Revision 1108

trunk/src/nh99/xxmcmc.cpp (revision 1108)
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 * $Id$
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 *
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 * Author: David Fournier
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 * Copyright (c) 2008-2012 Regents of the University of California 
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 * Copyright (c) 2008-2012 Regents of the University of California
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 */
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......
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  //int mcmc_wrap_flag=0;
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  //int mcmc_gui_length=10000;
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  int no_sd_mcmc=0;
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  int on2=-1;
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  int nvar1=0;
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  if ( (on2=option_match(ad_comm::argc,ad_comm::argv,"-nosdmcmc"))>-1)
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  {
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    no_sd_mcmc=1;
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  }
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  if (mcmc2_flag==1)
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  {
......
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    nvar1=initial_params::nvarcalc(); // get the number of active parameters
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  }
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  if (stddev_params::num_stddev_params==0) 
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  if (stddev_params::num_stddev_params==0)
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  {
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    cerr << " You must declare at least one object of type sdreport "
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         << endl << " to do the mcmc calculations" << endl;
......
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  }
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  {
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    //ofstream of_bf("testbf");
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    //if (adjm_ptr) set_labels_for_mcmc();
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    ivector number_offsets;
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    dvector lkvector;
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    //double current_bf=0;
......
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    int nvar_x=0;
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#if defined(USE_LAPLACE)
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    initial_params::set_inactive_random_effects();
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    nvar_x=initial_params::nvarcalc(); 
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    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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    int nvar_re=initial_params::nvarcalc();
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#endif
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......
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    int ibfcount=0;
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    double llbest;
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    double lbmax;
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    //int ntmp=0;
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    //if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-mcscov",ntmp))>-1)
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    //{
......
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    int ndvar=stddev_params::num_stddev_calc();
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    int numdvar=stddev_params::num_stddev_number_calc();
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    /*
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    if (adjm_ptr) 
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    if (adjm_ptr)
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    {
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      mcmc_display_matrix.allocate(1,numdvar,1,mcmc_gui_length);
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      number_offsets.allocate(1,numdvar);
......
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    dvector scale(1,nvar);
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    dmatrix values;
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    int have_hist_flag=0;
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    initial_params::xinit(x); 
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    initial_params::xinit(x);
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    dvector pen_vector(1,nvar);
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    {
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      initial_params::reset(dvar_vector(x),pen_vector); 
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      initial_params::reset(dvar_vector(x),pen_vector);
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      //cout << pen_vector << endl << endl;
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    }
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    initial_params::mc_phase=0;
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    initial_params::stddev_scale(scale,x);
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    initial_params::mc_phase=1;
......
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    {
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      diag_option=1;
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      cout << " Setting covariance matrix to diagonal with entries " << dscale
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           << endl;  
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