~Flim() {
lambda_.free();
ones_.free();
kappa_.free();
estimates_.free();
q_lambda_.free();
singleton_expectation_.free();
empirical_pair_.free();
empirical_singleton_.free();
}
void initializeKappa(int num_documents) {
gsl_vector_float_memcpy(kappa_, empirical_singleton_);
gsl_vector_float_scale(kappa_, num_documents);
gsl_vector_float_add_constant(kappa_, 1.0);
gsl_vector_float_scale(kappa_, 1.0 / (2.0 + num_documents));
for (int ii = 0; ii < kappa_.size(); ++ii) {
singleton_expectation_[ii] = kappa_[ii];
kappa_[ii] = logit(kappa_[ii]);
}
}
// [[Rcpp::export]]
Rcpp::List fitData(Rcpp::DataFrame ds) {
const size_t ncoeffs = NCOEFFS;
const size_t nbreak = NBREAK;
const size_t n = N;
size_t i, j;
Rcpp::DataFrame D(ds); // construct the data.frame object
RcppGSL::vector<double> y = D["y"]; // access columns by name,
RcppGSL::vector<double> x = D["x"]; // assigning to GSL vectors
RcppGSL::vector<double> w = D["w"];
gsl_bspline_workspace *bw;
gsl_vector *B;
gsl_vector *c;
gsl_matrix *X, *cov;
gsl_multifit_linear_workspace *mw;
double chisq, Rsq, dof, tss;
bw = gsl_bspline_alloc(4, nbreak); // allocate a cubic bspline workspace (k = 4)
B = gsl_vector_alloc(ncoeffs);
X = gsl_matrix_alloc(n, ncoeffs);
c = gsl_vector_alloc(ncoeffs);
cov = gsl_matrix_alloc(ncoeffs, ncoeffs);
mw = gsl_multifit_linear_alloc(n, ncoeffs);
gsl_bspline_knots_uniform(0.0, 15.0, bw); // use uniform breakpoints on [0, 15]
for (i = 0; i < n; ++i) { // construct the fit matrix X
double xi = gsl_vector_get(x, i);
gsl_bspline_eval(xi, B, bw); // compute B_j(xi) for all j
for (j = 0; j < ncoeffs; ++j) { // fill in row i of X
double Bj = gsl_vector_get(B, j);
gsl_matrix_set(X, i, j, Bj);
}
}
gsl_multifit_wlinear(X, w, y, c, cov, &chisq, mw); // do the fit
dof = n - ncoeffs;
tss = gsl_stats_wtss(w->data, 1, y->data, 1, y->size);
Rsq = 1.0 - chisq / tss;
Rcpp::NumericVector FX(151), FY(151); // output the smoothed curve
double xi, yi, yerr;
for (xi = 0.0, i=0; xi < 15.0; xi += 0.1, i++) {
gsl_bspline_eval(xi, B, bw);
gsl_multifit_linear_est(B, c, cov, &yi, &yerr);
FX[i] = xi;
FY[i] = yi;
}
Rcpp::List res =
Rcpp::List::create(Rcpp::Named("X")=FX,
Rcpp::Named("Y")=FY,
Rcpp::Named("chisqdof")=Rcpp::wrap(chisq/dof),
Rcpp::Named("rsq")=Rcpp::wrap(Rsq));
gsl_bspline_free(bw);
gsl_vector_free(B);
gsl_matrix_free(X);
gsl_vector_free(c);
gsl_matrix_free(cov);
gsl_multifit_linear_free(mw);
y.free();
x.free();
w.free();
return(res);
}
RcppExport SEXP R_lrgprApply( SEXP expression_, SEXP data_, SEXP pBigMat_, SEXP env_, SEXP terms_, SEXP EigenVectors_, SEXP EigenValues_, SEXP Wtilde_, SEXP rank_, SEXP chromosome_, SEXP location_, SEXP distance_, SEXP dcmp_features_, SEXP scale_, SEXP delta_, SEXP reEstimateDelta_, SEXP nthreads_, SEXP quiet_, SEXP cincl_){
//BEGIN_RCPP
CharacterVector expression( expression_ );
Environment env( env_ );
std::vector<int> terms = as<std::vector<int> >( terms_ );
RcppGSL::matrix<double> eigenVectors = EigenVectors_;
RcppGSL::vector<double> eigenValues = EigenValues_;
RcppGSL::matrix<double> Wtilde = Wtilde_;
int rank = as<int>( rank_ )
; std::vector<string> chromosome = as<std::vector<string> >(chromosome_);
std::vector<double> location = as<std::vector<double> >(location_);
double distance = as<double>( distance_ );
std::vector<int> dcmp_features = as<std::vector<int> >( dcmp_features_ );
bool scale = (bool) Rcpp::as<int>( scale_ );
double delta_global = as<double>( delta_ );
