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vtkPCAStatisticsGnuR Class Reference

A class for multivariate principal component analysis using R to calculate p-values. More...

#include <vtkPCAStatisticsGnuR.h>

Inheritance diagram for vtkPCAStatisticsGnuR:
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Collaboration diagram for vtkPCAStatisticsGnuR:
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Public Types

typedef vtkPCAStatistics Superclass
 
- Public Types inherited from vtkPCAStatistics
typedef
vtkMultiCorrelativeStatistics 
Superclass
 
enum  NormalizationType {
  NONE, TRIANGLE_SPECIFIED, DIAGONAL_SPECIFIED, DIAGONAL_VARIANCE,
  NUM_NORMALIZATION_SCHEMES
}
 
enum  ProjectionType { FULL_BASIS, FIXED_BASIS_SIZE, FIXED_BASIS_ENERGY, NUM_BASIS_SCHEMES }
 
- Public Types inherited from vtkMultiCorrelativeStatistics
typedef vtkStatisticsAlgorithm Superclass
 
- Public Types inherited from vtkStatisticsAlgorithm
typedef vtkTableAlgorithm Superclass
 
enum  InputPorts { INPUT_DATA = 0, LEARN_PARAMETERS = 1, INPUT_MODEL = 2 }
 
enum  OutputIndices { OUTPUT_DATA = 0, OUTPUT_MODEL = 1, ASSESSMENT = 2, OUTPUT_TEST = 2 }
 

Public Member Functions

virtual int IsA (const char *type)
 
vtkPCAStatisticsGnuRNewInstance () const
 
virtual void PrintSelf (ostream &os, vtkIndent indent)
 
- Public Member Functions inherited from vtkPCAStatistics
vtkPCAStatisticsNewInstance () const
 
virtual void SetNormalizationScheme (int)
 
virtual int GetNormalizationScheme ()
 
virtual void SetNormalizationSchemeByName (const char *sname)
 
virtual const char * GetNormalizationSchemeName (int scheme)
 
virtual vtkTable * GetSpecifiedNormalization ()
 
virtual void SetSpecifiedNormalization (vtkTable *)
 
void GetEigenvalues (int request, vtkDoubleArray *)
 
void GetEigenvalues (vtkDoubleArray *)
 
double GetEigenvalue (int request, int i)
 
double GetEigenvalue (int i)
 
void GetEigenvectors (int request, vtkDoubleArray *eigenvectors)
 
void GetEigenvectors (vtkDoubleArray *eigenvectors)
 
void GetEigenvector (int i, vtkDoubleArray *eigenvector)
 
void GetEigenvector (int request, int i, vtkDoubleArray *eigenvector)
 
virtual void SetBasisScheme (int)
 
virtual int GetBasisScheme ()
 
virtual const char * GetBasisSchemeName (int schemeIndex)
 
virtual void SetBasisSchemeByName (const char *schemeName)
 
virtual void SetFixedBasisSize (int)
 
virtual int GetFixedBasisSize ()
 
virtual void SetFixedBasisEnergy (double)
 
virtual double GetFixedBasisEnergy ()
 
virtual bool SetParameter (const char *parameter, int index, vtkVariant value)
 
- Public Member Functions inherited from vtkMultiCorrelativeStatistics
vtkMultiCorrelativeStatisticsNewInstance () const
 
virtual void Aggregate (vtkDataObjectCollection *, vtkMultiBlockDataSet *)
 
- Public Member Functions inherited from vtkStatisticsAlgorithm
vtkStatisticsAlgorithmNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent)
 
virtual void SetColumnStatus (const char *namCol, int status)
 
virtual void ResetAllColumnStates ()
 
virtual int RequestSelectedColumns ()
 
virtual void ResetRequests ()
 
virtual vtkIdType GetNumberOfRequests ()
 
virtual vtkIdType GetNumberOfColumnsForRequest (vtkIdType request)
 
void AddColumn (const char *namCol)
 
void AddColumnPair (const char *namColX, const char *namColY)
 
virtual void SetLearnOptionParameterConnection (vtkAlgorithmOutput *params)
 
virtual void SetLearnOptionParameters (vtkDataObject *params)
 
virtual void SetInputModelConnection (vtkAlgorithmOutput *model)
 
virtual void SetInputModel (vtkDataObject *model)
 
virtual void SetLearnOption (bool)
 
virtual bool GetLearnOption ()
 
virtual void SetDeriveOption (bool)
 
virtual bool GetDeriveOption ()
 
virtual void SetAssessOption (bool)
 
virtual bool GetAssessOption ()
 
virtual void SetTestOption (bool)
 
virtual bool GetTestOption ()
 
virtual void SetNumberOfPrimaryTables (vtkIdType)
 
virtual vtkIdType GetNumberOfPrimaryTables ()
 
virtual void SetAssessNames (vtkStringArray *)
 
virtual vtkStringArray * GetAssessNames ()
 
virtual const char * GetColumnForRequest (vtkIdType r, vtkIdType c)
 
virtual int GetColumnForRequest (vtkIdType r, vtkIdType c, vtkStdString &columnName)
 

Static Public Member Functions

static int IsTypeOf (const char *type)
 
static vtkPCAStatisticsGnuRSafeDownCast (vtkObjectBase *o)
 
static vtkPCAStatisticsGnuRNew ()
 
