Add test for getDrugPK

DESCRIPTION

@@ -20,6 +20,7 @@ Imports:
   ggplot2  (>= 3.2),
   ggpubr,
   grid,
+  here,
   httr,
   jpeg,
   jsonlite,
@@ -44,7 +45,6 @@ Imports:
   tidyr,
 Suggests:
     devtools,
-    here,
     rsconnect,
     testthat,
     yaml,

R/getDrugPK.R

@@ -1,11 +1,11 @@
 # Get the pharmacokinetic and pharmacodynamic value for a drug based on
 # patient covariates
 getDrugPK <- function(
-  drug = "propofol",
-  weight = 70,
-  height = 170,
-  age = 50,
-  sex = "male",
+  drug,
+  weight,
+  height,
+  age,
+  sex,
   drugDefaults
 )
 {

R/globalVariables.R

@@ -1,3 +1,4 @@
+library(here)
 
 facetFont <-      c(  20,   18,   18,   16,   14,   14,   14,   13,   13,   12,   11,   10,    9,    9,   8,  8)
 labelFont <-      c(  16,   15,   14,   13,   12,   11,   9,    8,    8,    7,    6,    6,    5,    5,   5,  5)
@@ -57,3 +58,15 @@ maxtimes <- data.frame(
   times = c(10, 30, 60, 90, 120, 180, 240, 300, 360, 480, 600, 720, 1440, 1680, 1920, 2880, 4320, 5760,7200, 1000000 ),
   steps = c( 1,  5, 10, 15,  15,  30,  30,  60,  60,  60, 120, 120, 240,  240, 240,  480,   480,  720, 720, 1440)
 )
+
+eventDefaults <- read.csv(here("data", "Event Defaults.csv"), stringsAsFactors = FALSE)
+
+drugUnitsExpand <- function(units) {
+  strsplit(units, ",")
+}
+
+drugDefaults_global <- (function() {
+  drugDefaults <- read.csv(here("data", "Drug Defaults.csv"), stringsAsFactors = FALSE, na.strings = "")
+  drugDefaults$Units <- drugUnitsExpand(drugDefaults$Units)
+  drugDefaults
+})()

global.R

@@ -41,10 +41,9 @@ for (file in list.files("R", pattern = "\\.R$")) {
 #CANCEL <- readPNG("www/cancel.png", native=TRUE)
 enableBookmarking(store = "url")
 
-eventDefaults_global <- read.csv("data/Event Defaults.csv", stringsAsFactors = FALSE)
-eventDefaults <- eventDefaults_global
-
-drugDefaults_global <- read.csv("data/Drug Defaults.csv", stringsAsFactors = FALSE, na.strings = "")
+drugUnitsSimplify <- function(units) {
+  unlist(lapply(units, paste, collapse = ","))
+}
 
 # Load individual drug routines
 for (drug in drugDefaults_global$Drug) {
@@ -88,14 +87,6 @@ nothingtoPlot <- staticPlot(
   )
 )
 
-drugUnitsExpand <- function(units) {
-  strsplit(units, ",")
-}
-drugUnitsSimplify <- function(units) {
-  unlist(lapply(units, paste, collapse = ","))
-}
-drugDefaults_global$Units <- drugUnitsExpand(drugDefaults_global$Units)
-
 blanks <- rep("", 6)
 doseTableInit <- data.frame(
   Drug = c("propofol","fentanyl","remifentanil","rocuronium", blanks),

