void QFRDRFCSFitFunctionSimulator::replotFitFunction() {
    JKQTPdatastore* ds=ui->pltFunction->getDatastore();
    QScopedPointer<QFFitFunction> ffunc(getFitFunction(NULL));

    if (!ffunc) return;

    try {
        ui->pltFunction->set_doDrawing(false);
        ui->pltFunction->clearGraphs();
        ds->clear();
        updateTau();
        if (tauN) {


            /////////////////////////////////////////////////////////////////////////////////
            // retrieve fit parameters and errors. run calcParameters to fill in calculated parameters and make sure
            // we are working with a complete set of parameters
            /////////////////////////////////////////////////////////////////////////////////

            double* fullParams=(double*)qfCalloc(ffunc->paramCount(), sizeof(double));
            double* errors=(double*)qfCalloc(ffunc->paramCount(), sizeof(double));
            double Nparticle=0;
            bool hasNParticle=false;
            for (int p=0; p<ffunc->paramCount(); p++) {
                QFFitFunction::ParameterDescription d=ffunc->getDescription(p);
                QString id=d.id;
                if (params.contains(id)) {
                    fullParams[p]=params[id].value;
                    errors[p]=params[id].error;
                } else {
                    fullParams[p]=d.initialValue;
                    /*double value=0;
                    if (overrideFitFunctionPreset(id, value)) d.initialValue=value;*/

                    errors[p]=0;
                }
            }
            ffunc->calcParameter(fullParams, errors);
            used_params.clear();
            for (int p=0; p<ffunc->paramCount(); p++) {
                QFFitFunction::ParameterDescription d=ffunc->getDescription(p);
                QString id=d.id.toLower();
                bool visible=ffunc->isParameterVisible(ffunc->getParameterNum(id), fullParams);
                if (visible) {
                    if (id=="n_particle") {
                        Nparticle=fullParams[p];
                        hasNParticle=true;
                    }
                    if (id=="1n_particle" && !hasNParticle) {
                        Nparticle=1.0/fullParams[p];
                        hasNParticle=true;
                    }
                    used_params[id]=fullParams[p];
                }
            }

            used_params["tau_min"]=ui->edtMinTau->value();
            used_params["tau_max"]=ui->edtMaxTau->value();
            used_params["runs"]=ui->spinRuns->value();
            used_params["noise_enabled"]=ui->chkNoise->isChecked();
            used_params["model_function"]=ffunc->id();

            csv="";

            // evaluate correlation function and determine small-lag amplitude
            double tau0avg=0;
            for (int r=0; r<runs; r++) {
                for (int i=0; i<tauN; i++) {
                    corr[r*tauN+i]=ffunc->evaluate(tau[i], fullParams);
                }
                tau0avg=tau0avg+corr[r*tauN];
            }
            tau0avg=tau0avg/double(runs);
            if (!hasNParticle) Nparticle=1.0/tau0avg;

