Revision 1935 trunk/src/nh99/xxmcmc.cpp

xxmcmc.cpp (revision 1935)
160 160
    //double total_spread=2500;
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    uostream * pofs_sd = NULL;
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#if defined(USE_LAPLACE)
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    initial_params::set_inactive_random_effects();
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    //int nvar_x=initial_params::nvarcalc();
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    initial_params::set_active_random_effects();
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    int nvar_re=initial_params::nvarcalc();
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#endif
169 166

  
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    int nvar=initial_params::nvarcalc(); // get the number of active parameters
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    //int scov_option=0;
......
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      number_offsets=stddev_params::copy_all_number_offsets();
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    }
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    */
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#if defined(USE_LAPLACE)
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    if (mcmc2_flag==0)
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    {
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      initial_params::set_inactive_random_effects();
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      nvar=initial_params::nvarcalc(); // get the number of active parameters
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    }
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#endif
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    dvector x(1,nvar);
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    dvector scale(1,nvar);
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    dmatrix values;
......
379 374
      // get lower and upper bounds
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      independent_variables y(1,nvar);
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#if defined(USE_LAPLACE)
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      independent_variables parsave(1,nvar_re);
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      initial_params::restore_start_phase();
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#else
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      independent_variables parsave(1,nvar);
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#endif
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      initial_params::restore_start_phase();
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      // read in the mcmc values to date
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      int ii=1;
......
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      ii=1;
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      initial_params::restore_all_values(parsave,ii);
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#if defined(USE_LAPLACE)
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      if (mcmc2_flag==0)
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      {
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        initial_params::set_inactive_random_effects();
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      }
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#endif
459 448

  
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      gradient_structure::set_NO_DERIVATIVES();
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      ofstream ogs("sims");
......
594 583
          {
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            if (psvflag || (mcrestart_flag == -1) )
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            {
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#           if defined(USE_LAPLACE)
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              (*pofs_psave) << nvar_re;
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#           else
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              (*pofs_psave) << nvar;
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#           endif
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            }
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          }
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        }
......
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          }
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        }
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        ii=1;
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#if defined(USE_LAPLACE)
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        if (random_effects_flag)
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        {
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          initial_params::restore_start_phase();
......
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        {
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          initial_params::restore_all_values(parsave,ii);
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        }
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#else
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        initial_params::restore_all_values(parsave,ii);
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#endif
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        initial_params::set_all_simulation_bounds(symbds);
717 698

  
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        // option of generating uniform or normal random variables
......
738 719
              symbds(2), chd,lpinv,-1*(chdinv*bmn1),pprobe,rng);
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          ll=-get_monte_carlo_value(nvar,y);
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#if defined(USE_LAPLACE)
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          if (random_effects_flag)
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          {
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            initial_params::restore_start_phase();
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          }
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#endif
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          //cout << ll << " " << llc << endl;
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          double ldiff=lprob-lpinv;
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          logr= ll - ldiff - llc;
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