bool reEstimateDelta = Rcpp::as<int>( reEstimateDelta_ );
int nthreads = as<int>( nthreads_ );
bool quiet = Rcpp::as<int>( quiet_ );
std::vector<int> cincl = as<std::vector<int> >( cincl_ );
// Make sure all eigen values are non-negative
for(unsigned int i=0; i<eigenValues->size; i++){
if( gsl_vector_get( eigenValues, i) < 0 ) gsl_vector_set( eigenValues, i, 0);
}
featureBatcher fbatch( data_, pBigMat_, 10000, cincl);
// Get original number of threads
int n_threads_original = omp_get_max_threads();
// Set threads to 1
omp_set_num_threads( nthreads );
// Intel paralellism
#ifdef INTEL
mkl_set_num_threads( 1 );
#endif
// disable nested OpenMP parallelism
omp_set_nested(0);
// Process exression, X_loop and env
Rexpress expr( as<string>( expression ), fbatch.get_N_indivs(), env );
RcppGSL::vector<double> y = expr.get_response();
int n_indivs = y->size;
// Check that sizes of and X_loop match
if( n_indivs != fbatch.get_N_indivs() ){
y.free();
throw invalid_argument("Dimensions of response and design matrix do not match\n");
}
// If # of samples in W and y is the same
bool useProxCon = ( Wtilde->size1 == y->size );
if( useProxCon && scale) gsl_matrix_center_scale(Wtilde);
// X_clean = model.matrix.default( y ~ sex:One + age )
// Replace marker with 1's so that design matrix for marker j can be created by multiplcation
RcppGSL::matrix<double> X_clean = expr.get_model_matrix_clean();
// If trying to access index beyond range
// Exit gracefully
if( terms[which_max(terms)] >= X_clean->size2 ){
y.free();
X_clean.free();
throw range_error("Element in \"terms\" is out of range");
}
gsl_matrix *Xu_clean = gsl_matrix_alloc( eigenVectors->size2, X_clean->size2 );
// Xu_clean = crossprod( decomp$vectors, X_clean)
gsl_blas_dgemm( CblasTrans, CblasNoTrans, 1.0, eigenVectors, X_clean, 0.0, Xu_clean );
// get indeces of columns that depend on X[,j]
vector<int> loopIndex = expr.get_loop_terms();
long batch_size = MAX( 1, fbatch.getBatchSize()/100.0 );
// Fit null model if necessary
if( R_IsNA( delta_global ) && ! reEstimateDelta ){
double log_L, sig_g, sig_e;
RcppGSL::matrix<double> X_null = expr.get_model_matrix_null();
LRGPR *lrgpr = new LRGPR( y, eigenVectors, eigenValues, X_null->size2, useProxCon ? Wtilde->size2 : 0);
// Must update W before X
if( useProxCon ) lrgpr->update_Wtilde( Wtilde );
lrgpr->update_X( X_null );
// Estimate delta
lrgpr->fit_mle( &log_L, &sig_g, &sig_e);
delta_global = sig_e / sig_g;
X_null.free();
delete lrgpr;
}
long tests_completed = 0;
Progress p(0, false);
std::vector<double> pValues( fbatch.get_N_features() );
std::fill(pValues.begin(), pValues.end(), NAN);
// Get map for marker in dcmp_features
// map_local = map[dcmp_features,]
vector<string> chromosome_local = get_values( chromosome, dcmp_features);
vector<double> location_local = get_values( location, dcmp_features);
time_t start_time;
time(&start_time);
gsl_matrix *X_set = NULL;
bool useThisChunk;
for(int i_set=0; i_set<fbatch.get_N_features(); i_set+=fbatch.getBatchSize()){
// Load data from binary matrix (or do noting if NumericMatrix is used)
useThisChunk = fbatch.loadNextChunk();
if( ! useThisChunk ) continue;
#pragma omp parallel
{
// Variables local to each thread
LRGPR *lrgpr = new LRGPR( y, eigenVectors, eigenValues, X_clean->size2, useProxCon ? Wtilde->size2 : 0);
gsl_matrix *X = gsl_matrix_alloc( X_clean->size1, X_clean->size2 );
gsl_matrix *Xu = gsl_matrix_alloc( eigenVectors->size2, X_clean->size2 );
