dataobject.h

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// Copyright (C) 2013 - 2019  Metrum Research Group
//
// This file is part of mrgsolve.
//
// mrgsolve 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 2 of the License, or
// (at your option) any later version.
//
// mrgsolve 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 mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
 
#ifndef DATAOBJECT_H
#define DATAOBJECT_H
 
#include <vector>
#include "odeproblem.h"
#include "RcppInclude.h"
 
typedef std::deque<double> uidtype;
 
class dataobject {
  
public:
  dataobject(Rcpp::NumericMatrix _data, 
             Rcpp::CharacterVector _parnames);
  
  dataobject(Rcpp::NumericMatrix _data, 
             Rcpp::CharacterVector _parnames, 
             Rcpp::CharacterVector _initnames);
  
  Rcpp::NumericMatrix Data;
  
  ~dataobject();
  
  unsigned int nrow() const  {return Data.nrow();}
  unsigned int ncol() const {return Data.ncol();}
  unsigned int nid() const {return Uid.size();}
  unsigned int idcol() const {return Idcol;}
  int start(int i) const {return Startrow.at(i);}
  int end(int i) const {return Endrow.at(i);}
  void map_uid();
  double get_uid(int i) const {return Uid.at(i);}
  uidtype return_uid()  {return Uid;}
  void copy_parameters(int this_row,odeproblem *prob);
  void copy_next_parameters(int id_n, bool from_data, int this_row, odeproblem *prob);
  void next_id(int id_n);
  void copy_inits(int this_row,odeproblem *prob);
  void reload_parameters(const Rcpp::NumericVector& param, odeproblem *prob);
  void idata_row();
  unsigned int get_idata_row(const double ID);  
  void locate_tran();
  void get_records(recstack& a, int NID, int neq, 
                   unsigned int& obscount, unsigned int& evcount, bool obsonly,
                   bool debug);
  void get_records_pred(recstack& a, int NID, int neq, unsigned int& obscount, 
                        unsigned int& evcount, bool obsonly,bool debug);
  // Function commented in dataobject.cpp
  // void expand_records(recstack& a, dataobject& idat, int& NID, 
  //                     unsigned int& obscount, unsigned int& evcount, bool debug);
  void check_idcol(dataobject& data);
  double get_value(const int row, const int col) const {return Data(row,col);}
  double get_id_value(const int row) const {return Data(row,Idcol);}
  Rcpp::IntegerVector get_col_n(const Rcpp::CharacterVector& what);
  void carry_out(const recstack& a, 
                 Rcpp::NumericMatrix& ans,
                 dataobject& idat,
                 const Rcpp::IntegerVector& data_carry,
                 const unsigned int data_carry_start,
                 const Rcpp::IntegerVector& idata_carry,
                 const unsigned int idata_carry_start);
  std::vector<unsigned int> col;
  Rcpp::CharacterVector Data_names;
  
  std::deque<double> Uid;  
  std::deque<int> Startrow;  
  std::deque<int> Endrow; 
  int Idcol; 
  std::map<double,int> idmap; 
  
  std::vector<int> par_from;  
  std::vector<int>  par_to;    
  Rcpp::CharacterVector parnames; 
  
  std::vector<int> cmt_from; 
  std::vector<int> cmt_to;  
  Rcpp::CharacterVector cmtnames; 
  
  bool any_copy; 
  bool done_copying; 
  int next_copy_row; 
  int last_copy_row; 
  
};
 
 
#endif