Fixes #423 export population to csv

NAMESPACE

@@ -36,6 +36,7 @@ export(createPopulationCharacteristics)
 export(createSimulationBatch)
 export(exportIndividualSimulations)
 export(exportPKAnalysesToCSV)
+export(exportPopulationToCSV)
 export(exportResultsToCSV)
 export(exportSensitivityAnalysisResultsToCSV)
 export(getAllContainerPathsIn)

R/create-individual.R

@@ -81,9 +81,10 @@ createIndividualCharacteristics <- function(
                                             ageUnit = "year(s)",
                                             gestationalAge = 40,
                                             gestationalAgeUnit = "week(s)",
-                                            moleculeOntogenies = NULL) {
+                                            moleculeOntogenies = NULL,
+                                            seed = NULL) {
 
-  # Assuming that if this function is called directly, PKSim was either initialized already
+  # Assuming that if this function is called directly, PK-Sim was either initialized already
   # or should be initialized automatically
   initPKSim()
 
@@ -99,6 +100,7 @@ createIndividualCharacteristics <- function(
   validateIsNumeric(gestationalAge)
   validateIsString(gestationalAgeUnit)
   validateIsOfType(moleculeOntogenies, MoleculeOntogeny, nullAllowed = TRUE)
+  validateIsNumeric(seed, nullAllowed = TRUE)
 
   moleculeOntogenies <- c(moleculeOntogenies)
   individualCharacteristics <- IndividualCharacteristics$new()
@@ -109,7 +111,7 @@ createIndividualCharacteristics <- function(
   individualCharacteristics$weight <- createSnapshotParameter(weight, weightUnit)
   individualCharacteristics$height <- createSnapshotParameter(height, heightUnit)
   individualCharacteristics$gestationalAge <- createSnapshotParameter(gestationalAge, gestationalAgeUnit)
-
+  individualCharacteristics$seed <- seed
   for (moleculeOntogeny in moleculeOntogenies) {
     individualCharacteristics$addMoleculeOntogeny(moleculeOntogeny)
   }

R/create-population.R

@@ -19,15 +19,15 @@ 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 properites Species and population. WEIGHT AND AGE DO NOT MATTER as long as we can create an invidiual
+    # 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(
       species = populationCharacteristics$species,
       population = populationCharacteristics$population,
       age = 30
     )
   }
   else {
-    # create an individual with similar properites Species and population. WEIGHT AND AGE DO NOT MATTER as long as we can create an invidiual
+    # 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(
       species = populationCharacteristics$species,
       population = populationCharacteristics$population,
@@ -38,7 +38,7 @@ createPopulation <- function(populationCharacteristics) {
 
   derivedParameters <- list()
 
-  # Even though those parameters are derived parmaeters, we keep them in the population for consistency purpose with the PKSim export.
+  # Even though those parameters are derived parameters, we keep them in the population for consistency purpose with the PKSim export.
   standardDerivedParametersToKeep <- c(StandardPath$Weight, StandardPath$BMI, StandardPath$BSA)
 
   for (derivedParameterPath in individual$derivedParameters$paths) {
@@ -52,7 +52,7 @@ createPopulation <- function(populationCharacteristics) {
     }
   }
 
-  # other parameters to remvove that should not have been exported in the first place
+  # other parameters to remove that should not have been exported in the first place
   standardDistributedParametersToRemove <- c(toPathString(StandardContainer$Organism, "MeanBW"), toPathString(StandardContainer$Organism, "MeanHeight"))
   for (parameterToRemove in standardDistributedParametersToRemove) {
     if (population$has(parameterToRemove)) {
@@ -85,6 +85,7 @@ createPopulation <- function(populationCharacteristics) {
 #' @param gestationalAgeMax max gestational age for the population (optional, for human species only)
 #' @param gestationalAgeUnit Unit in which the gestational age value is defined. Default is kg/m2
 #' @param moleculeOntogenies Optional list of \code{MoleculeOntogeny} that will be used to retrieve ontogeny information for molecules.
+#' @param seed Optional Seed parameter used to generate random values. This is only useful in order to reproduce the same population
 #'
 #' @return An instance of \code{PopulationCharacteristics} to be used in conjunction with \code{createPopulation}
 #'
@@ -109,8 +110,8 @@ createPopulationCharacteristics <- function(
                                             gestationalAgeMin = NULL,
                                             gestationalAgeMax = NULL,
                                             gestationalAgeUnit = "week(s)",
-
-                                            moleculeOntogenies = NULL) {
+                                            moleculeOntogenies = NULL,
+                                            seed = NULL) {
 
   # Assuming that if this function is called directly, PKSim was either initialized already
   # or should be initialized automatically
@@ -142,6 +143,7 @@ createPopulationCharacteristics <- function(
   validateIsString(gestationalAgeUnit)
 
   validateIsOfType(moleculeOntogenies, MoleculeOntogeny, nullAllowed = TRUE)
+  validateIsInteger(seed, nullAllowed = TRUE)
 
   moleculeOntogenies <- c(moleculeOntogenies)
   populationCharacteristics <- PopulationCharacteristics$new()
@@ -154,6 +156,7 @@ createPopulationCharacteristics <- function(
   populationCharacteristics$height <- createParameterRange(heightMin, heightMax, heightUnit)
   populationCharacteristics$gestationalAge <- createParameterRange(gestationalAgeMin, gestationalAgeMax, gestationalAgeUnit)
   populationCharacteristics$BMI <- createParameterRange(BMIMin, BMIMax, BMIUnit)
+  populationCharacteristics$seed <-seed
 
   for (moleculeOntogeny in moleculeOntogenies) {
     populationCharacteristics$addMoleculeOntogeny(moleculeOntogeny)

