C++ CharacterVector::size方法代码示例

// [[Rcpp::export]]
Rcpp::RawVector magick_image_write( XPtrImage input, Rcpp::CharacterVector format, Rcpp::IntegerVector quality,
                                    Rcpp::IntegerVector depth, Rcpp::CharacterVector density, Rcpp::CharacterVector comment){
  if(!input->size())
    return Rcpp::RawVector(0);
  XPtrImage image = copy(input);
#if MagickLibVersion >= 0x691
  //suppress write warnings see #74 and #116
  image->front().quiet(true);
#endif
  if(format.size())
    for_each ( image->begin(), image->end(), Magick::magickImage(std::string(format[0])));
  if(quality.size())
    for_each ( image->begin(), image->end(), Magick::qualityImage(quality[0]));
  if(depth.size())
    for_each ( image->begin(), image->end(), Magick::depthImage(depth[0]));
  if(density.size()){
    for_each ( image->begin(), image->end(), Magick::resolutionUnitsImage(Magick::PixelsPerInchResolution));
    for_each ( image->begin(), image->end(), Magick::densityImage(Point(density[0])));
  }
  if(comment.size())
    for_each ( image->begin(), image->end(), Magick::commentImage(std::string(comment.at(0))));
  Magick::Blob output;
  writeImages( image->begin(), image->end(),  &output );
  Rcpp::RawVector res(output.length());
  std::memcpy(res.begin(), output.data(), output.length());
  return res;
}

//' @rdname convert
//' @keywords internal manip
// [[Rcpp::export]]
Rcpp::List icd9ShortToPartsCpp(const Rcpp::CharacterVector icd9Short, const Rcpp::String minorEmpty) {

	Rcpp::CharacterVector major(icd9Short.size());
	Rcpp::CharacterVector minor(icd9Short.size());

	for (int i = 0; i < icd9Short.size(); ++i) {
		Rcpp::String thisShort = icd9Short[i];
		if (thisShort == NA_STRING) { // .is_na() is private?
			minor[i] = NA_STRING; // I think set_na() might be an alternative.
			continue;
		}

		std::string s(thisShort.get_cstring()); // TODO maybe better to use as?
		s = strimCpp(s); // in place or rewrite?
		std::string::size_type sz = s.size();

		if (icd9IsASingleE(s.c_str())) { // E code
			switch (sz) {
			case 2:
			case 3:
			case 4:
				major[i] = s.substr(0, sz);
				minor[i] = minorEmpty;
				break;
			case 5:
				major[i] = s.substr(0, 4);
				minor[i] = s.substr(4, 1);
				break;
			default:
				major[i] = NA_STRING;
				minor[i] = NA_STRING;
				continue;
			}
		} else { // not an E code
			switch (sz) {
			case 1:
			case 2:
			case 3:
				major[i] = s.substr(0, sz);
				minor[minorEmpty];
				continue;
			case 4:
			case 5:
				major[i] = s.substr(0, 3);
				minor[i] = s.substr(3, sz - 3);
				continue;
			default:
				major[i] = NA_STRING;
				minor[i] = NA_STRING;
				continue;
			}
		}

	} // for

	return icd9MajMinToParts(icd9AddLeadingZeroesMajor(major), minor);
}

// [[Rcpp::export]]
Rcpp::List CPL_sfc_from_wkt(Rcpp::CharacterVector wkt) {
	std::vector<OGRGeometry *> g(wkt.size());
	OGRGeometryFactory f;
	for (int i = 0; i < wkt.size(); i++) {
		char *wkt_str = wkt(i);
#if GDAL_VERSION_MAJOR <= 2 && GDAL_VERSION_MINOR <= 2
		handle_error(f.createFromWkt(&wkt_str, NULL, &(g[i])));
#else
		handle_error(f.createFromWkt( (const char*) wkt_str, NULL, &(g[i])));
#endif
	}
	return sfc_from_ogr(g, true);
}

std::vector<char *> create_options(Rcpp::CharacterVector lco, bool quiet) {
	if (lco.size() == 0)
		quiet = true; // nothing to report
	if (! quiet)
		Rcpp::Rcout << "options:        "; // #nocov
	std::vector<char *> ret(lco.size() + 1);
	for (int i = 0; i < lco.size(); i++) {
		ret[i] = (char *) (lco[i]);
		if (! quiet)
			Rcpp::Rcout << ret[i] << " "; // #nocov
	}
	ret[lco.size()] = NULL;
	if (! quiet)
		Rcpp::Rcout << std::endl;         // #nocov
	return ret;
}