gsl_vector_view col_view, col_view2;
double log_L, sig_g, sig_e;
double delta;
gsl_vector *marker_j = gsl_vector_alloc( y->size );
gsl_matrix *Wtilde_local = NULL;
vector<int> exclude_prev;
// Initialize with meaningless data
exclude_prev.push_back(-10);
#pragma omp for //schedule(static, batch_size)
for(int j=0; j<fbatch.getBatchSize(); j++){
// If element j+i_set is not include include list, than skip
if( ! fbatch.contains_element(j+i_set) ){
continue;
}
#pragma omp critical
tests_completed++;
fbatch.getFeautureInChunk( j, marker_j );
// replace missings values with the mean
gsl_vector_set_missing_mean( marker_j );
// Copy clean version of matrices to active variables
gsl_matrix_memcpy( X, X_clean );
gsl_matrix_memcpy( Xu, Xu_clean );
for(int k=0; k<loopIndex.size(); k++){
// X_design[,loopIndex[k]] = X_design[,loopIndex[k]] * marker_j
col_view = gsl_matrix_column( (gsl_matrix*)(X), loopIndex[k] );
gsl_vector_mul( &col_view.vector, marker_j );
// Xu[,loopIndex[k]] = crossprod( U, X_design[,loopIndex[k]] * marker_j)
col_view2 = gsl_matrix_column( (gsl_matrix*)(Xu), loopIndex[k] );
gsl_blas_dgemv( CblasTrans, 1.0, eigenVectors, &col_view.vector, 0.0, &col_view2.vector );
}
// Proximal contamination
//////////////////////////
// Must update W before X
// If a MAP was specified
if( chromosome.size() > 1 ){
vector<int> idx = get_markers_in_window( (string) chromosome[j+i_set], location[j+i_set], chromosome_local, location_local, distance);
vector<int> exclude = get_values( dcmp_features, idx);
/*cout << j+i_set <<": " << endl;
cout << "idx: " << endl;
print_vector(idx);
cout << "exclude: " << endl;
print_vector(exclude);*/
// If exclude != exclude_prev, Wtilde_local should be updated
if( ! equal(exclude.begin(), exclude.end(), exclude_prev.begin()) ){
if( exclude.size() > 0 ){
// Wtilde_local = X[,exclude]
///////////////////////////////
if( Wtilde_local != NULL ) gsl_matrix_free( Wtilde_local );
Wtilde_local = fbatch.getFeatures( exclude );
gsl_matrix_set_missing_mean_col( Wtilde_local );
if( scale ){
gsl_matrix_center_scale(Wtilde_local);
}
}else{
if( Wtilde_local != NULL ) gsl_matrix_free( Wtilde_local );
Wtilde_local = NULL;
}
// Update W_tilde based on marker window
// if argument is NULL, proximal contamination is not used
///////////////////////////////////
// If a global Wtilde is given
if( useProxCon ){
if( Wtilde_local == NULL ){
lrgpr->update_Wtilde( Wtilde );
}
if( Wtilde_local != NULL ){
gsl_matrix *Wcbind = gsl_matrix_alloc( Wtilde->size1, Wtilde_local->size2 + Wtilde->size2);
gsl_matrix_cbind( Wtilde, Wtilde_local, Wcbind);
lrgpr->update_Wtilde( Wcbind );
gsl_matrix_free(Wcbind);
}
}else{
// this doesn't have to be dont every time
lrgpr->update_Wtilde( Wtilde_local );
}
}
// save exclude for next marker
exclude_prev = exclude;
}else{
if( useProxCon ) lrgpr->update_Wtilde( Wtilde );
}
lrgpr->update_Xu( X, Xu );
if( reEstimateDelta ){
// Estimate delta
lrgpr->fit_mle( &log_L, &sig_g, &sig_e);
delta = sig_e / sig_g;
}else{
// Use pre-specified delta value
lrgpr->fit_fixed_delta( delta_global, &log_L, &sig_g, &sig_e );
delta = delta_global;
}
#pragma omp critical
pValues[j+i_set] = lrgpr->wald_test( terms );
} // END for
delete lrgpr;
gsl_matrix_free( X );
gsl_matrix_free( Xu );
gsl_vector_free( marker_j );
if( Wtilde_local != NULL ) gsl_matrix_free( Wtilde_local );
} // End parallel
