Code is mostly out of date, for up-to-date qfaBayes code see R package QFABayes:

https://r-forge.r-project.org/scm/viewvc.php/pkg/qfaBayes/?root=qfa

C code within the R package is found in the src directory.




#################################################################################

SHM
IHM
JHM

Things To Do:
Makefile build main should depend on data
condor grab data and main from within folder i.e. SHM/data100 
no need for .o files etc. 
makefile to cp main to second location


Data




git clone "****"

git commit -m 'jh'
git add "file"
git rm "file"
git push -u origin master




Set up git
  git config --global user.name "Your Name"
  git config --global user.email j.j.heydari@ncl.ac.uk
      
Next steps:
  mkdir Model-in-C
  cd Model-in-C
  git init
  touch README
  git add README
  git commit -m 'first commit'
  git remote add origin git@github.com:jhncl/Model-in-C.git
  git push -u origin master
      
Existing Git Repo?
  cd existing_git_repo
  git remote add origin git@github.com:jhncl/Model-in-C.git
  git push -u origin master

git pull



spare code 

/*READ IN*/

gsl_matrix *getParticleMatrix(char *filename)
{
    int line_length = 10000000;    
    int nrows, ncols;
       
    FILE* f;  
    char *pch;
    char line[10000000];
    gsl_matrix *particles;
    
    
    f=fopen(filename, "r");
    if(NULL==f)
    {
        fprintf(stderr, "Cannot open file %s\n", filename);
        exit(1);
    }

    nrows = 0, ncols = 0;
    /*Scan once to get the dimensions
        there doesn't seem to be a realloc matrix function
    */

    while(fgets(line, line_length, f) != NULL){
        pch = strtok(line," ");
        while(nrows == 0 && pch != NULL )
        {
            ncols++;
            pch = strtok(NULL," ");
        }
        nrows++;
    }
    
    fclose(f);
        
    /*Create matrix and fill up*/
    particles = gsl_matrix_alloc(nrows, ncols);
    nrows = 0; ncols = 0;
    f=fopen(filename, "r");
      
    while(fgets(line, line_length, f) != NULL){
        pch = strtok(line," ");
        while(pch != NULL )
        {
            gsl_matrix_set(particles, nrows, ncols, atof(pch));
            ncols++;
            pch = strtok(NULL," ");
        }
        ncols = 0;
        nrows++;
    }
    fclose(f);
    
    return(particles);    
}    

double meanParticleMatrix(gsl_matrix* matrix,int col,int start,int end){
	int i;
	double mean=0;
	for (i=start;i<=end;i++){
		mean=mean+gsl_matrix_get(matrix,i,col);
	}
	mean=mean/(end-start+1);
	return(mean);
}

int datadouble(char filename[], char filename2[], double datavec[],int length,struct_data *D)
{
int i;
double P,K,r;
gsl_matrix* matrixA=getParticleMatrix(filename);
gsl_matrix* matrixB=getParticleMatrix(filename2);
i=D->SHIFTmn+2*D->L+3-1;
P=exp(meanParticleMatrix(matrixA,i,1,D->CAPiter));

for (i=0;i<D->SHIFTmn;i++){
K=exp(meanParticleMatrix(matrixA,i,1,D->CAPiter));
r=exp(meanParticleMatrix(matrixA,i+D->SHIFTmn+2*D->L+4-1,1,D->CAPiter));
D->y[i]=(r/log(2*gsl_max(0,K-P)/gsl_max(0,K-2*P)))*(log(K/P)/log(2));
}
i=D->SHIFTmn+2*D->L+3-1;
P=exp(meanParticleMatrix(matrixB,i,1,D->CAPiter));
for (i=0;i<(D->MAXmn-D->SHIFTmn);i++){
K=exp(meanParticleMatrix(matrixB,i,1,D->CAPiter));
r=exp(meanParticleMatrix(matrixB,i+(D->MAXmn-D->SHIFTmn)+2*D->L+4-1,1,D->CAPiter));
D->y[D->SHIFTmn+i]=(r/log(2*gsl_max(0,K-P)/gsl_max(0,K-2*P)))*(log(K/P)/log(2));
}
return 0;
}




	for (i=0;i<1000;i++){
			D_para->alpha_c[1]=MCMC_base_adaptive(
				RNG,D,D_para,D_priors,&D_MH->accept_nu,&D_MH->halpha_c,D_para->alpha_c[1],MCMC_alpha_c,-999,-999,-999);

			D_para->sigma_gamma=MCMC_base_adaptive(
				RNG,D,D_para,D_priors,&D_MH->accept_Z,&D_MH->hsigma_gamma,D_para->sigma_gamma,MCMC_sigma_gamma,-999,-999,-999);
			D_para->upsilon_c[1]=MCMC_base_adaptive(
				RNG,D,D_para,D_priors,&D_MH->accept_up,&D_MH->hupsilon_c,D_para->upsilon_c[1],MCMC_upsilon_c,-999,-999,-999);
			D_para->sigma_upsilon=MCMC_base_adaptive(
				RNG,D,D_para,D_priors,&D_MH->accept_Z,&D_MH->hsigma_upsilon,D_para->sigma_upsilon,MCMC_sigma_upsilon,-999,-999,-999);
			D_para->sigma_nu=MCMC_base_adaptive(RNG,D,D_para,D_priors,&D_MH->accept_Z,&D_MH->hsigma_nu,D_para->sigma_nu,MCMC_sigma_nu,-999,-999,-999);
			D_para->Z_p=gauss_sample(RNG,D,0,D->L,D_para->Z_l,exp(D_para->sigma_Z),D_priors->Z_mu,D_priors->eta_Z_p);
			D_para->sigma_Z=gsl_min(10,MCMC_base(
				RNG,D,D_para,D_priors,&D_MH->accept_Z,&D_MH->hsigma_Z,D_para->sigma_Z,MCMC_sigma_Z,-999,-999,-999));        
			D_para->nu_p=gauss_sample(RNG,D,0,D->L,D_para->nu_l,exp(D_para->sigma_nu),D_priors->nu_mu,D_priors->eta_nu_p);

			for (l=0;l<D->L;l++){
				D_para->delta_l[l]=aug_delta_l(RNG,D,D_para,D_priors,l);
				D_para->gamma_cl[l]=MCMC_base_adaptive(
					RNG,D,D_para,D_priors,&D_MH->accept_Z,&D_MH->hgamma_cl,D_para->gamma_cl[l],MCMC_gamma_cl,-999,l,-999);
				D_para->Z_l[l]=MCMC_base_adaptive(RNG,D,D_para,D_priors,&D_MH->accept_Z,&D_MH->hZ_l,D_para->Z_l[l],MCMC_Z_l,-999,l,-999);
				D_para->nu_l[l]=MCMC_base_adaptive(RNG,D,D_para,D_priors,&D_MH->accept_Z,&D_MH->hnu_l,D_para->nu_l[l],MCMC_nu_l,-999,l,-999);
			}
	}