source: branches/0.6-stable/test/fisher_test.cc @ 2317

// $Id: fisher_test.cc 2317 2010-08-20 04:10:07Z peter $

/*
  Copyright (C) 2008, 2009, 2010 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include <climits>

#include "Suite.h"

#include "yat/statistics/Fisher.h"

using namespace theplu::yat;
void test_p_value(test::Suite&);
void test_p_value_approximative(test::Suite&);
void test_p_value_exact(test::Suite&);
void test_large_numbers(test::Suite&);

int main(int argc, char* argv[])
{  
  test::Suite suite(argc, argv);

  statistics::Fisher f;
  if (!suite.equal(f.oddsratio(1,4,5,1), 0.05)) {
    suite.add(false);
    suite.err() << "oddsratio failed\n";
  }
  double a, b, c, d;
  f.expected(a,b,c,d);
  if (!suite.equal(a, 30.0/11.0)) {
    suite.add(false);
    suite.err() << "expected a failed\n";
  }
  if (!suite.equal(b, 25.0/11.0)) {
    suite.add(false);
    suite.err() << "expected b failed\n";
  }
  if (!suite.equal(c, 36.0/11.0)) {
    suite.add(false);
    suite.err() << "expected c failed\n";
  }
  if (!suite.equal(d, 30.0/11.0)) {
    suite.add(false);
    suite.err() << "expected d failed\n";
  }
  if (!suite.equal(f.Chi2(), 4.4122222222222222222222)) { 
    suite.add(false);
    suite.err() << "Chi2 failed\n";
  }
  if (!suite.equal(f.minimum_size(),10)) {
    suite.add(false);
    suite.err() << "minimum_size failed\n";
  }
  test_p_value(suite);
  test_large_numbers(suite);
  return suite.return_value();
}


void test_p_value(test::Suite& suite)
{
  test_p_value_exact(suite);
  test_p_value_approximative(suite);
}


void test_p_value_approximative(test::Suite& suite)
{
  suite.err() << "testing p_value_approximative\n";
  statistics::Fisher f;
  f.minimum_size() = 0;
  f.oddsratio(10,20,20,50);
  suite.add(suite.equal(f.p_value(), 2*f.p_value_one_sided()));
  f.oddsratio(10,20,10,20);
  suite.add(suite.equal(f.p_value(), 1.0));
  suite.add(suite.equal(f.p_value_one_sided(), 0.5));
}


void test_p_value_exact(test::Suite& suite)
{
  suite.err() << "test p_value_exact\n";
  statistics::Fisher f;
  f.minimum_size() = 1000;
  f.oddsratio(10,20,10,20);
  suite.add(suite.equal(f.p_value(), 1.0));

  f.oddsratio(10, 20, 20, 200);
  suite.add(suite.equal_fix(f.p_value(), 0.000811906062767622,1e-16));
  suite.add(suite.equal_fix(f.p_value_one_sided(), 0.000811906062767622,1e-16));

  // testing symmetry
  statistics::Fisher f2;
  f2.minimum_size() = 1000;
  f2.oddsratio(20, 200, 10, 20);
  suite.add(suite.equal(f2.p_value(), f.p_value()));

  f.oddsratio(1, 1, 1, 2);
  suite.add(suite.equal(f.p_value(), 1.0, 2));
  suite.add(suite.equal(f.p_value_one_sided(), 0.7));

  f.oddsratio(1, 1, 2, 1);
  suite.add(suite.equal(f.p_value(), 1.0, 2));
  suite.add(suite.equal(f.p_value_one_sided(), 0.9));

}

void test_large_numbers(test::Suite& suite)
{
  // skip test if unsigned int is 16 bit
  if (UINT_MAX == ( 1 << 16))
    return;

  statistics::Fisher f;
  double oddsratio = f.oddsratio(1166,63326825-1166,1095,66074759-1095);
  if (oddsratio<0.5 || oddsratio>2) {
    suite.err() << "oddsratio: " << oddsratio << "\n";
    suite.err() << "expected ~ 1\n";
    suite.xadd(false);
  }
  f.p_value();
  f.p_value_one_sided();
}