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// File ContingencyTableGenerator.h
// Author: Julien Dutheil
// Created on: Fri Dec 10 2010 16:19
//
/*
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
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _CONTINGENCYTABLEGENERATOR_H_
#define _CONTINGENCYTABLEGENERATOR_H_
#include "RandomFactory.h"
#include "RandomTools.h"
#include "../Matrix/Matrix.h"
// From the STL:
#include <cmath>
#include <vector>
namespace bpp
{
/**
* @brief Generate a random contingency matrix with given marginal counts.
*
* This procedure was adapted from the original fortran code described in:
* Patefield, W. M. (1981) Algorithm AS159. An efficient method of
* generating r x c tables with given row and column totals.
* _Applied Statistics_ *30*, 91-97.
* This algorithm is the one also used in R function chisq.test for instance.
*
* The code was adpated from file rcont.c, edited by Martin Maechler, Dec 2003,
* available in the R software source distribution.
*
* @param nrowt Marginal counts.
* @param ncolt Marginal counts.
* @return A random matrix of counts with the same marginals as specified.
*/
class ContingencyTableGenerator
{
private:
std::vector<size_t> nrowt_;
std::vector<size_t> ncolt_;
size_t nrow_;
size_t ncol_;
size_t nrowm_;
size_t ncolm_;
std::vector<size_t> jwork_; //workspace
size_t ntot_; //total number of observations
std::vector<double> fact_; //log factorial
public:
ContingencyTableGenerator(const std::vector<size_t>& nrowt, const std::vector<size_t>& ncolt);
public:
RowMatrix<size_t> rcont2(const RandomFactory& generator = *RandomTools::DEFAULT_GENERATOR);
};
} //end of namespace bpp.
#endif //_CONTINGENCYTABLEGENERATOR_H_
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