            // calc noise
            if (ui->chkNoise->isChecked()) {
                MTRand rng;
                if (ui->cmbNoiseModel->currentIndex()==0) {
                    double I=ui->spinAvgCountRate->value()*1000.0;
                    double I2=sqr(I);
                    double NN=Nparticle;
                    if (NN<=0) NN=1.0;
                    for (int r=0; r<runs; r++) {
                        double corr0=corr[r*tauN];
                        for (int i=0; i<tauN; i++) {
                            double corrT=corr[r*tauN+i];
                            double M=ui->spinMeasDuration->value()/tau[i];
                            double m=tau[0]/tau[i];
                            double var=((1.0+sqr(corr0))*(1.0+sqr(corrT))/(1.0-sqr(corr0))+2.0*m*sqr(corrT))/M/NN/NN+(2.0*(1.0+sqr(corrT))/NN/I+(1.0+corrT/NN)/I2)/M;
                            corr[r*tauN+i]=corr[r*tauN+i]+rng.randNorm(0,1)*sqrt(var);
                        }
                    }
                    used_params["noise_model"]=QString("Koppel");
                    used_params["noise_intensity_kHz"]=I;
                    used_params["noise_measurement_duration"]=ui->spinMeasDuration->value();
                } else if (ui->cmbNoiseModel->currentIndex()==1) {
                    for (int r=0; r<runs; r++) {
                        for (int i=0; i<tauN; i++) {
                            corr[r*tauN+i]=corr[r*tauN+i]+rng.randNorm(0, 1)*(ui->spinNoiseLevel->value()/100.0*tau0avg);
                        }
                    }
                    used_params["noise_model"]=QString("gaussian");
                    used_params["noise_level"]=ui->spinNoiseLevel->value();
                } else if (ui->cmbNoiseModel->currentIndex()==2) {
                    for (int r=0; r<runs; r++) {
                        for (int i=0; i<tauN; i++) {
                            corr[r*tauN+i]=corr[r*tauN+i]+(rng.rand()*2.0-1.0)*ui->spinNoiseLevel->value()/100.0*tau0avg;
                        }
                    }
                    used_params["noise_model"]=QString("uniform");
                    used_params["noise_level"]=ui->spinNoiseLevel->value();
                } else if (ui->cmbNoiseModel->currentIndex()==3) {
                    for (int r=0; r<runs; r++) {
                        for (int i=0; i<tauN; i++) {
                            corr[r*tauN+i]=corr[r*tauN+i]+rng.randNorm(0, 1)*(ui->spinNoiseLevel->value()/100.0*corr[r*tauN+i]);
                        }
                    }
                    used_params["noise_model"]=QString("local gaussian");
                    used_params["noise_level"]=ui->spinNoiseLevel->value();
                } else if (ui->cmbNoiseModel->currentIndex()==4) {
                    for (int r=0; r<runs; r++) {
                        for (int i=0; i<tauN; i++) {
                            corr[r*tauN+i]=corr[r*tauN+i]+(rng.rand()*2.0-1.0)*ui->spinNoiseLevel->value()/100.0*corr[r*tauN+i];
                        }
                    }
                    used_params["noise_model"]=QString("local uniform");
                    used_params["noise_level"]=ui->spinNoiseLevel->value();
                }
            }


            for (int i=0; i<tauN; i++) {
                csv=csv+CDoubleToQString(tau[i]);
                for (int r=0; r<runs; r++) {
                    csv=csv+", "+CDoubleToQString(corr[r*tauN+i]);
                }
                csv=csv+"\n";
            }


            size_t c_tau = ds->addCopiedColumn(tau, tauN, "tau");

            for (int r=0; r<runs; r++) {
                size_t c_fit = ds->addCopiedColumn(&(corr[r*tauN]), tauN, QString("function_r%1").arg(r));
                /////////////////////////////////////////////////////////////////////////////////
                // plot fit model and additional function graphs
                /////////////////////////////////////////////////////////////////////////////////
                JKQTPxyLineGraph* g_fit=new JKQTPxyLineGraph(ui->pltFunction->get_plotter());
                g_fit->set_drawLine(true);
                g_fit->set_title(tr("run %1").arg(r));
                g_fit->set_xColumn(c_tau);
                g_fit->set_yColumn(c_fit);
                ui->pltFunction->addGraph(g_fit);
            }
        }

        ui->pltFunction->zoomToFit();
        ui->pltFunction->set_doDrawing(true);
        ui->pltFunction->update_plot();
    } catch(std::exception& E) {
        services->log_error(tr("error during plotting, error message: %1\n").arg(E.what()));
    }

}
Пример #2
0
//extern "C"{
SEXP sampler(
		/*prior params*/
		double *a1, double *a2, /* prior for tau2*/
		double *b1, double *b2, /* prior for sigma2 */
		double *alphaW, double *betaW, /* prior for w */
		double *v0, /* gamma */
		double *varKsi, /*vector length qKsiUpdate!!*/

