コード例 #1
0
//' @title Get covariate identifiers
//' 
//' @description
//' \code{getCovariateIds} returns a vector of integer covariate identifiers in an OHDSI Cyclops data object
//' 
//' @param object    An OHDSI Cyclops data object
//' 
// [[Rcpp::export("getCovariateIds")]]
std::vector<int64_t> cyclopsGetCovariateIds(Environment object) {
    using namespace bsccs;
	XPtr<ModelData> data = parseEnvironmentForPtr(object);
	ProfileVector covariates;
	size_t i = 0;
	if (data->getHasOffsetCovariate()) i++;
// 	if (data->getHasInterceptCovariate()) i++;
	for (; i < data->getNumberOfColumns(); ++i) {
		covariates.push_back(data->getColumn(i).getNumericalLabel());
	}
	return covariates;
}
コード例 #2
0
// [[Rcpp::export(".cyclopsFinalizeData")]]
void cyclopsFinalizeData(
        Environment x,
        bool addIntercept, 
        SEXP sexpOffsetCovariate,
        bool offsetAlreadyOnLogScale, 
        bool sortCovariates,
        SEXP sexpCovariatesDense,
        bool magicFlag = false) {
    using namespace bsccs;
    XPtr<ModelData> data = parseEnvironmentForPtr(x);
    
    if (data->getIsFinalized()) {
        ::Rf_error("OHDSI data object is already finalized");
    }
    
    if (addIntercept) {
        if (data->getHasInterceptCovariate()) {
            ::Rf_error("OHDSI data object already has an intercept");
        }
        // TODO add intercept as INTERCEPT_TYPE if magicFlag ==  true
        data->insert(0, DENSE); // add to front, TODO fix if offset
        data->setHasInterceptCovariate(true);
       // CompressedDataColumn& intercept = data->getColumn(0);
        const size_t numRows = data->getNumberOfRows();
        for (size_t i = 0; i < numRows; ++i) {
            data->getColumn(0).add_data(i, static_cast<real>(1.0));
        }
    } 
    
    if (!Rf_isNull(sexpOffsetCovariate)) {
        // TODO handle offset        
        IdType covariate = as<IdType>(sexpOffsetCovariate);
        int index;
        if (covariate == -1) { // TODO  Bad, magic number
            //std::cout << "Trying to convert time to offset" << std::endl;
            //data->push_back(NULL, NULL, offs.begin(), offs.end(), DENSE); // TODO Do not make copy
            //data->push_back(NULL, &(data->getTimeVectorRef()), DENSE);
            data->moveTimeToCovariate(true);
            index = data->getNumberOfColumns() - 1;
        } else {
            index = data->getColumnIndexByName(covariate);         		
 	    	if (index == -1) {
                std::ostringstream stream;
     			stream << "Variable " << covariate << " not found.";
                stop(stream.str().c_str());
     			//error->throwError(stream); 
            }
        }
        data->moveToFront(index);
        data->getColumn(0).add_label(-1); // TODO Generic label for offset?        
        data->setHasOffsetCovariate(true);   
    } 
    
    if (data->getHasOffsetCovariate() && !offsetAlreadyOnLogScale) {
        //stop("Transforming the offset is not yet implemented");        
        data->getColumn(0).transform([](real x) {
            return std::log(x);
        });
    }
    
    if (!Rf_isNull(sexpCovariatesDense)) {
        // TODO handle dense conversion
        ProfileVector covariates = as<ProfileVector>(sexpCovariatesDense);
        for (auto it = covariates.begin(); it != covariates.end(); ++it) {
        	IdType index = data->getColumnIndex(*it);
        	data->getColumn(index).convertColumnToDense(data->getNumberOfRows());      
        }             
    }
                        
    data->setIsFinalized(true);
}                        
コード例 #3
0
//' @title Get total number of covariates
//' 
//' @description
//' \code{getNumberOfCovariates} returns the total number of covariates in an OHDSI Cyclops data object
//' 
//' @param object    An OHDSI Cyclops data object
//'
// [[Rcpp::export("getNumberOfCovariates")]]
int cyclopsGetNumberOfColumns(Environment object) {	
	XPtr<bsccs::ModelData> data = parseEnvironmentForPtr(object);	
	return static_cast<int>(data->getNumberOfColumns());
}