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// File: MixtureOfSubstitutionModels.h
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// Created by: Laurent Gueguen
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// Date: lundi 13 septembre 2010, à 21h 31
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Copyright or © or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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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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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _MIXTUREOFSUBSTITUTIONMODELS_H_
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#define _MIXTUREOFSUBSTITUTIONMODELS_H_
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#include <Bpp/Numeric/Prob.all>
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#include <Bpp/Numeric/VectorTools.h>
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#include "AbstractMixedSubstitutionModel.h"
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#include <cstring> // C lib for string copy
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* @brief Substitution models defined as a mixture of several
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* substitution models.
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* @author Laurent Guéguen
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* All the models can be of different types (for example T92 or
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* GY94), and each model has a specific probability and rate.
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* The probabilities and rates of the models are independent
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* parameters, handled directly, under the constraint that the
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* expectation of the rates on the distribution of the models must
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* If there are @f$n@f$ models, @f$p_i@f$ is the probability of
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* model i (@f$\sum_{i=1}^{n} p_i = 1@f$) and the probabilities
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* are defined by relative probabilities parameters @f$rp_i@f$
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* (called "relprobai") with:
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* 1 <= i < n, p_i = (1-rp_1)*(1-rp_2)...(1-rp_{i-1})*rp_{i}
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* p_n = (1-rp_1)*(1-rp_2)...(1-rp_{n-1})
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* \forall 1 <= i < n, rp_i = \frac{p_i}{1-(p_1+...+p_{i-1})}
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* where @f$p_i@f$ stands for the probability of model @f$i@f$.
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* If there are @f$n@f$ models, @f$\rho_i@f$ is the rate and @f$p_i@f$
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* is the probability of model i (@f$\sum_{i=1}^{n} p_i * \rho_i =
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* 1@f$), the rates are defined by relative rates parameters
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* @f$r_i@f$ (called "relratei") with:
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* 1 <= i < n, \rho_i = (1-r_1)*(1-r_2)...(1-r_{i-1})*\frac{r_{i}}{p_i}
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* \rho_n = \frac{(1-r_1)*(1-r_2)*...*(1-r_{n-1})}{p_n}
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* \forall 1 <= i < n, r_i = \frac{\rho_i*p_i}{1-(p_1*\rho_1+...+p_{i-1}*\rho_{i-1})} < 1.
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* Mixture(model1=HKY85(kappa=3), model2=T92(theta=0.1),
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* model2=L95(gamma=2), relrate1=0.2, relrate2=0.9,
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* relproba1=0.1,relproba2=0.8)
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* define a model as a mixture of 3 different models: HKY85 has
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* probability 0.1 and rate 2, T92 has probability 0.4 and rate 1.8,
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* and L95 has probability 0.5 and rate 0.16.
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* The parameters are named \c "Mixture.relrate1", \c
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* "Mixture.relrate2", \c "Mixture.relproba1", \c
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* "Mixture.relproba2"... in addition to the parameters of the
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* submodels that are prefixed by "Mixture.i_", where i is the order
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class MixtureOfSubstitutionModels :
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public AbstractMixedSubstitutionModel
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*@brief Constructor of a MixtureOfSubstitutionModels, where all
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*the models have rate 1 and equal probability.
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*@param alpha pointer to the Alphabet
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*@param vpModel vector of pointers to SubstitutionModels. All the
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* SubstitutionModels are owned by the instance.
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MixtureOfSubstitutionModels(const Alphabet* alpha,
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std::vector<SubstitutionModel*> vpModel);
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*@brief Constructor of a MixtureOfSubstitutionModels.
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*@param alpha pointer to the Alphabet
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*@param vpModel vector of pointers to SubstitutionModels. All the
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* SubstitutionModels are owned by the instance.
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*@param vproba vector of the probabilities of the models
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*@param vrate vector of the rates of the models
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* See above the constraints on the rates and the probabilities of
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MixtureOfSubstitutionModels(const Alphabet* alpha,
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std::vector<SubstitutionModel*> vpModel,
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Vdouble& vproba, Vdouble& vrate);
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MixtureOfSubstitutionModels(const MixtureOfSubstitutionModels&);
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MixtureOfSubstitutionModels& operator=(const MixtureOfSubstitutionModels&);
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~MixtureOfSubstitutionModels();
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MixtureOfSubstitutionModels* clone() const { return new MixtureOfSubstitutionModels(*this); }
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std::string getName() const { return "MixtureOfSubstitutionModels"; }
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void updateMatrices();
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* @brief Sets the rates of the submodels to follow the constraint
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* that the mean rate of the mixture equals rate_.
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* @param vd a vector of positive values such that the rates of
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* the respective submodels are in the same proportions (ie this
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* vector does not need to be normalized).
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virtual void setVRates(Vdouble& vd);
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* @brief applies setFreq to all the models of the mixture and
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* recovers the parameters values.
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void setFreq(std::map<int,double>&);
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} // end of namespace bpp.
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#endif // _MIXTUREOFSUBSTITUTIONMODELS_H_
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src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h