		/*model dimensions*/
		int *q, /*length of ksi*/
		int *qKsiUpdate, /*length of updated ksi*/
		int *p,   /*length alpha*/
		int *pPen,   /*length penalized alpha/ tau2 / gamma*/
		int *n,   /* no. of  obs.*/
		int *d,   /*vector (length p): group sizes*/

		/*parameter vectors*/
		double *beta,
		double *alpha,
		double *ksi,
		double *tau2,
		double *gamma,
		double *sigma2,
		double *w,

		/* (precomputed) constants */
		double *y,
		double *X,
		double *G,
		double *scale,
		double *offset,

		/*info about updateBlocks*/
		int *blocksAlpha,
		int *indA1Alpha,
		int *indA2Alpha,

		int *blocksKsi,
		int *indA1Ksi,
		int *indA2Ksi,

		/*MCMC parameters*/
		int *pcts,
		int *burnin,
		int *thin,
		int *totalLength,
		int *verbose,
		double *ksiDF,
		int *scaleMode,
		double *modeSwitching,
		int *family,
		double *acceptKsi,
		double *acceptAlpha,

		/*return matrices*/
		double *betaMatR,
		double *alphaMatR,
		double *ksiMatR,
		double *gammaMatR,
		double *probV1MatR,
		double *tau2MatR,
		double *sigma2MatR,
		double *wMatR,
		double *likMatR,
		double *logPostMatR
)
{
	// ############################################### //
	// ######## unwrap/initialize args ############### //
	// ############################################### //
	int pIncluded=0, i=0, j=0, startPen = *p-*pPen, qKsiNoUpdate = *q - *qKsiUpdate,
			save = 0, keep = *burnin,  nrv =1,  info=0,
			nSamp=(*totalLength-*burnin)/(*thin), oneInt = 1, zeroInt = 0;

	double *p1 =Calloc(*pPen, double);

	double infV  = 100000, oneV = 1.0, zeroV = 0.0, minusOneV =-1.0;
	double *one=&oneV, *zero=&zeroV, *minusOne=&minusOneV, *inf=&infV, acceptance=0;
	double invSigma2 = 1 / *sigma2, sqrtInvSigma2 = R_pow(invSigma2, 0.5);
	double  *penAlphaSq, *alphaLong, *varAlpha, *priorMeanAlpha, *modeAlpha, *offsetAlpha;;
	penAlphaSq	= Calloc(*pPen, double);
	for(int i=*p-*pPen; i<*p; i++) penAlphaSq[i- *p + *pPen] = R_pow(alpha[i], 2.0);
	alphaLong = Calloc(*q, double);
	F77_CALL(dgemm)("N","N", q, &oneInt, p, one, G, q, alpha, p, zero, alphaLong, q);
	varAlpha = Calloc(*p, double);
	for(int i=0; i<startPen; i++) varAlpha[i] = *inf; /*unpenalized*/
	for(int i=startPen; i<*p; i++) varAlpha[i] = tau2[i-startPen]*gamma[i-startPen]; /*penalized*/
	priorMeanAlpha	= Calloc(*p, double);
	setToZero(priorMeanAlpha, *p);
	modeAlpha = Calloc(*p, double);
	F77_CALL(dcopy)(p, alpha, &oneInt, modeAlpha, &oneInt);
	offsetAlpha = Calloc(*n, double);
	F77_CALL(dcopy)(n, offset, &oneInt, offsetAlpha, &oneInt);


