protected override void Context()
{
base.Context();
var pKAnalyses = new PopulationSimulationPKAnalyses();
_populationSimulation = new PopulationSimulation {
PKAnalyses = pKAnalyses
};
var pkParameter = new QuantityPKParameter {
QuantityPath = "Liver", Name = "P"
};
var dimension = A.Fake <IDimension>();
var unit = A.Fake <Unit>();
A.CallTo(() => unit.Name).Returns("UNIT");
A.CallTo(() => _displayUnitRetriever.PreferredUnitFor(pkParameter, null)).Returns(unit);
pkParameter.Dimension = dimension;
pkParameter.SetNumberOfIndividuals(2);
pkParameter.SetValue(0, 10);
pkParameter.SetValue(1, 11);
A.CallTo(() => dimension.BaseUnitValueToUnitValue(unit, 10)).Returns(100.10);
A.CallTo(() => dimension.BaseUnitValueToUnitValue(unit, 11)).Returns(110.20);
pKAnalyses.AddPKAnalysis(pkParameter);
}
private void addPKParametersForOutput(ISimulation simulation, int numberOfIndividuals, SimulationResults runResults, Action <int> performIndividualScalingAction,
QuantitySelection selectedQuantity, PopulationSimulationPKAnalyses popAnalyses, string moleculeName,
PKCalculationOptions pkCalculationOptions, IReadOnlyList <PKCalculationOptionsFactory.ApplicationParameters> allApplicationParameters)
{
var availablePKParameters = _pkParameterRepository.All().Where(p => PKParameterCanBeUsed(p, pkCalculationOptions)).ToList();
//create pk parameter for each quantities
foreach (var pkParameter in availablePKParameters)
{
var quantityPKParameter = new QuantityPKParameter {
Name = pkParameter.Name, QuantityPath = selectedQuantity.Path, Dimension = pkParameter.Dimension
};
quantityPKParameter.SetNumberOfIndividuals(numberOfIndividuals);
popAnalyses.AddPKAnalysis(quantityPKParameter);
}
//add the values for each individual
foreach (var individualResult in runResults.AllIndividualResults)
{
performIndividualScalingAction(individualResult.IndividualId);
_pkCalculationOptionsFactory.UpdateAppliedDose(simulation, moleculeName, pkCalculationOptions, allApplicationParameters);
var values = individualResult.ValuesFor(selectedQuantity.Path);
var pkValues = _pkValuesCalculator.CalculatePK(individualResult.Time.Values, values.Values, pkCalculationOptions);
foreach (var pkParameter in availablePKParameters)
{
var quantityPKParameter = popAnalyses.PKParameterFor(selectedQuantity.Path, pkParameter.Name);
quantityPKParameter.SetValue(individualResult.IndividualId, pkValues.ValueOrDefaultFor(pkParameter.Name));
}
}
}
protected override void Context()
{
base.Context();
_numberOfVariations = 5;
_pkParameter1 = new QuantityPKParameter {
QuantityPath = "Output1", Name = "AUC"
};
_pkParameter1.SetNumberOfIndividuals(_numberOfVariations);
_pkParameter1.SetValue(0, 10);
_pkParameter1.SetValue(1, 11);
_pkParameter1.SetValue(2, 12);
_pkParameter1.SetValue(4, _defaultPK1Value);
_pkParameter2 = new QuantityPKParameter {
QuantityPath = "Output2", Name = "Cmax"
};
_pkParameter2.SetNumberOfIndividuals(_numberOfVariations);
_pkParameter2.SetValue(0, 20);
_pkParameter2.SetValue(1, 21);
_pkParameter2.SetValue(2, 22);
_pkParameter2.SetValue(3, 23);
_pkParameter2.SetValue(4, _defaultPK2Value);
_sensitivityParameter1 = A.Fake <SensitivityParameter>().WithName("SP1");
A.CallTo(() => _sensitivityParameter1.DefaultValue).Returns(10);
_sensitivityParameter2 = A.Fake <SensitivityParameter>().WithName("SP2");
A.CallTo(() => _sensitivityParameter2.DefaultValue).Returns(20);
_sensitivityParameter3 = A.Fake <SensitivityParameter>().WithName("SP3");
A.CallTo(() => _sensitivityParameter3.DefaultValue).Returns(0);
A.CallTo(() => _sensitivityParameter3.VariationRangeValue).Returns(0.8);
_pkAnalyses.AddPKAnalysis(_pkParameter1);
_pkAnalyses.AddPKAnalysis(_pkParameter2);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter1);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter2);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter3);
var pv11 = new ParameterVariation {
ParameterName = _sensitivityParameter1.Name, VariationId = 0, Variation = new[] { 15d, 200d, 300d }
};
var pv12 = new ParameterVariation {
ParameterName = _sensitivityParameter1.Name, VariationId = 1, Variation = new[] { 20d, 200d, 300d }
};
var pv21 = new ParameterVariation {
ParameterName = _sensitivityParameter2.Name, VariationId = 2, Variation = new[] { 100d, 21d, 300d }
};
var pv22 = new ParameterVariation {
ParameterName = _sensitivityParameter2.Name, VariationId = 3, Variation = new[] { 100d, 31d, 300d }
};
_variationData.DefaultValues = new[] { 100d, 200d, 300d };
_variationData.AddVariation(pv11);
_variationData.AddVariation(pv12);
_variationData.AddVariation(pv21);
_variationData.AddVariation(pv22);
}
private QuantityPKParameter createPKAnalyses(string path)
{
var pk = new QuantityPKParameter {
QuantityPath = path
};
pk.Name = "AUC";
_numberOfIndividuals = 100000;
pk.SetNumberOfIndividuals(_numberOfIndividuals);
for (int i = 0; i < _numberOfIndividuals; i++)
{
pk.SetValue(i, (float)_random.NextDouble() * 100);
}
return(pk);
}
