ContingencyTableTest.cpp

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//
// File: ContingencyTableTest.cpp
// Created by: Julien Dutheil
// Created on: Thu Dec 09 14:20 2010
//

/*
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
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In this respect, the user's attention is drawn to the risks associated
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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
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*/

#include "ContingencyTableTest.h"
#include "../Random/ContingencyTableGenerator.h"

#include "../../App/ApplicationTools.h"
#include "../VectorTools.h"
#include "../Random/RandomTools.h"

#include <iostream>
#include <algorithm>

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_);
  }
}