In Open-Systems-Pharmacology/OSPSuite-R: R package to manipulate OSPSuite Models

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.showtext = TRUE
)

Population simulations

Population simulations can be easily performed in R by combining the simulation loaded from a *.pkml file with the population information created in PK-Sim and exported to CSV format (for details, please refer to OSPS online documentation) or created directly in R (see Creating populations).

Loading population file

The method loadPopulation creates an object of the Population class that can be passed to the runSimulations() method (see Running simulations and retrieving the results).

library(ospsuite)
# Load population information from csv
popFilePath <- system.file("extdata", "pop.csv", package = "ospsuite")
myPopulation <- loadPopulation(csvPopulationFile = popFilePath)
print(myPopulation)

Creating populations {#SectionCreatePopulation}

Similar to creating individual parameter sets (see Creating individuals), a population is created from population characteristics created by calling the method createPopulationCharacteristics(). To see the list of available values for the arguments species and population (only for human), use the enums Species and HumanPopulation, respectively. The returned object of type PopulationCharacteristics is then passed to the function createPopulation to generate a set of parameter values. The algorithm behind is the same used in PK-Sim when creating an population. Molecule ontogenies can be added as described in the vignette Creating individuals.

library(ospsuite)

# If no unit is specified, the default units are used. For "height" it is "dm", for "weight" it is "kg", for "age" it is "year(s)".
populationCharacteristics <- createPopulationCharacteristics(
  species             = Species$Human,
  population          = HumanPopulation$Asian_Tanaka_1996,
  numberOfIndividuals = 50,
  proportionOfFemales = 50,
  weightMin           = 30,
  weightMax           = 98,
  weightUnit          = "kg",
  heightMin           = NULL,
  heightMax           = NULL,
  ageMin              = 0,
  ageMax              = 80,
  ageUnit             = "year(s)"
)
print(populationCharacteristics)

# Create population from population characteristics
result <- createPopulation(populationCharacteristics = populationCharacteristics)
myPopulation <- result$population
print(myPopulation)

Running population simulation

To run a population simulation, the Population object created by the createPopulation method must be passed to the runSimulation() method:

library(ospsuite)

# Load simulation
simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
sim <- loadSimulation(simFilePath)

# Run population simulation
simulationResults <- runSimulations(simulations = sim, population = myPopulation)[[1]]
print(simulationResults)

Population simulations are run in parallel on multi-core machines - one core simulates a subset of all individuals defined in the population. By default, the number of cores used equals the maximal number of logical cores available minus one.

The user can change the default behavior by providing custom SimulationRunOptions().

# Load simulation
simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
sim <- loadSimulation(simFilePath)

# Create a SimulationRunOptions object
simRunOptions <- SimulationRunOptions$new()
print(simRunOptions)

# Change the maximal number of cores to use and show a progress bar during simulation
simRunOptions$numberOfCores <- 3
simRunOptions$showProgress <- TRUE

# Run population simulation with custom options
populationResults <- runSimulations(simulations = sim, population = myPopulation, simulationRunOptions = simRunOptions)[[1]]
print(populationResults)

Simulated time-value pairs for a specific output from the SimulationResults-object returned by the runSimulation method can be accessed with the method getOutputValues. The user can provide either the path(s) of the output (which can be a molecule, a parameter, or an observer), or the object(s) of the type Molecule, Parameter, or Quantity (for observers) with the argument quantitiesOrPaths. If no output is specified, all outputs available in the simulation results are returned.

The paths of all available outputs can be accessed via

populationResults$allQuantityPaths

getOutputValues() returns a list with two entries: data and metadata:

• data is a dataframe with two predefined columns (IndividualId and Time) as well as one column for each requested output
  • IndividualId
  • Time a vector with simulated time values (in minutes, equal for all outputs)
  • a vector with simulated entries for each output requested.

The values of IndividualId, Time, and the simulated outputs, are appended for each simulated individual. Note that this results in non-monotonously increasing column Time.

# Get simulated results by path
resultsPath <- populationResults$allQuantityPaths[[1]]
print(resultsPath)

resultsData <- getOutputValues(populationResults, quantitiesOrPaths = resultsPath)

resultsTime <- resultsData$data$Time
resultsValues <- resultsData$data$`Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)`

plot(resultsTime, resultsValues, type = "l")

To get the results for a specific individual or a set of individuals, the argument individualIds of the method getOutputValues() can be specified:

# Get simulated results by path
resultsPath <- populationResults$allQuantityPaths[[1]]
print(resultsPath)

# Get only the results for individuals with IDs 1 and 2
resultsData <- getOutputValues(populationResults, quantitiesOrPaths = resultsPath, individualIds = c(1, 2))

resultsTime <- resultsData$data$Time
resultsValues <- resultsData$data$`Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)`

plot(resultsTime, resultsValues, type = "l")

For more information about running simulations, please refer to Running simulations and retrieving the results.

Open-Systems-Pharmacology/OSPSuite-R documentation built on Feb. 14, 2025, 4:48 p.m.