tests/testthat/test-getDrugPK.R

@@ -0,0 +1,111 @@
+context("getDrugPKtest")
+
+#library(shiny)
+library(here)
+
+source(here('data', 'drugs', 'propofol.R'))
+
+test_that("it returns the same value", {
+  drug <- "propofol"
+  weight <- 70
+  height <- 170
+  age <- 50
+  sex <- "male"
+  drugDefaults <- drugDefaults_global
+#  drugDefaults <- shiny::reactiveVal(drugDefaults_global)/
+
+
+  actual <- getDrugPK(drug, weight, height, age, sex, drugDefaults)
+  expected <- list(
+    drug = "propofol",
+    PK = list(
+      default = list(
+        v1 = 6.283078,
+        v2 = 20.17078,
+        v3 = 1004.196,
+        cl1 = 1.551355,
+        cl2 = 1.516118,
+        cl3 = 2.97701,
+        k10 = 0.24691,
+        k12 = 0.2413017,
+        k13 = 0.473814,
+        k21 = 0.07516406,
+        k31 = 0.002964571,
+        ka_PO = 0,
+        bioavailability_PO = 0,
+        tlag_PO = 0,
+        ka_IM = 0,
+        bioavailability_IM = 0,
+        tlag_IM = 0,
+        ka_IN = 0,
+        bioavailability_IN = 0,
+        tlag_IN = 0,
+        customFunction = "",
+        lambda_1 = 0.9834275,
+        lambda_2 = 0.05572286,
+        lambda_3 = 0.001004003,
+        ke0 = 0.3973057,
+        p_coef_bolus_l1 = 0.1555113,
+        p_coef_bolus_l2 = 0.00321584,
+        p_coef_bolus_l3 = 0.0004304708,
+        e_coef_bolus_l1 = -0.1054142,
+        e_coef_bolus_l2 = 0.003740444,
+        e_coef_bolus_l3 = 0.0004315614,
+        e_coef_bolus_ke0 = 0.1012422,
+        p_coef_infusion_l1 = 0.158132,
+        p_coef_infusion_l2 = 0.05771132,
+        p_coef_infusion_l3 = 0.4287546,
+        e_coef_infusion_l1 = -0.1071906,
+        e_coef_infusion_l2 = 0.06712584,
+        e_coef_infusion_l3 = 0.4298409,
+        e_coef_infusion_ke0 = 0.2548219,
+        p_coef_PO_l1 = 0,
+        p_coef_PO_l2 = 0,
+        p_coef_PO_l3 = 0,
+        p_coef_PO_ka = 0,
+        e_coef_PO_l1 = 0,
+        e_coef_PO_l2 = 0,
+        e_coef_PO_l3 = 0,
+        e_coef_PO_ke0 = 0,
+        e_coef_PO_ka = 0,
+        p_coef_IM_l1 = 0,
+        p_coef_IM_l2 = 0,
+        p_coef_IM_l3 = 0,
+        p_coef_IM_ka = 0,
+        e_coef_IM_l1 = 0,
+        e_coef_IM_l2 = 0,
+        e_coef_IM_l3 = 0,
+        e_coef_IM_ke0 = 0,
+        e_coef_IM_ka = 0,
+        p_coef_IN_l1 = 0,
+        p_coef_IN_l2 = 0,
+        p_coef_IN_l3 = 0,
+        p_coef_IN_ka = 0,
+        e_coef_IN_l1 = 0,
+        e_coef_IN_l2 = 0,
+        e_coef_IN_l3 = 0,
+        e_coef_IN_ke0 = 0,
+        e_coef_IN_ka = 0
+      )
+    ),
+    tPeak = 1.6,
+    pkEvents = "default",
+    reference = "Not Available",
+    weight = 70,
+    height = 170,
+    age = 50,
+    sex = "male",
+    upperTypical        = drugDefaults$Upper,
+    lowerTypical        = drugDefaults$Lower,
+    typical             = drugDefaults$Typical,
+    MEAC                = drugDefaults$MEAC,
+    Concentration.Units = drugDefaults$Concentration.Units,
+    Bolus.Units         = drugDefaults$Bolus.Units,
+    Infusion.Units      = drugDefaults$Infusion.Units,
+    Units               = drugDefaults$Units,
+    Default.Units       = drugDefaults$Default.Units,
+    emerge              = drugDefaults$Emerge
+  )
+
+  expect_equal_rounded(actual, expected)
+})