", tz = "Australia/Melbourne"),
-      lubridate::as_datetime("2020-10-25 09:00:00", tz = "Australia/Melbourne"),
-      length.out = 7
+    SCr_ = c(
+      units::set_units(seq(2.0, 4.5, by = 0.25), "mg/dl"),
+      units::set_units(seq(2.5, 4.0, by = 0.25), "mg/dl"),
+      units::set_units(seq(3.0, 4.2, by = 0.10), "mg/dl")
     ),
-    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
+    bCr_ = c(
+      rep(units::set_units(1.8, "mg/dl"), 11 + 7),
+      rep(units::set_units(3.0, "mg/dl"), 13)
     )
-  ),
-  SCr_ = c(
-    units::set_units(seq(2.0, 4.5, by = 0.25), "mg/dl"),
-    units::set_units(seq(2.5, 4.0, 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 + 7),
-    rep(units::set_units(3.0, "mg/dl"), 13)
   )
-)
 
-data <- data_[sample(nrow(data_)), ]
+  data <- data_[sample(nrow(data_)), ]
+})