VTK
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | List of all members
vtkContingencyStatisticsGnuR Class Reference

A class for bivariate correlation contigency tables, conditional probabilities, and information entropy. The p-value are calculated using R. More...

#include <vtkContingencyStatisticsGnuR.h>

Inheritance diagram for vtkContingencyStatisticsGnuR:
[legend]
Collaboration diagram for vtkContingencyStatisticsGnuR:
[legend]

Public Types

typedef vtkContingencyStatistics Superclass
 
- Public Types inherited from vtkContingencyStatistics
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 Types inherited from vtkTableAlgorithm
typedef vtkAlgorithm Superclass
 
- Public Types inherited from vtkAlgorithm
typedef vtkObject Superclass
 
enum  DesiredOutputPrecision { SINGLE_PRECISION, DOUBLE_PRECISION, DEFAULT_PRECISION }
 

Public Member Functions

virtual int IsA (const char *type)
 
vtkContingencyStatisticsGnuRNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent)
 
- Public Member Functions inherited from vtkContingencyStatistics
vtkContingencyStatisticsNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent)
 
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)
 
virtual bool SetParameter (const char *parameter, int index, vtkVariant value)
 
- Public Member Functions inherited from vtkTableAlgorithm
vtkTableAlgorithmNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent)
 
virtual int ProcessRequest (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
vtkTableGetOutput ()
 
vtkTableGetOutput (int index)
 
void SetInputData (vtkDataObject *obj)
 
void SetInputData (int index, vtkDataObject *obj)
 
- Public Member Functions inherited from vtkAlgorithm
vtkAlgorithmNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent)
 
int HasExecutive ()
 
vtkExecutiveGetExecutive ()
 
virtual void SetExecutive (vtkExecutive *executive)
 
virtual int ModifyRequest (vtkInformation *request, int when)
 
vtkInformation * GetInputPortInformation (int port)
 
vtkInformation * GetOutputPortInformation (int port)
 
int GetNumberOfInputPorts ()
 
int GetNumberOfOutputPorts ()
 
void UpdateProgress (double amount)
 
vtkInformation * GetInputArrayInformation (int idx)
 
void RemoveAllInputs ()
 
vtkDataObjectGetOutputDataObject (int port)
 
virtual void RemoveInputConnection (int port, vtkAlgorithmOutput *input)
 
virtual void RemoveInputConnection (int port, int idx)
 
virtual void RemoveAllInputConnections (int port)
 
int GetNumberOfInputConnections (int port)
 
int GetTotalNumberOfInputConnections ()
 
vtkAlgorithmOutputGetInputConnection (int port, int index)
 
vtkAlgorithmGetInputAlgorithm (int port, int index, int &algPort)
 
vtkAlgorithmGetInputAlgorithm (int port, int index)
 
vtkExecutiveGetInputExecutive (int port, int index)
 
vtkInformation * GetInputInformation (int port, int index)
 
vtkInformation * GetOutputInformation (int port)
 
virtual void UpdateInformation ()
 
virtual void PropagateUpdateExtent ()
 
virtual void UpdateWholeExtent ()
 
void ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
 
virtual double ComputePriority ()
 
int SetUpdateExtentToWholeExtent (int port)
 
int SetUpdateExtentToWholeExtent ()
 
void SetUpdateExtent (int port, int extent[6])
 
int ProcessRequest (vtkInformation *request, vtkCollection *inInfo, vtkInformationVector *outInfo)
 
virtual int ComputePipelineMTime (vtkInformation *request, vtkInformationVector **inInfoVec, vtkInformationVector *outInfoVec, int requestFromOutputPort, unsigned long *mtime)
 
virtual vtkInformation * GetInformation ()
 
virtual void SetInformation (vtkInformation *)
 
virtual void Register (vtkObjectBase *o)
 
virtual void UnRegister (vtkObjectBase *o)
 
virtual void SetAbortExecute (int)
 
virtual int GetAbortExecute ()
 
virtual void AbortExecuteOn ()
 
virtual void AbortExecuteOff ()
 
virtual void SetProgress (double)
 
virtual double GetProgress ()
 
void SetProgressText (const char *ptext)
 
virtual char * GetProgressText ()
 
virtual unsigned long GetErrorCode ()
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)
 
virtual void SetInputArrayToProcess (int idx, vtkInformation *info)
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, const char *fieldAssociation, const char *attributeTypeorName)
 
vtkDataObjectGetInputDataObject (int port, int connection)
 
virtual void SetInputConnection (int port, vtkAlgorithmOutput *input)
 
virtual void SetInputConnection (vtkAlgorithmOutput *input)
 
virtual void AddInputConnection (int port, vtkAlgorithmOutput *input)
 