R/dot-net-wrapper.R

@@ -88,7 +88,16 @@ DotNetWrapper <- R6::R6Class(
         rClr::clrSet(self$ref, propertyName, as.integer(value))
       }
     },
-
+    wrapNullableIntegerProperty = function(propertyName, value) {
+      if(missing(value)){
+        return(rClr::clrGet(self$ref, propertyName))
+      }
+      if(is.null(value)){
+        return()
+      } else {
+        rClr::clrSet(self$ref, propertyName, as.integer(value))
+      }
+    },
     wrapIndexProperty = function(propertyName, value) {
       # Special method needed because Index are 0-based in .NET but 1-based in R
       if (missing(value)) {

R/individual-characteristics.R

@@ -40,6 +40,10 @@ IndividualCharacteristics <- R6::R6Class(
     #' @field allMoleculeOntogenies All molecule ontogenies defined for this individual characteristics.
     allMoleculeOntogenies = function(value) {
       private$readOnlyProperty("allMoleculeOntogenies", value, private$.moleculeOntogenies)
+    },
+    #' @field seed Seed used to generate the population
+    seed = function(value) {
+      private$wrapNullableIntegerProperty("Seed", value)
     }
   ),
   private = list(
@@ -85,6 +89,9 @@ IndividualCharacteristics <- R6::R6Class(
       for (moleculeOntogeny in self$allMoleculeOntogenies) {
         moleculeOntogeny$printMoleculeOntogeny()
       }
+      if(!is.null(self$seed)){
+        private$printLine("Seed", self$seed)
+      }
       invisible(self)
     },
 

R/population-characteristics.R

@@ -48,6 +48,10 @@ PopulationCharacteristics <- R6::R6Class(
     #' @field allMoleculeOntogenies All molecule ontogenies defined for this individual characteristics.
     allMoleculeOntogenies = function(value) {
       private$readOnlyProperty("allMoleculeOntogenies", value, private$.moleculeOntogenies)
+    },
+    #' @field seed Seed used to generate the population
+    seed = function(value) {
+      private$wrapNullableIntegerProperty("Seed", value)
     }
   ),
   private = list(
@@ -92,9 +96,13 @@ PopulationCharacteristics <- R6::R6Class(
       private$printRange("Weight", self$weight)
       private$printRange("Height", self$height)
       private$printRange("BMI", self$BMI)
+
       for (moleculeOntogeny in self$allMoleculeOntogenies) {
         moleculeOntogeny$printMoleculeOntogeny()
       }
+      if(!is.null(self$seed)){
+        private$printLine("Seed", self$seed)
+      }
       invisible(self)
     },
 

R/printable.R

@@ -1,6 +1,6 @@
 #' @title Printable
 #' @docType class
-#' @description  Base class that implements some basic functionalities for printing to console
+#' @description  Base class that implements some basic properties for printing to console
 #'
 Printable <- R6::R6Class(
   "Printable",

R/utilities-population.R

@@ -66,3 +66,27 @@ populationAsDataFrame <- function(population) {
 
   data.frame(columns, stringsAsFactors = FALSE, check.names = FALSE)
 }
+
+#' Saves the population to csv file
+#'
+#' @param population Population to export to csv (typically imported from file using \code{loadPopulation})
+#' @param filePath Full path where the population will be saved.
+#'
+#' @examples
+#' csvPath <- system.file("extdata", "pop.csv", package = "ospsuite")
+#'
+#' # Load the population
+#' population <- loadPopulation(csvPath)
+#'
+#' # Exports the population
+#' exportPopulationToCSV(population, tempfile())
+#' @export
+exportPopulationToCSV <- function(population, filePath) {
+  validateIsOfType(population, Population)
+  validateIsString(filePath)
+  filePath <- expandPath(filePath)
+  df <- populationAsDataFrame(population)
+  write.csv(df, file = filePath, row.names = FALSE)
+  invisible()
+}
+

packages.config

@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
-  <package id="OSPSuite.Assets" version="10.0.80"/>
-  <package id="OSPSuite.Core" version="10.0.80"/>
-  <package id="OSPSuite.Infrastructure" version="10.0.80"/>
-  <package id="OSPSuite.Infrastructure.Import" version="10.0.80"/>
-  <package id="OSPSuite.Infrastructure.Autofac" version="10.0.80"/>
-  <package id="OSPSuite.R" version="10.0.80 "/>
+  <package id="OSPSuite.Assets" version="10.0.84"/>
+  <package id="OSPSuite.Core" version="10.0.84"/>
+  <package id="OSPSuite.Infrastructure" version="10.0.84"/>
+  <package id="OSPSuite.Infrastructure.Import" version="10.0.84"/>
+  <package id="OSPSuite.Infrastructure.Autofac" version="10.0.84"/>
+  <package id="OSPSuite.R" version="10.0.84 "/>
   <package id="OSPSuite.Serializer" version="3.0.0.1"/>
   <package id="OSPSuite.Utility" version="4.0.0.4"/>
   <package id="LumenWorksCsvReader" version="4.0.0"/>

tests/testthat/test-population.R

@@ -120,3 +120,13 @@ test_that("It can retrieve all ids define ina population", {
   population <- loadPopulation(populationFileName)
   expect_length(population$allIndividualIds, 10)
 })
+
+context("exportPopulationToCSV")
+
+test_that("It can export valid population to CSV", {
+  executeWithTestFile(function(csvFile) {
+    population <- loadPopulation(populationFileName)
+    exportPopulationToCSV(population, csvFile)
+    expect_true(file.exists(csvFile))
+  })
+})