PrincipalComponentAnalysis.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_NUMERIC_STAT_MVA_PRINCIPALCOMPONENTANALYSIS_H
#define BPP_NUMERIC_STAT_MVA_PRINCIPALCOMPONENTANALYSIS_H


#include "../../Matrix/Matrix.h"
#include "DualityDiagram.h"

namespace bpp
{
class PrincipalComponentAnalysis :
  public DualityDiagram
{
private:
  std::vector<double> columnMeans_;
  std::vector<double> columnSd_;

public:
  PrincipalComponentAnalysis(
      const Matrix<double>& data,
      unsigned int nbAxes,
      const std::vector<double>& rowW,
      const std::vector<double>& colW,
      bool centered = true,
      bool scaled = true,
      double tol = 0.0000001,
      bool verbose = true);

  PrincipalComponentAnalysis(
      const Matrix<double>& data,
      unsigned int nbAxes,
      bool centered = true,
      bool scaled = true,
      double tol = 0.0000001,
      bool verbose = true);

  virtual ~PrincipalComponentAnalysis() {}

  PrincipalComponentAnalysis* clone() const { return new PrincipalComponentAnalysis(*this); }

public:
  static void center(Matrix<double>& matrix, const std::vector<double>& rowW);

  static void scale(Matrix<double>& matrix, const std::vector<double>& rowW);

public:
  const std::vector<double>& getColumnMeans() const { return columnMeans_; }
  const std::vector<double>& getColumnSd() const { return columnSd_; }
};
} // end of namespace bpp.
#endif // BPP_NUMERIC_STAT_MVA_PRINCIPALCOMPONENTANALYSIS_H