    DataFrameJoinVisitors::DataFrameJoinVisitors(const Rcpp::DataFrame& left_, const Rcpp::DataFrame& right_, Rcpp::CharacterVector names_left, Rcpp::CharacterVector names_right, bool warn_ ) :
        left(left_), right(right_),
        visitor_names_left(names_left),
        visitor_names_right(names_right),
        nvisitors(names_left.size()),
        visitors(nvisitors),
        warn(warn_)
    {
        std::string name_left, name_right ;

        IntegerVector indices_left  = Language( "match", names_left,  RCPP_GET_NAMES(left)  ).fast_eval() ;
        IntegerVector indices_right = Language( "match", names_right, RCPP_GET_NAMES(right) ).fast_eval() ;

        for( int i=0; i<nvisitors; i++){
            name_left  = names_left[i] ;
            name_right = names_right[i] ;

            if( indices_left[i] == NA_INTEGER ){
              stop( "'%s' column not found in lhs, cannot join" ) ;
            }
            if( indices_right[i] == NA_INTEGER ){
              stop( "'%s' column not found in rhs, cannot join" ) ;
            }

            visitors[i] = join_visitor( left[indices_left[i]-1], right[indices_right[i]-1], name_left, name_right, warn ) ;

        }
    }

SEXP rawSymmetricMatrixToDist(SEXP object)
{
BEGIN_RCPP
	Rcpp::S4 rawSymmetric = object;
	Rcpp::NumericVector levels = Rcpp::as<Rcpp::NumericVector>(rawSymmetric.slot("levels"));
	Rcpp::CharacterVector markers = Rcpp::as<Rcpp::CharacterVector>(rawSymmetric.slot("markers"));
	Rcpp::RawVector data = Rcpp::as<Rcpp::RawVector>(rawSymmetric.slot("data"));
	R_xlen_t size = markers.size(), levelsSize = levels.size();

	Rcpp::NumericVector result(size*(size - 1)/2, 0);
	int counter = 0;
	for(R_xlen_t row = 0; row < size; row++)
	{
		for(R_xlen_t column = row+1; column < size; column++)
		{
			int byte = data(column * (column + (R_xlen_t)1)/(R_xlen_t)2 + row);
			if(byte == 255) result(counter) = std::numeric_limits<double>::quiet_NaN();
			else result(counter) = levels(byte);
			counter++;
		}
	}
	result.attr("Size") = (int)size;
	result.attr("Labels") = markers;
	result.attr("Diag") = false;
	result.attr("Upper") = false;
	result.attr("class") = "dist";
	return result;
END_RCPP
}

SEXP hclustThetaMatrix(SEXP mpcrossRF_, SEXP preClusterResults_)
{
BEGIN_RCPP
	Rcpp::List preClusterResults = preClusterResults_;
	bool noDuplicates;
	R_xlen_t preClusterMarkers = countPreClusterMarkers(preClusterResults_, noDuplicates);
	if(!noDuplicates)
	{
		throw std::runtime_error("Duplicate marker indices in call to hclustThetaMatrix");
	}

	Rcpp::S4 mpcrossRF = mpcrossRF_;
	Rcpp::S4 rf = mpcrossRF.slot("rf");

