private PKParameterSensitivity calculateParameterSensitivity(SensitivityParameter sensitivityParameter, int sensitivityParameterIndex, VariationData variationData, QuantityPKParameter pkParameter)
{
var defaultParameterValue = sensitivityParameter.DefaultValue;
var defaultPKValue = pkParameter.Values[variationData.DefaultVariationId];
var allVariations = variationData.VariationsFor(sensitivityParameter.Name);
if (float.IsNaN(defaultPKValue) || defaultPKValue == 0 || defaultParameterValue == 0 || !allVariations.Any())
{
return(null);
}
var sensitivity = new PKParameterSensitivity
{
ParameterName = sensitivityParameter.Name,
PKParameterName = pkParameter.Name,
QuantityPath = pkParameter.QuantityPath,
Value = double.NaN
};
var delta = (from variation in allVariations
let deltaP = difference(variation.Variation[sensitivityParameterIndex], defaultParameterValue)
let deltaPK = difference(pkParameter.Values[variation.VariationId], defaultPKValue)
select deltaPK / deltaP).Sum();
sensitivity.Value = delta * defaultParameterValue / defaultPKValue / allVariations.Count;
if (Math.Abs(sensitivity.Value) < Constants.SENSITIVITY_THRESHOLD)
{
sensitivity.Value = 0.0;
}
return(sensitivity);
}
protected override void Context()
{
sut = new SensitivityAnalysisRunResult();
_pkParameterSensitivity1 = new PKParameterSensitivity
{
ParameterName = "P1",
PKParameterName = "AUC",
QuantityPath = "Organism|Liver|Drug|Concentration",
Value = 0.8,
ParameterPath = "P1-Path"
};
_pkParameterSensitivity2 = new PKParameterSensitivity
{
ParameterName = "P2",
PKParameterName = "AUC2",
QuantityPath = "Organism|Liver|Drug|Concentration",
Value = 0.8,
ParameterPath = "P2-Path"
};
_pkParameterSensitivity3 = new PKParameterSensitivity
{
ParameterName = "P2",
PKParameterName = "AUC",
QuantityPath = "Organism|Kidney|Drug|Concentration",
Value = 0.8,
ParameterPath = "P3-Path"
};
sut.AddPKParameterSensitivity(_pkParameterSensitivity1);
sut.AddPKParameterSensitivity(_pkParameterSensitivity2);
sut.AddPKParameterSensitivity(_pkParameterSensitivity3);
}
private IReadOnlyList <PKParameterSensitivity> pkParameterSensitivitiesFrom(string fileFullPath, char delimiter)
{
using (var reader = new CsvReaderDisposer(fileFullPath, delimiter))
{
var pkParameterSensitivityList = new List <PKParameterSensitivity>();
var csv = reader.Csv;
var headers = csv.GetFieldHeaders();
if (!headers.ContainsAll(new[] { PARAMETER, PK_PARAMETER, QUANTITY_PATH, VALUE }))
{
return(pkParameterSensitivityList);
}
while (csv.ReadNextRecord())
{
var pkParameterSensitivity = new PKParameterSensitivity
{
PKParameterName = csv[PK_PARAMETER],
ParameterName = csv[PARAMETER],
QuantityPath = csv[QUANTITY_PATH],
Value = csv.DoubleAt(VALUE)
};
pkParameterSensitivityList.Add(pkParameterSensitivity);
}
return(pkParameterSensitivityList);
}
}
private void addParameterSensitivity(PKParameterSensitivity parameterSensitivity, DataTable dataTable, SensitivityAnalysis sensitivityAnalysis)
{
var row = dataTable.NewRow();
var sensitivityParameter = sensitivityAnalysis.SensitivityParameterByName(parameterSensitivity.ParameterName);
row[Captions.SensitivityAnalysis.Output] = parameterSensitivity.QuantityPath;
row[Captions.SensitivityAnalysis.PKParameterName] = _pkParameterRepository.DisplayNameFor(parameterSensitivity.PKParameterName);
row[Captions.SensitivityAnalysis.PKParameterDescription] = _pkParameterRepository.DescriptionFor(parameterSensitivity.PKParameterName);
row[Captions.SensitivityAnalysis.ParameterName] = parameterSensitivity.ParameterName;
row[Captions.SensitivityAnalysis.ParameterDisplayPath] = parameterDisplayPathFor(sensitivityParameter);
row[Captions.SensitivityAnalysis.ParameterPath] = parameterFullPathFor(sensitivityParameter);
row[Captions.SensitivityAnalysis.Value] = parameterSensitivity.Value;
dataTable.Rows.Add(row);
}
