ThreeNaMarkov.hpp

// Unfit: Data fitting and optimization software
//
// Copyright (C) 2012- Dr Martin Buist & Dr Alberto Corrias
// Contacts: martin.buist _at_ nus.edu.sg; alberto _at_ nus.edu.sg
//
// See the 'Contributors' file for a list of those who have contributed
// to this work.
//
// This program 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.
//
// This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
//
#ifndef UNFIT_EXAMPLES_THREENAMARKOV_HPP_
#define UNFIT_EXAMPLES_THREENAMARKOV_HPP_

#include <vector>
#include "GenericCostFunction.hpp"

namespace Unfit
{
namespace Examples
{
class ThreeNaMarkov : public GenericCostFunction
{
 public:
  ThreeNaMarkov(const std::vector<double> &open_prob, double dt)
    : open_prob_ {open_prob},
      dt_ {dt}
  {}

  std::vector<double> operator()(const std::vector<double> &param)
  {
    // Initial conditions
    double O = 0.0;
    double C = 1.0;
    double I = 0.0;
    // Rate constants
    const double kco = param[0];
    const double koc = param[1];
    const double koi = param[2];
    const double kio = param[3];
    // Residual initialization
    auto residuals = open_prob_;
    residuals[0] -= O;

    for (auto i = 1u; i < residuals.size(); ++i) {
      const double deltaC = dt_*(koc*O - kco*C);
      const double deltaI = dt_*(koi*O - kio*I);
      I += deltaI;
      C += deltaC;
      O = 1.0 - C - I;
      // NOTE: equivalent behaviour of "O = 1-C-I" is
      // double deltaO = dt_*(kco*C + kio*I - (koc+koi)*O);
      // O += deltaO;
      residuals[i] -= O;
    }
    return (residuals);
  }
 private:
  const std::vector<double> open_prob_;
  const double dt_;
};

}  // namespace Examples
}  // namespace Unfit

#endif