	double *ksiUpdate, *priorMeanKsi, *modeKsi,  *offsetKsi;
	int safeQKsiUpdate = imax2(1, *qKsiUpdate);
	//ksiUpdate contains the last qKsiUpdate elements in ksi
	ksiUpdate = Calloc(safeQKsiUpdate, double);
	F77_CALL(dcopy)(&safeQKsiUpdate, &ksi[*q-safeQKsiUpdate], &oneInt, ksiUpdate, &oneInt);
	priorMeanKsi = Calloc(safeQKsiUpdate, double);
	setToZero(priorMeanKsi, safeQKsiUpdate);
	for(int i=0; i<*qKsiUpdate; i++) priorMeanKsi[i] = 1.0;
	modeKsi = Calloc(safeQKsiUpdate, double);
	setToZero(modeKsi, safeQKsiUpdate);
	for(int i=0; i<*qKsiUpdate; i++) modeKsi[i] = ksi[i+qKsiNoUpdate];
	// offsetKsi = offset + X_d=1*alpha : use lin.predictor of grps with ksi==1 as offset
	offsetKsi = Calloc(*n, double);
	F77_CALL(dcopy)(n, offset, &oneInt, offsetKsi, &oneInt);
	if(qKsiNoUpdate < *q){
		if(qKsiNoUpdate > 0){
			F77_CALL(dgemm)("N","N", n, &oneInt, &qKsiNoUpdate, one, X, n, alpha, &qKsiNoUpdate, one, offsetKsi, n);
		}
	}

	double	*eta, *resid, rss, *XAlpha, *XKsiUpdate, *etaOffset;
	eta	= Calloc(*n, double);
	F77_CALL(dgemm)("N","N", n, &oneInt, q, one, X, n, beta, q, zero, eta, n);
	resid = Calloc(*n, double);
	rss = 0;
	for(int i=0; i<*n; i++) {
		resid[i] = y[i]-eta[i] - offset[i];
		rss += R_pow(resid[i], 2.0);
	}
	XAlpha = Calloc(*p * (*n), double);
	updateXAlpha(XAlpha, X, G, ksi, q, qKsiUpdate, p, n);
	XKsiUpdate = Calloc( *n * safeQKsiUpdate, double);
	setToZero(XKsiUpdate, *n * safeQKsiUpdate);
	if(qKsiNoUpdate < *q){
		updateXKsi(XKsiUpdate, X, alphaLong, q, &qKsiNoUpdate, n);
	}
	etaOffset	= Calloc(*n, double);
	for(int i=0; i<*n; i++) etaOffset[i] = eta[i]+offset[i];


	// ############################################################ //
	// ######## set up blocks for blockwise updates ############### //
	// ############################################################ //

	XBlockQR *AlphaBlocks = Calloc(*blocksAlpha, XBlockQR);
	XBlockQR *KsiBlocks = Calloc(*blocksKsi, XBlockQR);


	for(int i=0; i < *blocksAlpha; i++){
		(AlphaBlocks[i]).indA1 = indA1Alpha[i];
		(AlphaBlocks[i]).indA2 = indA2Alpha[i];

		(AlphaBlocks[i]).qA = (AlphaBlocks[i]).indA2 - (AlphaBlocks[i]).indA1 + 1;
		(AlphaBlocks[i]).qI = *p - (AlphaBlocks[i]).qA;

		(AlphaBlocks[i]).qraux = Calloc((AlphaBlocks[i]).qA, double);
		setToZero((AlphaBlocks[i]).qraux, (AlphaBlocks[i]).qA);
		(AlphaBlocks[i]).work = Calloc((AlphaBlocks[i]).qA, double);
		setToZero((AlphaBlocks[i]).work, (AlphaBlocks[i]).qA);
		(AlphaBlocks[i]).pivots = Calloc((AlphaBlocks[i]).qA, int);
		for(int j=0; j < (AlphaBlocks[i]).qA; j++) (AlphaBlocks[i]).pivots[j] = 0;

		(AlphaBlocks[i]).coefI = Calloc((AlphaBlocks[i]).qI, double);
		setToZero((AlphaBlocks[i]).coefI, (AlphaBlocks[i]).qI);

