Merge pull request #14 from esqLABS/simulation-parameterization

Simulation parameterization

app/logic/constants.R

@@ -3,6 +3,12 @@ box::use(config)
 #' @export
 ORGAN_TAB <- config$get("tab_items", config = "organ_tab")
 
+#' @export
+GENDERS <- c("male", "female")
+
+#' @export
+POPULATIONS <- c("European", "White American", "Black American", "Mexican American", "Asian", "Japanese")
+
 #' @export
 COFFEE_TYPES <- list(
   `Espresso` = list(caffeine = 64, water = 30),

app/logic/individual.R

@@ -4,6 +4,10 @@ box::use(
   dplyr[case_match]
 )
 
+box::use(
+  app / logic / constants[POPULATIONS, GENDERS],
+)
+
 set_individual <- function(simulation, user_data) {
   message("Applying individual characteristics to the simulation")
   # Create individual
@@ -38,20 +42,21 @@ set_individual <- function(simulation, user_data) {
 }
 
 create_individual <- function(user_data) {
+  unit_system <- user_data$unit
   ind_carac <- ospsuite::createIndividualCharacteristics(
     species = "Human",
     population = translate_population(user_data$ethnicity),
     gender = translate_gender(user_data$gender),
     age = as.double(user_data$age),
-    weight = as.double(user_data$weight),
-    height = as.double(convert_height(user_data$height)),
+    weight = convert_weight(user_data$weight, unit_system),
+    height = convert_height(user_data$height, unit_system),
     seed = 42
   )
   return(ospsuite::createIndividual(ind_carac))
 }
 
 translate_population <- function(population) {
-  rlang::arg_match(population, c("European", "White American", "Black American", "Mexican American", "Asian", "Japanese"))
+  rlang::arg_match(population, POPULATIONS)
   case_match(
     population,
     "European" ~ ospsuite::HumanPopulation$European_ICRP_2002,
@@ -64,15 +69,30 @@ translate_population <- function(population) {
 }
 
 translate_gender <- function(gender) {
-  rlang::arg_match(gender, c("male", "female"))
+  rlang::arg_match(gender, GENDERS)
   case_match(
     gender,
     "male" ~ ospsuite::Gender$Male,
     "female" ~ ospsuite::Gender$Female
   )
 }
+convert_height <- function(height, unit_system) {
+  height <- if (unit_system == "imperial") {
+    # feet to cm
+    height * 30.48
+  } else {
+    # meters to cm
+    height * 100
+  }
+  return(as.double(height))
+}
 
-convert_height <- function(height) {
-  # meters to cm
-  return(height * 100)
+convert_weight <- function(weight, unit_system) {
+  weight <- if (unit_system == "imperial") {
+    # lbs to kg
+    weight * 0.453592
+  } else {
+    weight
+  }
+  return(as.double(weight))
 }

app/logic/intakes.R

@@ -11,7 +11,7 @@ set_intakes <- function(simulation, intakes) {
   # Get all relevant paths
   time_paths <- purrr::map(ospsuite::getAllParametersMatching("**|Start time", simulation), "path")
   dose_paths <- purrr::map(ospsuite::getAllParametersMatching("**|Dose", simulation), "path")
-  volume_paths <- purrr::map(ospsuite::getAllParametersMatching("**|Volume of water/body weight", simulation), "path")
+  volume_paths <- purrr::map(ospsuite::getAllParametersMatching("Applications|Coffee Drinks|Solution|Application_*|ProtocolSchemaItem|Amount of water", simulation), "path")
 
   # Keep only enabled intakes
   enabled_intakes <- purrr::keep(intakes, ~ .x$selected)
@@ -20,9 +20,8 @@ set_intakes <- function(simulation, intakes) {
   # Add the caffeine and water content to the intake
   # Set the intake in the simulation
   for (i in seq_along(enabled_intakes)) {
-
     caffein_dose <- enabled_intakes[[i]]$type[[1]]$caffeine
-    water_volume <-enabled_intakes[[i]]$type[[1]]$water
+    water_volume <- enabled_intakes[[i]]$type[[1]]$water
     time <- enabled_intakes[[i]]$time
 
     # Set the caffeine dose
@@ -42,11 +41,16 @@ set_intakes <- function(simulation, intakes) {
     )
 
     # Set the volume of water
-    # TODO
+    ospsuite::setParameterValuesByPath(
+      parameterPaths = volume_paths[[i]],
+      values = water_volume,
+      unit = "ml",
+      simulation = simulation
+    )
   }
 
