/*=========================================================================

Program:   Visualization Toolkit
Module:    vtkContingencyStatisticsGnuR.h

Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
/*-------------------------------------------------------------------------
  Copyright 2011 Sandia Corporation.
  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
  the U.S. Government retains certain rights in this software.
  -------------------------------------------------------------------------*/
/**
 * @class   vtkContingencyStatisticsGnuR
 * @brief   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.
 *
 * @par Thanks:
 * Thanks to Philippe Pebay and David Thompson from Sandia National Laboratories
 * for implementing this class.
 * Updated by Philippe Pebay, Kitware SAS 2012
*/

#ifndef vtkContingencyStatisticsGnuR_h
#define vtkContingencyStatisticsGnuR_h

#include "vtkFiltersStatisticsGnuRModule.h" // For export macro
#include "vtkContingencyStatistics.h"

class vtkIdTypeArray;
class vtkTable;

class VTKFILTERSSTATISTICSGNUR_EXPORT vtkContingencyStatisticsGnuR : public vtkContingencyStatistics
{
public:
  vtkTypeMacro(vtkContingencyStatisticsGnuR, vtkContingencyStatistics);
  void PrintSelf(ostream& os, vtkIndent indent);
  static vtkContingencyStatisticsGnuR* New();

protected:
  vtkContingencyStatisticsGnuR();
  ~vtkContingencyStatisticsGnuR();

  virtual void CalculatePValues(vtkTable*);

private:
  vtkContingencyStatisticsGnuR(const vtkContingencyStatisticsGnuR&) VTK_DELETE_FUNCTION;
  void operator=(const vtkContingencyStatisticsGnuR&) VTK_DELETE_FUNCTION;
};

#endif