		(AlphaBlocks[i]).Xa = Calloc(((AlphaBlocks[i]).qA + *n) * (AlphaBlocks[i]).qA, double);
		setToZero((AlphaBlocks[i]).Xa, ((AlphaBlocks[i]).qA + *n) * (AlphaBlocks[i]).qA);
		(AlphaBlocks[i]).Xi = Calloc(*n * (AlphaBlocks[i]).qI, double);
		setToZero((AlphaBlocks[i]).Xi, *n * (AlphaBlocks[i]).qI );
		(AlphaBlocks[i]).ya = Calloc(((AlphaBlocks[i]).qA + *n), double);
		F77_CALL(dcopy)(n, y, &nrv, (AlphaBlocks[i]).ya, &nrv);
		setToZero((AlphaBlocks[i]).ya + *n, (AlphaBlocks[i]).qA);

		(AlphaBlocks[i]).m = Calloc((AlphaBlocks[i]).qA, double);
			setToZero((AlphaBlocks[i]).m, (AlphaBlocks[i]).qA);
		(AlphaBlocks[i]).err = Calloc((AlphaBlocks[i]).qA, double);
			setToZero((AlphaBlocks[i]).err, (AlphaBlocks[i]).qA);

	}
	initializeBlocksQR(AlphaBlocks, XAlpha, *n, *blocksAlpha, *p, varAlpha, scale);


	if(*qKsiUpdate > 0){
		for(int i=0; i < *blocksKsi; i++){
			(KsiBlocks[i]).indA1 = indA1Ksi[i];
			(KsiBlocks[i]).indA2 = indA2Ksi[i];

			(KsiBlocks[i]).qA = (KsiBlocks[i]).indA2 - (KsiBlocks[i]).indA1 + 1;
			(KsiBlocks[i]).qI = *qKsiUpdate - (KsiBlocks[i]).qA;

			(KsiBlocks[i]).qraux = Calloc((KsiBlocks[i]).qA, double);
			setToZero((KsiBlocks[i]).qraux, (KsiBlocks[i]).qA);
			(KsiBlocks[i]).work = Calloc((KsiBlocks[i]).qA, double);
			setToZero((KsiBlocks[i]).work, (KsiBlocks[i]).qA);
			(KsiBlocks[i]).pivots = Calloc((KsiBlocks[i]).qA, int);
			for(int j=0; j < (KsiBlocks[i]).qA; j++) (KsiBlocks[i]).pivots[j] = 0;

			(KsiBlocks[i]).coefI = Calloc((KsiBlocks[i]).qI, double);
			setToZero((KsiBlocks[i]).coefI, (KsiBlocks[i]).qI);

			(KsiBlocks[i]).Xa = Calloc(((KsiBlocks[i]).qA + *n) * (KsiBlocks[i]).qA, double);
			setToZero((KsiBlocks[i]).Xa, ((KsiBlocks[i]).qA + *n) * (KsiBlocks[i]).qA);
			(KsiBlocks[i]).Xi = Calloc(*n * (KsiBlocks[i]).qI, double);
			setToZero((KsiBlocks[i]).Xi, *n * (KsiBlocks[i]).qI );
			(KsiBlocks[i]).ya = Calloc(((KsiBlocks[i]).qA + *n), double);
			F77_CALL(dcopy)(n, y, &nrv, (KsiBlocks[i]).ya, &nrv);
			setToZero((KsiBlocks[i]).ya + *n, (KsiBlocks[i]).qA);

			(KsiBlocks[i]).m = Calloc((KsiBlocks[i]).qA, double);
			setToZero((KsiBlocks[i]).m, (KsiBlocks[i]).qA);
			(KsiBlocks[i]).err = Calloc((KsiBlocks[i]).qA, double);
			setToZero((KsiBlocks[i]).err, (KsiBlocks[i]).qA);
		}
		initializeBlocksQR(KsiBlocks, XKsiUpdate, *n, *blocksKsi, *qKsiUpdate, varKsi, scale);
	}