protected override void Context()
{
base.Context();
_parameterSensitivity1 = new PKParameterSensitivity {
PKParameterName = "AUC"
};
_parameterSensitivity2 = new PKParameterSensitivity {
PKParameterName = "C_max"
};
_sa = new SensitivityAnalysis {
Results = new SensitivityAnalysisRunResult()
};
_sa.Results.AddPKParameterSensitivity(_parameterSensitivity1);
_sa.Results.AddPKParameterSensitivity(_parameterSensitivity2);
}
protected override void Context()
{
base.Context();
_sensitivityAnalysis = new SensitivityAnalysis();
_sensitivityParameter = new SensitivityParameter().WithName("OLD_NAME");
_parameterSensitivity1 = new PKParameterSensitivity {
ParameterName = _sensitivityParameter.Name
};
_parameterSensitivity2 = new PKParameterSensitivity {
ParameterName = "Another name"
};
_sensitivityAnalysis.Results = new SensitivityAnalysisRunResult();
_sensitivityAnalysis.Results.AddPKParameterSensitivity(_parameterSensitivity1);
_sensitivityAnalysis.Results.AddPKParameterSensitivity(_parameterSensitivity2);
}
protected override void Context()
{
base.Context();
_sensitivityAnalysisRunResult = new SensitivityAnalysisRunResult();
_simulation = A.Fake <IModelCoreSimulation>().WithName("Sim");
var pkParameter = new PKParameterSensitivity
{
QuantityPath = "Liver",
PKParameterName = "AUC",
ParameterName = "P1",
Value = 0.5,
ParameterPath = "ParameterPath"
};
_sensitivityAnalysisRunResult.AddPKParameterSensitivity(pkParameter);
}
protected override void Context()
{
base.Context();
_pkParameterName = "AUC";
_outputPath = "Output";
_pk1 = new PKParameterSensitivity {
PKParameterName = _pkParameterName, QuantityPath = _outputPath, Value = 0.4
};
_pk2 = new PKParameterSensitivity {
PKParameterName = _pkParameterName, QuantityPath = _outputPath, Value = 0.1
};
_pk3 = new PKParameterSensitivity {
PKParameterName = _pkParameterName, QuantityPath = _outputPath, Value = -0.6
};
sut.AddPKParameterSensitivity(_pk1);
sut.AddPKParameterSensitivity(_pk2);
sut.AddPKParameterSensitivity(_pk3);
}
protected override void Context()
{
sut = new SensitivityAnalysisRunResult();
_pkParameterSensitivity1 = new PKParameterSensitivity
{
ParameterName = "P1",
PKParameterName = "AUC",
QuantityPath = "Organism|Liver|Volume",
Value = 0.8
};
_pkParameterSensitivity2 = new PKParameterSensitivity
{
ParameterName = "P2",
PKParameterName = "AUC2",
QuantityPath = "Organism|Liver|Volume",
Value = 0.8
};
sut.AddPKParameterSensitivity(_pkParameterSensitivity1);
sut.AddPKParameterSensitivity(_pkParameterSensitivity2);
}
protected override void Context()
{
_applicationSettings = A.Fake <IApplicationSettings>();
_sensitivityAnalysis = new SensitivityAnalysis();
_sensitivityAnalysisPKParameterAnalysis = new SensitivityAnalysisPKParameterAnalysis();
_sensitivityAnalysis.Results = new SensitivityAnalysisRunResult();
_pkParameterSensitivity = new PKParameterSensitivity
{
PKParameterName = "pkParameterName",
ParameterName = "parameterName",
QuantityPath = "quantityPath",
Value = 1.0
};
_pkParameterSensitivity2 = new PKParameterSensitivity
{
PKParameterName = "pkParameterName",
ParameterName = "parameterName",
QuantityPath = "quantityPath",
Value = 0.0
};
_pkParameterSensitivity3 = new PKParameterSensitivity
{
PKParameterName = "pkParameterName",
ParameterName = "parameterName",
QuantityPath = "quantityPath",
Value = double.NaN
};
_sensitivityAnalysis.Results.AddPKParameterSensitivity(_pkParameterSensitivity);
_sensitivityAnalysis.Results.AddPKParameterSensitivity(_pkParameterSensitivity2);
_view = A.Fake <ISensitivityAnalysisPKParameterAnalysisView>();
_presentationSettingsTask = A.Fake <IPresentationSettingsTask>();
var pkParameterRepository = A.Fake <IPKParameterRepository>();
sut = new SensitivityAnalysisPKParameterAnalysisPresenter(_view, _presentationSettingsTask, pkParameterRepository, _applicationSettings);
}