if( ! quiet ) Rcpp::Rcout << print_progress( tests_completed, fbatch.get_N_features_included(), 25, start_time);
if( Progress::check_abort() ){
y.free();
X_clean.free();
gsl_matrix_free(Xu_clean);
eigenVectors.free();
eigenValues.free();
Wtilde.free();
return wrap(0);
}
} // End set loop
// Restore original number of threads
omp_set_num_threads( n_threads_original );
if( ! quiet ) Rcpp::Rcout << endl;
y.free();
X_clean.free();
gsl_matrix_free(Xu_clean);
eigenVectors.free();
eigenValues.free();
Wtilde.free();
return( wrap(pValues) );
//END_RCPP
}
RcppExport SEXP R_lrgpr( SEXP Y_, SEXP X_, SEXP eigenVectors_, SEXP eigenValues_, SEXP delta_, SEXP nthreads_, SEXP Wtilde_, SEXP diagnostic_){
//BEGIN_RCPP
RcppGSL::matrix<double> X = X_;
RcppGSL::vector<double> y = Y_;
RcppGSL::matrix<double> eigenVectors = eigenVectors_;
RcppGSL::vector<double> eigenValues = eigenValues_;
RcppGSL::matrix<double> Wtilde = Wtilde_;
bool diagnostic = (bool) Rcpp::as<int>(diagnostic_);
// If # of samples in W and y is the same
bool useProxCon = ( Wtilde->size1 == y->size );
double delta = Rcpp::as<double>( delta_ );
double nthreads = Rcpp::as<double>( nthreads_ );
// Get original number of threads
int n_threads_original = omp_get_max_threads();
if( ! R_IsNA( nthreads ) ){
omp_set_num_threads( nthreads );
// Intel paralellism
#ifdef INTEL
mkl_set_num_threads( nthreads );
#endif
// disable nested OpenMP parallelism
omp_set_nested(0);
}
// Make sure all eigen values are non-negative
for(unsigned int i=0; i<eigenValues->size; i++){
if( gsl_vector_get( eigenValues, i) < 0 ) gsl_vector_set( eigenValues, i, 0);
}
//cout << "Create lrgpr" << endl;
LRGPR *lrgpr = new LRGPR( y, eigenVectors, eigenValues, X->size2, useProxCon ? Wtilde->size2 : 0);
// Must update W before X
if( useProxCon ) lrgpr->update_Wtilde( Wtilde );
//cout << "Scale" << endl;
gsl_matrix_set_missing_mean_col( X );
//cout << "Update X" << endl;
lrgpr->update_X( X );
double log_L, sig_g, sig_e;
if( isnan( delta ) ){
// Estimate delta
lrgpr->fit_mle( &log_L, &sig_g, &sig_e);
delta = sig_e / sig_g;
}else{
// Use pre-specified delta value
lrgpr->fit_fixed_delta( delta, &log_L, &sig_g, &sig_e );
}
double df;
RcppGSL::vector<double> Hii(y->size);
if( diagnostic && ! useProxCon){
gsl_vector_free(Hii);
Hii = lrgpr->get_hat_matrix_diag();
df = gsl_vector_sum_elements( Hii );
}else{
gsl_vector_set_all(Hii, NAN);
if( ! useProxCon ) df = lrgpr->get_effective_df();
else df = NAN;
}
// Restore original number of threads
omp_set_num_threads( n_threads_original );
RcppGSL::vector<double> alpha = gsl_vector_alloc( y->size );
RcppGSL::vector<double> Y_hat = lrgpr->get_fitted_response( alpha );
RcppGSL::matrix<double> Sigma = lrgpr->coeff_covariance();
RcppGSL::vector<double> pValues = lrgpr->wald_test_all();
RcppGSL::vector<double> beta = lrgpr->get_beta();
Rcpp::List res = Rcpp::List::create(Rcpp::Named("coefficients") = beta,
Rcpp::Named("p.values") = pValues,
Rcpp::Named("sigSq_e") = sig_e,
Rcpp::Named("sigSq_a") = sig_g,
Rcpp::Named("delta") = delta,
Rcpp::Named("df") = df,
Rcpp::Named("rank") = eigenValues->size,
Rcpp::Named("logLik") = log_L,
Rcpp::Named("fitted.values")= Y_hat,
Rcpp::Named("alpha") = alpha,
Rcpp::Named("Sigma") = Sigma,
Rcpp::Named("hii") = Hii );
X.free();
y.free();
eigenVectors.free();
eigenValues.free();
beta.free();
Wtilde.free();
delete lrgpr;
Hii.free();
alpha.free();
Y_hat.free();
Sigma.free();
pValues.free();
return res; // return the result list to R
//END_RCPP
}