virtual void AddInputConnection (vtkAlgorithmOutput *input)
 
virtual void SetInputDataObject (int port, vtkDataObject *data)
 
virtual void SetInputDataObject (vtkDataObject *data)
 
virtual void AddInputDataObject (int port, vtkDataObject *data)
 
virtual void AddInputDataObject (vtkDataObject *data)
 
vtkAlgorithmOutputGetOutputPort (int index)
 
vtkAlgorithmOutputGetOutputPort ()
 
vtkAlgorithmGetInputAlgorithm ()
 
vtkExecutiveGetInputExecutive ()
 
vtkInformation * GetInputInformation ()
 
virtual void Update (int port)
 
virtual void Update ()
 
virtual void SetReleaseDataFlag (int)
 
virtual int GetReleaseDataFlag ()
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
int UpdateExtentIsEmpty (vtkInformation *pinfo, vtkDataObject *output)
 
int UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
 
void SetUpdateExtent (int port, int piece, int numPieces, int ghostLevel)
 
void SetUpdateExtent (int piece, int numPieces, int ghostLevel)
 
void SetUpdateExtent (int extent[6])
 
int * GetUpdateExtent ()
 
int * GetUpdateExtent (int port)
 
void GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
 
void GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
 
void GetUpdateExtent (int extent[6])
 
void GetUpdateExtent (int port, int extent[6])
 
int GetUpdatePiece ()
 
int GetUpdatePiece (int port)
 
int GetUpdateNumberOfPieces ()
 
int GetUpdateNumberOfPieces (int port)
 
int GetUpdateGhostLevel ()
 
int GetUpdateGhostLevel (int port)
 

Static Public Member Functions

static int IsTypeOf (const char *type)
 
static
vtkContingencyStatisticsGnuR
SafeDownCast (vtkObjectBase *o)
 
static
vtkContingencyStatisticsGnuR
New ()
 
- Static Public Member Functions inherited from vtkContingencyStatistics
static int IsTypeOf (const char *type)
 
static vtkContingencyStatisticsSafeDownCast (vtkObjectBase *o)
 
static vtkContingencyStatisticsNew ()
 
- Static Public Member Functions inherited from vtkStatisticsAlgorithm
static int IsTypeOf (const char *type)
 
static vtkStatisticsAlgorithmSafeDownCast (vtkObjectBase *o)
 
- Static Public Member Functions inherited from vtkTableAlgorithm
static vtkTableAlgorithmNew ()
 
static int IsTypeOf (const char *type)
 
static vtkTableAlgorithmSafeDownCast (vtkObjectBase *o)
 
- Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithmNew ()
 
static int IsTypeOf (const char *type)
 
static vtkAlgorithmSafeDownCast (vtkObjectBase *o)
 
static void SetDefaultExecutivePrototype (vtkExecutive *proto)
 
static vtkInformationIntegerKey * INPUT_IS_OPTIONAL ()
 
static vtkInformationIntegerKey * INPUT_IS_REPEATABLE ()
 
static
vtkInformationInformationVectorKey * 
INPUT_REQUIRED_FIELDS ()
 
static
vtkInformationStringVectorKey * 
INPUT_REQUIRED_DATA_TYPE ()
 
static
vtkInformationInformationVectorKey * 
INPUT_ARRAYS_TO_PROCESS ()
 
static vtkInformationIntegerKey * INPUT_PORT ()
 
static vtkInformationIntegerKey * INPUT_CONNECTION ()
 
static vtkInformationIntegerKey * PRESERVES_DATASET ()
 
static vtkInformationIntegerKey * PRESERVES_GEOMETRY ()
 
static vtkInformationIntegerKey * PRESERVES_BOUNDS ()
 
static vtkInformationIntegerKey * PRESERVES_TOPOLOGY ()
 
static vtkInformationIntegerKey * PRESERVES_ATTRIBUTES ()
 
static vtkInformationIntegerKey * PRESERVES_RANGES ()
 
static vtkInformationIntegerKey * MANAGES_METAINFORMATION ()
 

Protected Member Functions

virtual vtkObjectBase * NewInstanceInternal () const
 
 vtkContingencyStatisticsGnuR ()
 
 ~vtkContingencyStatisticsGnuR ()
 
virtual void CalculatePValues (vtkTable *)
 
- Protected Member Functions inherited from vtkContingencyStatistics
 vtkContingencyStatistics ()
 