- Static Public Member Functions inherited from vtkPCAStatistics
static int IsTypeOf (const char *type)
 
static vtkPCAStatisticsSafeDownCast (vtkObjectBase *o)
 
static vtkPCAStatisticsNew ()
 
- Static Public Member Functions inherited from vtkMultiCorrelativeStatistics
static int IsTypeOf (const char *type)
 
static
vtkMultiCorrelativeStatistics
SafeDownCast (vtkObjectBase *o)
 
static
vtkMultiCorrelativeStatistics
New ()
 
- Static Public Member Functions inherited from vtkStatisticsAlgorithm
static int IsTypeOf (const char *type)
 
static vtkStatisticsAlgorithmSafeDownCast (vtkObjectBase *o)
 

Protected Member Functions

virtual vtkObjectBase * NewInstanceInternal () const
 
 vtkPCAStatisticsGnuR ()
 
 ~vtkPCAStatisticsGnuR ()
 
virtual vtkDoubleArray * CalculatePValues (vtkIdTypeArray *, vtkDoubleArray *)
 
- Protected Member Functions inherited from vtkPCAStatistics
 vtkPCAStatistics ()
 
 ~vtkPCAStatistics ()
 
virtual int FillInputPortInformation (int port, vtkInformation *info)
 
virtual void Derive (vtkMultiBlockDataSet *)
 
virtual void Test (vtkTable *, vtkMultiBlockDataSet *, vtkTable *)
 
virtual void Assess (vtkTable *, vtkMultiBlockDataSet *, vtkTable *)
 
virtual void SelectAssessFunctor (vtkTable *inData, vtkDataObject *inMeta, vtkStringArray *rowNames, AssessFunctor *&dfunc)
 
- Protected Member Functions inherited from vtkMultiCorrelativeStatistics
 vtkMultiCorrelativeStatistics ()
 
 ~vtkMultiCorrelativeStatistics ()
 
virtual void Learn (vtkTable *, vtkTable *, vtkMultiBlockDataSet *)
 
- Protected Member Functions inherited from vtkStatisticsAlgorithm
 vtkStatisticsAlgorithm ()
 
 ~vtkStatisticsAlgorithm ()
 
virtual int FillOutputPortInformation (int port, vtkInformation *info)
 
virtual int RequestData (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
void Assess (vtkTable *, vtkMultiBlockDataSet *, vtkTable *, int)
 

Additional Inherited Members

- Protected Attributes inherited from vtkPCAStatistics
int NormalizationScheme
 
int BasisScheme
 
int FixedBasisSize
 
double FixedBasisEnergy
 
- Protected Attributes inherited from vtkStatisticsAlgorithm
int NumberOfPrimaryTables
 
bool LearnOption
 
bool DeriveOption
 
bool AssessOption
 
bool TestOption
 
vtkStringArray * AssessNames
 
vtkStatisticsAlgorithmPrivateInternals
 
- Static Protected Attributes inherited from vtkPCAStatistics
static const char * BasisSchemeEnumNames [NUM_BASIS_SCHEMES+1]
 
static const char * NormalizationSchemeEnumNames [NUM_NORMALIZATION_SCHEMES+1]
 

Detailed Description

A class for multivariate principal component analysis using R to calculate p-values.

This class derives from the multi-correlative statistics algorithm and uses the covariance matrix and Cholesky decomposition computed by it. However, when it finalizes the statistics in learn operation, the PCA class computes the SVD of the covariance matrix in order to obtain its eigenvectors.

In the assess operation, the input data are

In the test operation, a Jarque-Bera-Srivastava test of n-d normality is performed.

Thanks:
Thanks to David Thompson, Philippe Pebay and Jackson Mayo from Sandia National Laboratories for implementing this class. Updated by Philippe Pebay, Kitware SAS 2012

Definition at line 55 of file vtkPCAStatisticsGnuR.h.

Member Typedef Documentation

Definition at line 58 of file vtkPCAStatisticsGnuR.h.

Constructor & Destructor Documentation

vtkPCAStatisticsGnuR::vtkPCAStatisticsGnuR ( )
protected
vtkPCAStatisticsGnuR::~vtkPCAStatisticsGnuR ( )
protected

Member Function Documentation

static int vtkPCAStatisticsGnuR::IsTypeOf ( const char *  type)
static
virtual int vtkPCAStatisticsGnuR::IsA ( const char *  type)
virtual

Reimplemented from vtkPCAStatistics.

static vtkPCAStatisticsGnuR* vtkPCAStatisticsGnuR::SafeDownCast ( vtkObjectBase *  o)
static
virtual vtkObjectBase* vtkPCAStatisticsGnuR::NewInstanceInternal ( ) const
protectedvirtual

Reimplemented from vtkPCAStatistics.

vtkPCAStatisticsGnuR* vtkPCAStatisticsGnuR::NewInstance ( ) const
virtual void vtkPCAStatisticsGnuR::PrintSelf ( ostream &  os,
vtkIndent  indent 
)
virtual

Reimplemented from vtkPCAStatistics.

static vtkPCAStatisticsGnuR* vtkPCAStatisticsGnuR::New ( )
static
virtual vtkDoubleArray* vtkPCAStatisticsGnuR::CalculatePValues ( vtkIdTypeArray *  ,
vtkDoubleArray *   
)
protectedvirtual

Calculate p-value. This will be overridden using the object factory with an R implementation if R is present.

Reimplemented from vtkPCAStatistics.


The documentation for this class was generated from the following file: