ContingencyTableTest.cpp

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//
// File: ContingencyTableTest.cpp
// Authors:
//   Julien Dutheil
// Created: 2010-12-09 14:20:00
//
 
/*
  Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
  
  This software is a computer program whose purpose is to provide classes
  for numerical calculus.
  
  This software is governed by the CeCILL license under French law and
  abiding by the rules of distribution of free software. You can use,
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".
  
  As a counterpart to the access to the source code and rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty and the software's author, the holder of the
  economic rights, and the successive licensors have only limited
  liability.
  
  In this respect, the user's attention is drawn to the risks associated
  with loading, using, modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean that it is complicated to manipulate, and that also
  therefore means that it is reserved for developers and experienced
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  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL license and that you accept its terms.
*/
 
#include <algorithm>
#include <iostream>
 
#include "../../App/ApplicationTools.h"
#include "../Random/ContingencyTableGenerator.h"
#include "../Random/RandomTools.h"
#include "../VectorTools.h"
#include "ContingencyTableTest.h"
 
using namespace bpp;
using namespace std;
 
ContingencyTableTest::ContingencyTableTest(const std::vector< std::vector<size_t> >& table, unsigned int nbPermutations, bool warn) :
  statistic_(0),
  pvalue_(0),
  df_(0),
  margin1_(table.size()),
  margin2_(0)
{
  // Compute marginals:
  size_t n = table.size();
  if (n < 2)
    throw Exception("ContingencyTableTest. Table size should be at least 2x2!");
  size_t m = table[0].size();
  if (m < 2)
    throw Exception("ContingencyTableTest. Table size should be at least 2x2!");
  margin2_.resize(m);
  for (size_t j = 0; j < m; ++j)
  {
    margin2_[j] = 0;
  }
  bool test = false;
  for (size_t i = 0; i < n; ++i)
  {
    if (table[i].size() != m)
      throw Exception("ContingencyTableTest. Input array has non-homogeneous dimensions!");
    for (size_t j = 0; j < m; ++j)
    {
      size_t c = table[i][j];
      if (c <= 5)
        test = true;
      margin1_[i] += c;
      margin2_[j] += c;
    }
  }
  for (size_t i = 0; i < n; ++i)
  {
    if (margin1_[i] == 0)
      throw Exception("ContingencyTableTest. Row " + TextTools::toString(i) + " sums to 0.");
  }
  for (size_t j = 0; j < m; ++j)
  {
    if (margin2_[j] == 0)
      throw Exception("ContingencyTableTest. Column " + TextTools::toString(j) + " sums to 0.");
  }
 
 
  size_t tot = VectorTools::sum(margin1_);
  df_ = static_cast<double>((m - 1) * (n - 1));
 
  RowMatrix<long double> expc(n, m);
  for (size_t i = 0; i < n; ++i)
  {
    for (size_t j = 0; j < m; ++j)
    {
      long double c = table[i][j];
      long double e = static_cast<long double>(margin1_[i] * margin2_[j]) / static_cast<long double>(tot);
      expc(i, j) = e;
      statistic_ += static_cast<double>(std::pow(c - e, 2.L) / e);
    }
  }
 
  if (nbPermutations > 0)
  {
    size_t count = 0;
    ContingencyTableGenerator ctgen(margin1_, margin2_);
    for (unsigned int k = 0; k < nbPermutations; ++k)
    {
      // Randomize:
      RowMatrix<size_t> table_rep = ctgen.rcont2();
      // Recompute statistic:
      double stat_rep = 0;
      for (size_t i = 0; i < n; ++i)
      {
        for (size_t j = 0; j < m; ++j)
        {
          long double c = table_rep(i, j);
          long double e = expc(i, j);
          stat_rep += static_cast<double>(std::pow(c - e, 2.L) / e);
        }
      }
      if (stat_rep >= statistic_)
        count++;
    }
    pvalue_ = static_cast<double>(count + 1) / static_cast<double>(nbPermutations + 1);
  }
  else
  {
    if (test && warn)
      ApplicationTools::displayWarning("Unsufficient observations, p-value might be incorrect.");
 
    // Compute p-value:
    pvalue_ = 1. - RandomTools::pChisq(statistic_, df_);
  }
}