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// File: Simplex.h
// Created by: Laurent Guéguen
// Created on: mardi 31 mai 2011, à 11h 02
//
/*
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 _SIMPLEX_H_
#define _SIMPLEX_H_
// From the STL:
#include <vector>
#include "../AbstractParameterAliasable.h"
namespace bpp
{
/**
* @brief A Simplex object, used to define sets of probabilities that
* sum 1.
*
* The probabilities are denoted @f$p_i@f$ for @f$i \in <1,n>@f$.
*
* If they are parametrized, the parameters are called \c "theta1",
* ..., \c "theta(n-1)".
*
* Two ways of parametrization are available:
*
* Global ratio:
*
* @f$\forall i<n, \theta_i=\frac{p_i}{1-(p_1+...+p_{i-1})}@f$.
*
* In the reverse,
* @f$\forall i<n, p_i= (1-\theta_1).(1-\theta_2)...\theta_{i}@f$
* and @f$p_n=(1-\theta_1).(1-\theta_2)...(1-\theta_{n-1})@f$.
*
*
* Local ratio:
*
* @f$\theta_i = \frac{p_i}{p_i+p_{i+1}} \forall i \in 1..\textrm{n-1}@f$.
*
* In the reverse if we denote @f$\alpha_i=\frac{1-\theta_i}{\theta_i}@f$,
* @f$p_i=\frac{\alpha_1...\alpha_{i-1}}{1+\sum_{k=1}^{n-1}\alpha_1...\alpha_k}@f$.
*
*/
class Simplex:
public AbstractParameterAliasable
{
private:
/*
*@brief The dimension+1 of the space simplex (ie the number of probabilities).
*
*/
size_t dim_;
/*
*@brief the method of parametrization.
*
* 0: No parametrization
* 1: Global ratio
* 2: Local ratio
*
*/
unsigned short method_;
std::vector<double> vProb_;
/*
*@brief just used with local ratio (method 2)
*
*/
std::vector<double> valpha_;
public:
/**
* @brief Builds a new Simplex object from a number of
* probabilities. They are initialized equal.
*
* @param dim The number of probabilities.
* @param method tells the method of parametrization (default 0)
* 0: No parametrization
* 1: Global ratio
* 2: Local ratio
* @param name The name passed to AbstractParameterAliasable constructor.
*
*/
Simplex(size_t dim, unsigned short method = 0, const std::string& name = "Simplex.");
/**
* @brief Builds a new Simplex object from a vector of probabilities
*
* @param probas The vector of probabilities.
* @param method tells the method of parametrization (default 0)
* 0: No parametrization
* 1: Global ratio
* 2: Local ratio
* @param name The name passed to AbstractParameterAliasable constructor.
*
*/
Simplex(const std::vector<double>& probas, unsigned short method = 0, const std::string& name = "Simplex.");
virtual ~Simplex() {}
Simplex* clone() const { return new Simplex(*this); }
public:
void fireParameterChanged(const ParameterList & parameters);
size_t dimension() const { return dim_; }
void setFrequencies(const std::vector<double>&);
double prob(size_t i) const { return vProb_[i];}
unsigned short getMethod() const { return method_;}
};
} //end of namespace bpp.
#endif //_SIMPLEDISCRETEDISTRIBUTION_H_
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