AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp

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//
// File: AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
// Created by: Julien Dutheil
// Created on: Wue Jun 15 09:42 2005
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

   This software is a computer program whose purpose is to provide classes
   for phylogenetic data analysis.

   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
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   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.
 */

#include "AbstractDiscreteRatesAcrossSitesTreeLikelihood.h"

#include <Bpp/Numeric/VectorTools.h>

using namespace bpp;

// From the STL:
#include <iostream>

using namespace std;

/******************************************************************************/

AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood(
  DiscreteDistribution* rDist,
  bool verbose)
throw (Exception) :
  rateDistribution_(rDist)
{
  AbstractTreeLikelihood::enableDerivatives(true);
}

/******************************************************************************/

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters() const
{
  if (!initialized_)
    throw Exception("AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(). Object is not initialized.");
  return rateDistribution_->getParameters().getCommonParametersWith(getParameters());
}

/******************************************************************************/

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters() const
{
  if (!initialized_)
    throw Exception("AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters(). Object is not initialized.");
  return getBranchLengthsParameters();
}

/******************************************************************************/

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters() const
{
  if (!initialized_)
    throw Exception("AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters(). Object is not initialized.");
  ParameterList tmp = getSubstitutionModelParameters();
  tmp.addParameters(getRateDistributionParameters());
  return tmp;
}

/******************************************************************************/

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass() const
{
  size_t nbSites   = getNumberOfSites();
  size_t nbClasses = getNumberOfClasses();
  VVdouble l(nbSites);
  for (size_t i = 0; i < nbSites; i++)
  {
    l[i].resize(nbClasses);
    for (size_t j = 0; j < nbClasses; j++)
    {
      l[i][j] = getLikelihoodForASiteForARateClass(i, j);
    }
  }
  return l;
}

/******************************************************************************/

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(size_t site, int state) const
{
  size_t nbClasses = getNumberOfClasses();
  double l = 0;
  for (size_t i = 0; i < nbClasses; i++)
  {
    l += getLikelihoodForASiteForARateClassForAState(site, i, state) * rateDistribution_->getProbability(i);
  }
  return l;
}

/******************************************************************************/

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(size_t site, int state) const
{
  size_t nbClasses = getNumberOfClasses();
  double l = 0;
  for (size_t i = 0; i < nbClasses; i++)
  {
    l += getLikelihoodForASiteForARateClassForAState(site, i, state) * rateDistribution_->getProbability(i);
  }
  // if(l <= 0.) cerr << "WARNING!!! Negative likelihood." << endl;
  return log(l);
}

/******************************************************************************/

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClass() const
{
  size_t nbSites   = getNumberOfSites();
  size_t nbClasses = getNumberOfClasses();
  VVdouble l(nbSites);
  for (size_t i = 0; i < nbSites; i++)
  {
    l[i] = Vdouble(nbClasses);
    for (size_t j = 0; j < nbClasses; j++)
    {
      l[i][j] = getLogLikelihoodForASiteForARateClass(i, j);
    }
  }
  return l;
}

/******************************************************************************/

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState() const
{
  size_t nbSites   = getNumberOfSites();
  size_t nbClasses = getNumberOfClasses();
  size_t nbStates  = getNumberOfStates();
  VVVdouble l(nbSites);
  for (size_t i = 0; i < nbSites; i++)
  {
    l[i].resize(nbClasses);
    for (size_t j = 0; j < nbClasses; j++)
    {
      l[i][j].resize(nbStates);
      for (size_t x = 0; x < nbStates; x++)
      {
        l[i][j][x] = getLikelihoodForASiteForARateClassForAState(i, j, static_cast<int>(x));
      }
    }
  }
  return l;
}

/******************************************************************************/

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState() const
{
  size_t nbSites   = getNumberOfSites();
  size_t nbClasses = getNumberOfClasses();
  size_t nbStates  = getNumberOfStates();
  VVVdouble l(nbSites);
  for (size_t i = 0; i < nbSites; i++)
  {
    l[i].resize(nbClasses);
    for (size_t j = 0; j < nbClasses; j++)
    {
      l[i][j].resize(nbStates);
      for (size_t x = 0; x < nbStates; x++)
      {
        l[i][j][x] = getLogLikelihoodForASiteForARateClassForAState(i, j, static_cast<int>(x));
      }
    }
  }
  return l;
}