	// ############################################### //
	// ########     start sampling     ############### //
	// ############################################### //


#ifdef Win32
	R_FlushConsole();
#endif
	/* sampling */
	GetRNGstate();
	for(i = 0; i < *totalLength; i++)
	{
		debugMsg("\n###########################################\n\n");
		//update alpha
		{
			//update varAlpha
			for(j=startPen; j<*p; j++) varAlpha[j] = tau2[j-startPen] * gamma[j-startPen];
			//update alpha
			updateCoefQR(y, XAlpha, AlphaBlocks,
					*blocksAlpha,
					alpha,
					varAlpha, *p,
					scale,
					*n, nrv, oneInt, info, *minusOne, *zero, *one, 1, priorMeanAlpha,
					*family, modeAlpha, eta, acceptAlpha, offsetAlpha, *modeSwitching, zeroInt);
		}


		//update ksi
		if(qKsiNoUpdate < *q){

			//update alphaLong = G %*% alpha
			F77_CALL(dgemm)("N","N", q, &oneInt, p, one, G, q, alpha, p, zero, alphaLong, q);

			//update design for ksi
			updateXKsi(XKsiUpdate, X, alphaLong, q, &qKsiNoUpdate, n);

			//update offsetKsi
			if(qKsiNoUpdate > 0){
				F77_CALL(dcopy)(n, offset, &oneInt, offsetKsi, &oneInt);
				F77_CALL(dgemm)("N","N", n, &oneInt, &qKsiNoUpdate, one, X, n, alpha, &qKsiNoUpdate, one, offsetKsi, n);
			}

			for(j = 0; j < *qKsiUpdate; j++){
				priorMeanKsi[j] = sign(  1/(1 + exp(-2*ksiUpdate[j]/varKsi[j])) - runif(0,1) );
			}


			if(*ksiDF>0){
				updateVarKsi(ksiUpdate, varKsi, ksiDF, priorMeanKsi, qKsiNoUpdate, *q);
			}


			updateCoefQR(y, XKsiUpdate, KsiBlocks,
					*blocksKsi,
					ksiUpdate, varKsi, *qKsiUpdate,
					scale,
					*n, nrv, oneInt, info, *minusOne, *zero, *one, 1, priorMeanKsi,
					*family, modeKsi, eta, acceptKsi, offsetKsi, *modeSwitching, *scaleMode);
			//write back to ksi
			F77_CALL(dcopy)(qKsiUpdate, ksiUpdate, &oneInt, &ksi[*q-*qKsiUpdate], &oneInt);


			//rescale ksi, alpha & put back in ksiUpdate
			if(*scaleMode > 0){
				rescaleKsiAlpha(ksi, alpha, varKsi, tau2, G, d, *p, *q, qKsiNoUpdate, *pPen, *scaleMode, modeAlpha, modeKsi, *family);
				F77_CALL(dcopy)(qKsiUpdate, &ksi[*q-*qKsiUpdate], &oneInt, ksiUpdate, &oneInt);
			}

			//update XAlpha
			updateXAlpha(XAlpha, X, G, ksi, q, qKsiUpdate, p, n);

			//update alphaLong = G %*% alpha
			F77_CALL(dgemm)("N","N", q, &oneInt, p, one, G, q, alpha, p, zero, alphaLong, q);

		} else {
			F77_CALL(dcopy)(q, alpha, &oneInt, alphaLong, &oneInt);
		}

		for(int i = *p-*pPen; i < *p; i++) penAlphaSq[i - *p + *pPen] = R_pow(alpha[i], 2.0);
		updateTau(penAlphaSq, gamma, tau2, *a1, *a2, *pPen);

		updateP1Gamma(penAlphaSq, tau2, p1, gamma, *v0, *w, *pPen);
		pIncluded = 0;
		for(j=0; j<*p - startPen; j++) pIncluded += (gamma[j] == 1.0);

		*w = rbeta( *alphaW + pIncluded, *betaW + *p - pIncluded );

