Bring 1.35.1 and 1.35.2 changes to release-1.35-stable

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: clinPK
 Type: Package
 Title: Clinical Pharmacokinetics Toolkit
-Version: 0.10.4
-Date: 2021-05-19
+Version: 0.10.5
+Date: 2021-06-11
 Authors@R: c(person("Ron", "Keizer", email = "ron@insight-rx.com", role
         = "aut"), person("Jasmine", "Hughes", email =
         "jasmine@insight-rx.com", role = "aut"), person("Dominic",

NAMESPACE

@@ -8,6 +8,7 @@ export(auc2dose)
 export(calc_abw)
 export(calc_aki_stage)
 export(calc_amts_for_conc)
+export(calc_baseline_scr)
 export(calc_bmi)
 export(calc_bsa)
 export(calc_creat)

R/calc_aki_stage.R

@@ -8,8 +8,9 @@
 #'   numeric (0.2)
 #' @param times creatinine sample times in hours
 #' @param method classification method, one of `KDIGO`, `RIFLE`, `pRIFLE` (case insensitive)
-#' @param baseline_scr baseline serum creatinine, required for `RIFLE` classifation. Will use value if numeric. If `character`, can be either `median` or `expected`. The latter will use the expected value based on sex and age.
+#' @param baseline_scr baseline serum creatinine, required for `RIFLE` classifation. Will use value if numeric. If `character`, can be either `median`, `median_before_treatment`, `lowest`, or `first`.
 #' @param baseline_egfr baseline eGFR, required for `RIFLE` classifations. Will take median of `egfr` values if `NULL`.
+#' @param first_dose_time time in hours of first dose relative to sCr value, used for calculate baseline serum creatinine in `median_before_treatment` approach.
 #' @param override_prifle_baseline by default, `pRIFLE` compares eGFR to 120 ml/min. Override by setting to TRUE.
 #' @param age age in years, needed when eGFR is used in the classification method
 #' @param egfr eGFR in ml/min/1.73m^2. Optional, can also be calcualted if `age`, `weight`, `height`, `sex`, `egfr_method` are specified as arguments.
@@ -39,6 +40,7 @@ calc_aki_stage <- function (
   method = "kdigo",
   baseline_scr = "median",
   baseline_egfr = NULL,
+  first_dose_time = NULL,
   age = NULL,
   egfr = NULL,
   egfr_method = NULL,
@@ -65,11 +67,18 @@ calc_aki_stage <- function (
       egfr_method <- "cockroft_gault"
     }
   }
+
+  ## Make sure values are ordered by time
+  if(!is.null(times)) {
+    idx   <- order(times)
+    times <- times[idx]
+    scr   <- scr[idx]
+    egfr  <- egfr[idx]
+  }
 
   if(is.null(scr) && method !='prifle') stop("No serum creatinine values provided.")
   if(is.null(times) && method !='prifle') stop("No sample times (days) provided.")
   if(class(times) == "Date") {
-    times <- times[order(times)]
     times <- as.numeric(difftime(times, min(times), units = "days"))
   }
   if((!class(times[1]) %in% c("numeric","integer")) && method !='prifle') {
@@ -96,17 +105,12 @@ calc_aki_stage <- function (
   }
   # pRIFLE does not require SCr
   if(class(baseline_scr) == "character" && method !='prifle') {
-    if(baseline_scr == "median") {
-      baseline_scr <- stats::median(scr)
-      if(verbose) message("No baseline SCr value specified, using *median* of supplied values.")
-    }
-    if(baseline_scr == "first" && method !='prifle') {
-      baseline_scr <- scr[1]
-      if(verbose) message("No baseline SCr value specified, using *first* of supplied values.")
-    }
-    if(baseline_scr == "expected" && method !='prifle') {
-      ## need to implement
-    }
+    baseline_scr <- calc_baseline_scr(baseline_scr, 
+                                      scr,
+                                      times,
+                                      method,
+                                      first_dose_time,
+                                      verbose)
   }
   if(method %in% ('prifle') && !(override_prifle_baseline)) baseline_egfr <- 120
 
@@ -129,7 +133,7 @@ calc_aki_stage <- function (
 
   ## Differences in SCr - don't need scr for pRIFLE
   if (method %in% c("kdigo", "rifle")) {
-    dat <- data.frame(scr = scr, t = times, deltat = c(0, diff(times)))
+    dat <- data.frame(scr = scr, t = times, deltat = c(0, diff(times)), baseline_scr = baseline_scr)
     dat$baseline_scr_diff <- (dat$scr - baseline_scr)
     dat$baseline_scr_reldiff <- dat$baseline_scr_diff / baseline_scr
     dat$stage <- rep(NA, length(scr))