/*******************************************************************************/

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate() const
{
  size_t nbSites   = getNumberOfSites();
  size_t nbClasses = getNumberOfClasses();
  VVdouble pb = getLikelihoodForEachSiteForEachRateClass();
  Vdouble l  = getLikelihoodForEachSite();
  for (size_t i = 0; i < nbSites; i++)
  {
    for (size_t j = 0; j < nbClasses; j++)
    {
      pb[i][j] = pb[i][j] * rateDistribution_->getProbability(j) / l[i];
    }
  }
  return pb;
}

/******************************************************************************/

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite() const
{
  size_t nbSites   = getNumberOfSites();
  size_t nbClasses = getNumberOfClasses();
  VVdouble lr = getLikelihoodForEachSiteForEachRateClass();
  Vdouble l  = getLikelihoodForEachSite();
  Vdouble rates(nbSites, 0.);
  for (size_t i = 0; i < nbSites; i++)
  {
    for (size_t j = 0; j < nbClasses; j++)
    {
      rates[i] += (lr[i][j] / l[i]) * rateDistribution_->getProbability(j) *  rateDistribution_->getCategory(j);
    }
  }
  return rates;
}

/******************************************************************************/

vector<size_t> AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbOfEachSite() const
{
  size_t nbSites = getNumberOfSites();
  VVdouble l = getLikelihoodForEachSiteForEachRateClass();
  vector<size_t> classes(nbSites);
  for (size_t i = 0; i < nbSites; i++)
  {
    classes[i] = VectorTools::whichMax<double>(l[i]);
  }
  return classes;
}

/******************************************************************************/

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite() const
{
  size_t nbSites = getNumberOfSites();
  VVdouble l = getLikelihoodForEachSiteForEachRateClass();
  Vdouble rates(nbSites);
  for (size_t i = 0; i < nbSites; i++)
  {
    rates[i] = rateDistribution_->getCategory(VectorTools::whichMax<double>(l[i]));
  }
  return rates;
}

/******************************************************************************/

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(
  VVVdouble& likelihoodArray)
{
  size_t nbSites   = likelihoodArray.size();
  size_t nbClasses = likelihoodArray[0].size();
  size_t nbStates  = likelihoodArray[0][0].size();
  for (size_t i = 0; i < nbSites; i++)
  {
    for (size_t c = 0; c < nbClasses; c++)
    {
      for (size_t s = 0; s < nbStates; s++)
      {
        likelihoodArray[i][c][s] = 1.;
      }
    }
  }
}

/******************************************************************************/

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(
  const VVVdouble& likelihoodArray)
{
  size_t nbSites   = likelihoodArray.size();
  size_t nbClasses = likelihoodArray[0].size();
  size_t nbStates  = likelihoodArray[0][0].size();
  for (size_t i = 0; i < nbSites; i++)
  {
    cout << "Site " << i << ":" << endl;
    for (size_t c = 0; c < nbClasses; c++)
    {
      cout << "Rate class " << c;
      for (size_t s = 0; s < nbStates; s++)
      {
        cout << "\t" << likelihoodArray[i][c][s];
      }
      cout << endl;
    }
    cout << endl;
  }
}

/******************************************************************************/

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities(int nodeId, size_t siteIndex) const
{
  VVVdouble p3 = getTransitionProbabilitiesPerRateClass(nodeId, siteIndex);
  VVdouble p2;
  Vdouble probs = rateDistribution_->getProbabilities();
  p2.resize(getNumberOfStates());
  for (size_t i = 0; i < p2.size(); i++)
  {
    p2[i].resize(getNumberOfStates());
    for (size_t j = 0; j < p2.size(); j++)
    {
      for (size_t k = 0; k < getNumberOfClasses(); k++)
      {
        p2[i][j] += p3[k][i][j] * probs[k];
      }
    }
  }
  return p2;
}

/******************************************************************************/