 ~vtkContingencyStatistics ()
 
virtual void Derive (vtkMultiBlockDataSet *)
 
virtual void Learn (vtkTable *, vtkTable *, vtkMultiBlockDataSet *)
 
virtual void Test (vtkTable *, vtkMultiBlockDataSet *, vtkTable *)
 
virtual void Assess (vtkTable *, vtkMultiBlockDataSet *, vtkTable *)
 
virtual void SelectAssessFunctor (vtkTable *outData, vtkDataObject *inMeta, vtkStringArray *rowNames, AssessFunctor *&dfunc)
 
virtual void SelectAssessFunctor (vtkTable *outData, vtkMultiBlockDataSet *inMeta, vtkIdType pairKey, vtkStringArray *rowNames, AssessFunctor *&dfunc)
 
- Protected Member Functions inherited from vtkStatisticsAlgorithm
 vtkStatisticsAlgorithm ()
 
 ~vtkStatisticsAlgorithm ()
 
virtual int FillInputPortInformation (int port, vtkInformation *info)
 
virtual int FillOutputPortInformation (int port, vtkInformation *info)
 
virtual int RequestData (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
void Assess (vtkTable *, vtkMultiBlockDataSet *, vtkTable *, int)
 
- Protected Member Functions inherited from vtkTableAlgorithm
 vtkTableAlgorithm ()
 
 ~vtkTableAlgorithm ()
 
virtual int RequestInformation (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
 
virtual int RequestUpdateExtent (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
- Protected Member Functions inherited from vtkAlgorithm
 vtkAlgorithm ()
 
 ~vtkAlgorithm ()
 
virtual void SetNumberOfInputPorts (int n)
 
virtual void SetNumberOfOutputPorts (int n)
 
int InputPortIndexInRange (int index, const char *action)
 
int OutputPortIndexInRange (int index, const char *action)
 
int GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)
 
virtual vtkExecutiveCreateDefaultExecutive ()
 
virtual void ReportReferences (vtkGarbageCollector *)
 
virtual void SetNumberOfInputConnections (int port, int n)
 
int GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
 
int GetInputArrayAssociation (int idx, vtkDataObject *input)
 
vtkDataArray * GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)
 
vtkDataArray * GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkDataArray * GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 
vtkDataArray * GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkDataArray * GetInputArrayToProcess (int idx, vtkDataObject *input)
 
vtkDataArray * GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkAbstractArray * GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)
 
vtkAbstractArray * GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArray * GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 
vtkAbstractArray * GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArray * GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
 
vtkAbstractArray * GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkInformation * GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
 
virtual void SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
 
void SetInputDataInternal (int port, vtkDataObject *input)
 
void AddInputDataInternal (int port, vtkDataObject *input)
 
virtual void SetErrorCode (unsigned long)
 

Additional Inherited Members

- Public Attributes inherited from vtkAlgorithm
int AbortExecute
 
- Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKey * PORT_REQUIREMENTS_FILLED ()
 
- Protected Attributes inherited from vtkStatisticsAlgorithm
int NumberOfPrimaryTables
 
bool LearnOption
 
bool DeriveOption
 
bool AssessOption
 
bool TestOption
 
vtkStringArray * AssessNames
 
vtkStatisticsAlgorithmPrivateInternals
 
- Protected Attributes inherited from vtkAlgorithm
vtkInformation * Information
 
double Progress
 
char * ProgressText
 
unsigned long ErrorCode
 
- Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutiveDefaultExecutivePrototype
 

Detailed Description

A class for bivariate correlation contigency tables, conditional probabilities, and information entropy. The p-value are calculated using R.

Given a pair of columns of interest, this class provides the following functionalities, depending on the operation in which it is executed: Learn: calculate contigency tables and corresponding discrete joint probability distribution. Derive: calculate conditional probabilities, information entropies, and pointwise mutual information. Assess: given two columns of interest with the same number of entries as input in port INPUT_DATA, and a corresponding bivariate probability distribution, Test: calculate Chi-square independence statistic and, if VTK to R interface is available, retrieve corresponding p-value for independence testing.

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

Definition at line 52 of file vtkContingencyStatisticsGnuR.h.

Member Typedef Documentation

Definition at line 55 of file vtkContingencyStatisticsGnuR.h.

Constructor & Destructor Documentation

vtkContingencyStatisticsGnuR::vtkContingencyStatisticsGnuR ( )
protected
vtkContingencyStatisticsGnuR::~vtkContingencyStatisticsGnuR ( )
protected

Member Function Documentation

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

Reimplemented from vtkContingencyStatistics.

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

Reimplemented from vtkContingencyStatistics.

vtkContingencyStatisticsGnuR* vtkContingencyStatisticsGnuR::NewInstance ( ) const
void vtkContingencyStatisticsGnuR::PrintSelf ( ostream &  os,
vtkIndent  indent 
)
static vtkContingencyStatisticsGnuR* vtkContingencyStatisticsGnuR::New ( )
static
virtual void vtkContingencyStatisticsGnuR::CalculatePValues ( vtkTable )
protectedvirtual

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

Reimplemented from vtkContingencyStatistics.


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