void CollapsedSampler::update(){//{{{
Sampler::update();
sampleTheta();
updateSums();
if((doLog)&&(save))appendFile();
}//}}}
void MCMCPkPg::sample( PkPgModel& model, PkPgResult& Result )//(SEXP dyn_eval, SEXP rho)
{
cIter = 0;
//int tidx = 0;
//int chain = 0;
// Result.InitializeSummary( model );
int total_iter = nBURN + nTHIN * nSAMPLE;
acceptTheta=zeros<mat>( model.N, total_iter );
for( cIter = 0; cIter < total_iter; cIter++ ){
//std::cout << "iteration: "<< cIter << std::endl;
Rprintf("iteration: %d\n", cIter+1);
//for( chain = 0; chain < NCHAIN; chain++ ){
//Rprintf("Update Omega theta\n");
sampleOtheta( model, Result );
if(flgSNP == 1){
//Rprintf("Update Omega SNP\n");
sampleOsnp( model, Result );
//Rprintf("Update Z\n");
sampleZ( model, Result );
//Rprintf("Update Beta Pg\n");
sampleBetaPg( model, Result );
//Rprintf("Update Rho\n");
sampleRho( model, Result );
}
//Rprintf("Update Beta Pk\n");
sampleBetaPk( model, Result );
// update Z*Rho
// SNPs ---------------------------------------------------------------------
//Rprintf("Update means\n");
Result.update_mth( model );
// PK -----------------------------------------------------------------------
//Rprintf("Sample Sigma\n");
sampleSigma( model, Result );
//Rprintf("Update Fit\n");
update_fit( model, Result );
//Rprintf("Sample Theta\n");
sampleTheta( model, Result ); // make sure Result.mTheta is up to date
//Rprintf("Update Theta Bar\n");
update_theta_bar( model, Result );
//Rprintf("Update Sigma Theta\n");
update_sigma_theta( model, Result );
// update_fit_parallel( model, Result );
//mcmc_Sth();
// RJ -----------------------------------------------------------------------
//
// record
if( ( cIter >= nBURN ) && ( ( cIter - nBURN ) % nTHIN == 0 ) ) {
Result.SaveDraws( model );
}
}
Result.SaveFinal( model );
} // END MCMC_main ---------------------------------------------------------------------