		// update beta
		for(j = 0; j < *q; j++){
			beta[j] = alphaLong[j]*ksi[j];
		}

		//update eta, eta+offset
		F77_CALL(dgemm)("N", "N", n, &oneInt, q, one, X, n, beta, q, zero, eta, n);
		for(int i=0; i<*n; i++) etaOffset[i] = eta[i] + offset[i];

		//update sigma_eps
		if(*family == 0){
			//resid = y - eta - offset
			F77_CALL(dcopy)(n, y, &nrv, resid, &nrv);  //resid <- y
			F77_CALL(daxpy)(n, minusOne, etaOffset, &nrv, resid, &nrv); //resid <- resid - eta - offset

			//rss = resid'resid
			rss = F77_CALL(ddot)(n, resid, &oneInt, resid, &oneInt);

			//update sigma2
			invSigma2 = rgamma(*n/2 + *b1, 1/(rss/2 + *b2));
			sqrtInvSigma2 = R_pow(invSigma2, 0.5);
			scale[0] = sqrtInvSigma2;
			*sigma2 = 1 / invSigma2;
		}


		if(i >= *burnin){
			/* report progress */
			if(*verbose){
				for(j=0; j<9; j++){
					if(i == pcts[j]){
						Rprintf(".");
						#ifdef Win32
							R_FlushConsole();
						#endif
						break;
					}
				}
			}
			/* save samples*/
			if(i == keep){
				for(j = 0; j < *q; j++){
					(betaMatR)[save + j*nSamp] = beta[j];
					(ksiMatR)[save + j*nSamp] = ksi[j];
				}
				for(j=0; j < *p; j++){
					(alphaMatR)[save + j*nSamp] = alpha[j];
				}
				for(j=0; j < *pPen; j++){
					(tau2MatR)[save + j*nSamp] = tau2[j];
					(gammaMatR)[save + j*nSamp] = gamma[j];
					(probV1MatR)[save + j*nSamp] = p1[j];
				}
				(wMatR)[save] = *w;
				(sigma2MatR)[save] = *sigma2;
				likMatR[save] = logLik(y, etaOffset, *family, scale, *n);
				(logPostMatR)[save] = updateLogPost(y, 	alpha, varAlpha,
						ksi, varKsi, scale, *b1, *b2, gamma, *w, *alphaW, *betaW,
						tau2, *a1, *a2,	*n, *q, *p, *pPen, pIncluded, qKsiNoUpdate, priorMeanKsi, *family, likMatR[save]);
				keep = keep + *thin;
				save ++;
				R_CheckUserInterrupt();
			}
		} else {
			if(*verbose){
				if(i == (*burnin-1)){
					Rprintf("b");
					#ifdef Win32
						R_FlushConsole();
					#endif
				}
			}
		}
	} /* end for i*/

	PutRNGstate();

	if(*verbose) Rprintf(".");
	if(*family > 0) {
		acceptance = 0.0;
		for(j=0; j<*blocksAlpha; j++) acceptance += acceptAlpha[j];
		acceptance = 0.0;
		if(qKsiNoUpdate < *q){
			for(j=0; j<*blocksKsi; j++) acceptance += acceptKsi[j];
		}
	}

	Free(etaOffset); Free(XKsiUpdate); Free(XAlpha);  Free(resid); Free(eta);
	Free(offsetKsi); Free(modeKsi); Free(priorMeanKsi);	Free(ksiUpdate);
	Free(offsetAlpha);
	Free(modeAlpha);
	Free(priorMeanAlpha);
	Free(varAlpha);
	Free(alphaLong);
	Free(penAlphaSq);
	freeXBlockQR(AlphaBlocks, *blocksAlpha);
	if(qKsiNoUpdate < *q) freeXBlockQR(KsiBlocks, *blocksKsi);
	Free(p1);
	return(R_NilValue);
}/* end sampler ()*/