Add getAllStateVariablesPaths

NAMESPACE

@@ -55,6 +55,7 @@ export(getAllParametersForSensitivityAnalysisMatching)
 export(getAllParametersMatching)
 export(getAllQuantitiesMatching)
 export(getAllQuantityPathsIn)
+export(getAllStateVariablesPaths)
 export(getBaseUnit)
 export(getContainer)
 export(getDimensionForUnit)

R/create-population.R

@@ -19,16 +19,16 @@ createPopulation <- function(populationCharacteristics) {
 
   # NOTE THIS IS A WORKAROUND UNTIL THE CODE IN PKSIM IS UPDATED
   if (populationCharacteristics$species == Species$Human) {
-    # create an individual with similar properties Species and population. WEIGHT AND AGE DO NOT MATTER as long as we can create an invidiual
-    individualCharacteristics <- ospsuite::createIndividualCharacteristics(
+    # create an individual with similar properties Species and population. WEIGHT AND AGE DO NOT MATTER as long as we can create an invdiviual
+    individualCharacteristics <- createIndividualCharacteristics(
       species = populationCharacteristics$species,
       population = populationCharacteristics$population,
       age = 30
     )
   }
   else {
-    # create an individual with similar properties Species and population. WEIGHT AND AGE DO NOT MATTER as long as we can create an invidiual
-    individualCharacteristics <- ospsuite::createIndividualCharacteristics(
+    # create an individual with similar properties Species and population. WEIGHT AND AGE DO NOT MATTER as long as we can create an indiviual
+    individualCharacteristics <- createIndividualCharacteristics(
       species = populationCharacteristics$species,
       population = populationCharacteristics$population,
     )

R/utilities-simulation.R

@@ -425,6 +425,22 @@ getAllParametersForSensitivityAnalysisMatching <- function(paths, simulation) {
   )
 }
 
+#' Get the paths of all state variable quantities of the simulation
+#'
+#' @param simulation \code{Simulation} object
+#' @details List of paths of all molecules in all compartments and all parameters that are
+#' state variables.
+#'
+#' @return A list of paths
+#' @export
+getAllStateVariablesPaths <- function(simulation) {
+  validateIsOfType(simulation, type = Simulation)
+  allMoleculesPaths <- getAllMoleculePathsIn(container = simulation)
+  allStateVariableParamsPaths <- getAllEntityPathsIn(container = simulation, entityType = Parameter, method = "AllStateVariableParameterPathsIn")
+  allQantitiesPaths <- append(allMoleculesPaths, allStateVariableParamsPaths)
+  return(allQantitiesPaths)
+}
+
 #' Export simulation PKMLs for given `individualIds`. Each pkml file will contain the orginial simulation updated with parameters of the corresponding individual.
 #'
 #' @param population A population object typically loaded with `loadPopulation`

tests/testthat/test-utilities-simulation.R

@@ -340,3 +340,10 @@ test_that("It can run multiple simulation batches with multiple parameters and m
   expect_equal(names(res[[2]])[[2]], ids[[4]])
 })
 
+context("getAllStateVariablesPaths")
+
+test_that("It returns the correct paths of the state variables", {
+  sim <- loadTestSimulation(simulationName = "simple", loadFromCache = FALSE)
+  stateVariablePaths <- getAllStateVariablesPaths(simulation = sim)
+  expect_equal(length(stateVariablePaths), 5)
+})