   # Set remaining intakes to 0
-  for (j in (i+1):length(dose_paths)) {
+  for (j in (i + 1):length(dose_paths)) {
     if (j > length(dose_paths)) break
 
     ospsuite::setParameterValuesByPath(
@@ -66,14 +70,14 @@ set_intakes <- function(simulation, intakes) {
     ospsuite::setParameterValuesByPath(
       parameterPaths = volume_paths[[j]],
       values = 0,
-      unit = "l/kg",
+      unit = "ml",
       simulation = simulation
     )
   }
 }
 
 
-convert_time_to_min <- function(time){
+convert_time_to_min <- function(time) {
   # Convert time to minutes from midnight
   time <- as.POSIXct(time, format = "%H:%M")
 

app/logic/plot.R

@@ -3,7 +3,7 @@ box::use(
   ospsuite
 )
 
-get_plot <- function(simulation_results){
+get_plot <- function(simulation_results) {
   message("Generating time profile plot")
   dc <- ospsuite::DataCombined$new()
 
@@ -14,8 +14,5 @@ get_plot <- function(simulation_results){
 
   dc$addSimulationResults(simulation_results[[1]])
 
-  return(ospsuite::plotIndividualTimeProfile(dc,defaultPlotConfiguration = pc))
-
+  return(ospsuite::plotIndividualTimeProfile(dc, defaultPlotConfiguration = pc))
 }
-
-

app/logic/simulation.R

@@ -4,9 +4,17 @@ box::use(
 )
 
 
-load_simulation <- function(){
+load_simulation <- function() {
   message("Initializing Simulation")
   simulation <- ospsuite::loadSimulation("app/logic/coffee-sim.pkml")
-  ospsuite::setOutputInterval(simulation, 0, 24*60-1, resolution = 1/2)
+  ospsuite::setOutputInterval(simulation, 0, 24 * 60 - 1, resolution = 1 / 2)
+  ospsuite::setOutputs(
+    c(
+      "Organism|PeripheralVenousBlood|Caffeine|Plasma (Peripheral Venous Blood)",
+      "Organism|Brain|Intracellular|Caffeine|Concentration",
+      "Organism|Heart|Intracellular|Caffeine|Concentration"
+    ),
+    simulation
+  )
   return(simulation)
 }

app/main.R

@@ -61,6 +61,5 @@ server <- function(id) {
       app_data$destroy_intro_screen <- TRUE
       result_screen$server("result_screen", app_data)
     })
-
   })
 }

app/view/intro_screen.R

@@ -3,7 +3,7 @@ box::use(
   shiny[moduleServer, NS, tagList, observeEvent],
 )
 box::use(
-  app/logic/constants[COFFEE_TYPES],
+  app/logic/constants[COFFEE_TYPES, POPULATIONS],
   app/view/react[intro_screen_page], # Import the component.
 )
 
@@ -14,10 +14,10 @@ ui <- makeModuleUIDestroyable(
     tagList(
       intro_screen_page(
         id = ns("stepper"),
-        ethinicity_options = c("European", "White American", "Black American","Mexican American", "Asian", "Japanese"),
+        ethinicity_options = POPULATIONS,
         metabolism_options = c("low", "normal", "high"),
         coffee_type_options = COFFEE_TYPES,
-        unit="metric",
+        unit = "metric",
         unit_options = c("metric", "imperial"),
         init_shiny_data = list(
           ethnicity = "European",
@@ -60,21 +60,20 @@ server <- makeModuleServerDestroyable(
       # Observe User Data changes
       observeEvent(input$stepper_userdata, {
         app_data$user_data <- input$stepper_userdata
-        print(app_data$user_data) #! dev
+        print(app_data$user_data) # ! dev
       })
 
       # Observe Intake Data changes
       observeEvent(input$stepper_intake, {
         app_data$intake_data <- input$stepper_intake$intakes
         app_data$destroy_intro_screen <- TRUE
-        print(app_data$intake_data) #! dev
+        print(app_data$intake_data) # ! dev
       })
 
       # Remove loader when calcularion finished
       observeEvent(app_data$destroy_intro_screen, {
         destroyModule()
       })
-
     })
   }
 )

app/view/result_screen.R

@@ -12,8 +12,8 @@ box::use(
 ui <- function(id) {
   ns <- NS(id)
   tagList(
-    uiOutput(ns("result_screen")),
-    fluidRow(column(plotOutput(ns("plot")), width = 10, offset = 1))
+    uiOutput(ns("result_screen"))
+
   )
 }
 
@@ -34,7 +34,8 @@ server <- function(id, app_data) {
         div(
           style = "margin-top: 2rem;",
           organ_info_tabpanel$ui(session$ns("organ_info_tabpanel"))
-        )
+        ),
+        fluidRow(column(plotOutput(session$ns("plot")), width = 10, offset = 1))
       )
     })