R/calc_baseline_scr.R

@@ -0,0 +1,56 @@
+#' Calculate baseline sCr
+#' 
+#' @inheritParams calc_aki_stage
+#' @param baseline_scr baseline serum creatinine method (character). See calc_aki_stage() for availabloptions.
+#' 
+#' @export
+calc_baseline_scr <- function(
+  baseline_scr, 
+  scr,
+  times,
+  method,
+  first_dose_time = NULL,
+  verbose) {
+  if(baseline_scr == "median_before_treatment") {
+    if(is.null(first_dose_time)) {
+      baseline_scr <- stats::median(scr, na.rm = TRUE)
+      if(verbose) message("To calculate median baseline before treatment start need time of first dose. Using median over whole treatment period.")
+    } else {
+      if((!class(first_dose_time) %in% c("numeric","integer"))) {
+        stop("`first_dose_times` argument should be supplied as numeric (hours).")
+      }
+      if(any(times <= first_dose_time)) {
+        baseline_scr <- stats::median(scr[times <= first_dose_time], na.rm = TRUE)
+        if(verbose) message("No baseline SCr value specified, using *median* of supplied values before first dose.")
+      } else {
+        if(any(times < 48)) {
+          baseline_scr <- stats::median(scr[times < 48], na.rm = TRUE)
+          if(verbose) message("No baseline before first dose, using *median* of supplied values in first 48 hours.")
+        } else {
+          baseline_scr <- stats::median(scr, na.rm = TRUE)
+          if(verbose) message("No baseline in first 48 hours, using *median* of supplied values.")
+        }
+      }
+    }
+  }
+  if(baseline_scr == "median") {
+    baseline_scr <- stats::median(scr)
+    if(verbose) message("No baseline SCr value specified, using *median* of supplied values.")
+  }
+  if(baseline_scr == "first" && method !='prifle') {
+    baseline_scr <- scr[1]
+    if(verbose) message("No baseline SCr value specified, using *first* of supplied values.")
+  }
+  if(baseline_scr == "lowest") {
+    baseline_scr <- min(scr)
+    if(verbose) message("No baseline SCr value specified, using *lowest* of supplied values.")
+  }
+  if(baseline_scr == "expected" && method !='prifle') {
+    ## TODO: need to implement
+  }
+  if(! class(baseline_scr) %in% c("numeric", "integer")) {
+    stop("Requested baseline calculation method not recognized.")
+  }
+
+  baseline_scr
+}

R/weight2kg.R

@@ -1,7 +1,7 @@
 #' Convert any weight unit to kg
 #'
 #' @param value weight in any allowed unit
-#' @param unit unit of weight, one of "lbs", "pound", "pounds", "oz", "ounce", "ounces"
+#' @param unit unit of weight, one of "lbs", "pound", "pounds", "oz", "ounce", "ounces", "g", "gram", "grams"
 #' @examples
 #' weight2kg(250, unit = "oz")
 #' weight2kg(250, unit = "pounds")
@@ -12,13 +12,16 @@ weight2kg <- function(value = NULL, unit = NULL) {
     stop("No weight value specified.")
   }
   if(!is.null(unit) && !is.na(unit)) {
-    if(tolower(unit) %in% c("kg", "lbs", "pound", "pounds", "oz", "ounce", "ounces")) {
+    if(tolower(unit) %in% c("kg", "lbs", "pound", "pounds", "oz", "ounce", "ounces", "g", "gram", "grams")) {
       if(tolower(unit) %in% c("lbs", "pound", "pounds")) {
         value <- value / 2.20462
       }
       if(tolower(unit) %in% c("oz", "ounce", "ounces")) {
         value <- value / 35.274
       }
+      if (tolower(unit) %in% c("g", "gram", "grams")) {
+        value <- value / 1000
+      }
     } else {
       warning(paste0("Unit (", unit,") not recognized, returning original weight."))
     }

tests/testthat/test_calc_aki_stage.R

@@ -159,3 +159,46 @@ test_that("calc_aki_stage errors if can't coerce scr to numeric", {
     )
   )
 })
+
+test_that("calc_aki_stage correctly calculates baseline_scr", {
+  test11 <- calc_aki_stage(
+    method = "kDIGO",
+    scr = c(0.5, 1.5),
+    t = c(0, 24),
+    egfr = c(50, 30),
+    baseline_scr = "median",
+    first_dose_time = 50,
+    verbose = FALSE
+  )
+  expect_equal(test11$data$baseline_scr, c(1,1))
+  test12 <- calc_aki_stage(
+    method = "kDIGO",
+    scr = c(0.5, 1.0, 1.5),
+    t = c(0, 10, 24),
+    egfr = c(50, 40, 30),
+    baseline_scr = "median_before_treatment",
+    first_dose_time = 12,
+    verbose = FALSE
+  )
+  expect_equal(test12$data$baseline_scr, c(0.75, 0.75, 0.75))
+  expect_equal(
+    calc_aki_stage(
+      method = "kDIGO",
+      scr = c(0.5, 1.0, 1.5),
+      t = c(0, 10, 24),
+      egfr = c(50, 40, 30),
+      baseline_scr = "lowest",
+      first_dose_time = 12,
+      verbose = FALSE
+    )$data$baseline_scr, rep(0.5, 3))
+  expect_error(
+    calc_aki_stage(
+      method = "kDIGO",
+      scr = c(0.5, 1.0, 1.5),
+      t = c(0, 10, 24),
+      egfr = c(50, 40, 30),
+      baseline_scr = "typo",
+      first_dose_time = 12,
+      verbose = FALSE
+    )$data$baseline_scr)
+})

tests/testthat/test_weight2kg.R

@@ -34,3 +34,7 @@ test_that("vectorized input works", {
     c(4.0823362, 4.5359291)
   )
 })
+
+test_that("weight2kg supports grams as input unit", {
+  expect_equal(weight2kg(1000, "g"), 1)
+})