	Rcpp::S4 theta = rf.slot("theta");
	Rcpp::RawVector data = theta.slot("data");
	Rcpp::NumericVector levels = theta.slot("levels");
	Rcpp::CharacterVector markers = theta.slot("markers");
	if(markers.size() != preClusterMarkers)
	{
		throw std::runtime_error("Number of markers in precluster object was inconsistent with number of markers in mpcrossRF object");
	}
	R_xlen_t resultDimension = preClusterResults.size();
	//Allocate enough storage. This symmetric matrix stores the *LOWER* triangular part, in column-major storage. Excluding the diagonal. 
	Rcpp::NumericVector result(((resultDimension-(R_xlen_t)1)*resultDimension)/(R_xlen_t)2);
	for(R_xlen_t column = 0; column < resultDimension; column++)
	{
		Rcpp::IntegerVector columnMarkers = preClusterResults(column);
		for(R_xlen_t row = column + 1; row < resultDimension; row++)
		{
			Rcpp::IntegerVector rowMarkers = preClusterResults(row);
			double total = 0;
			R_xlen_t counter = 0;
			for(R_xlen_t columnMarkerCounter = 0; columnMarkerCounter < columnMarkers.size(); columnMarkerCounter++)
			{
				R_xlen_t marker1 = columnMarkers[columnMarkerCounter]-(R_xlen_t)1;
				for(R_xlen_t rowMarkerCounter = 0; rowMarkerCounter < rowMarkers.size(); rowMarkerCounter++)
				{
					R_xlen_t marker2 = rowMarkers[rowMarkerCounter]-(R_xlen_t)1;
					R_xlen_t column = std::max(marker1, marker2);
					R_xlen_t row = std::min(marker1, marker2);
					Rbyte thetaDataValue = data((column*(column+(R_xlen_t)1))/(R_xlen_t)2 + row);
					if(thetaDataValue != 0xFF)
					{
						total += levels(thetaDataValue);
						counter++;
					}
				}
			}
			if(counter == 0) total = 0.5;
			else total /= counter;
			result(((resultDimension-(R_xlen_t)1)*resultDimension)/(R_xlen_t)2 - ((resultDimension - column)*(resultDimension-column-(R_xlen_t)1))/(R_xlen_t)2 + row-column-(R_xlen_t)1) = total;
		}
	}
	return result;
END_RCPP
}

SEXP collapsedList(Rcpp::List ll) {
    if (ll.length() == 0) return R_NilValue;
    Rcpp::List::iterator it = ll.begin(); 
    switch(TYPEOF(*it)) {
        case REALSXP: {
            Rcpp::NumericVector v(ll.begin(), ll.end());
            Rcpp::RObject ro = ll[0];
            if (ro.hasAttribute("class")) {
                Rcpp::CharacterVector cv = ro.attr("class");
                if ((cv.size() == 1) && std::string(cv[0]) == "Date") {
                    Rcpp::DateVector dv(v);
                    return dv;
                }
                if ((cv.size() == 2) && std::string(cv[1]) == "POSIXt") {
                    Rcpp::DatetimeVector dtv(v);
                    return dtv;
                }
            }
            return v;
            break;              // not reached ...
        }
        case INTSXP: {
            Rcpp::IntegerVector v(ll.begin(), ll.end());
            return v;
            break;              // not reached ...
        }
        case LGLSXP: {
            Rcpp::LogicalVector v(ll.begin(), ll.end());
            return v;
            break;              // not reached ...
        }
        case STRSXP: {              // minor code smell that this is different :-/
            int n = ll.size();
            Rcpp::CharacterVector v(n);
            for (int i=0; i<n; i++) {
                std::string s = Rcpp::as<std::string>(ll[i]);
                v[i] = s;
            }
            return v;
            break;              // not reached ...
        }
    }
    return ll;
}

// [[Rcpp::export]]
XPtrImage magick_image_readpath(Rcpp::CharacterVector paths, Rcpp::CharacterVector density, Rcpp::IntegerVector depth, bool strip = false){
  XPtrImage image = create();
#if MagickLibVersion >= 0x689
  Magick::ReadOptions opts = Magick::ReadOptions();
#if MagickLibVersion >= 0x690
  opts.quiet(1);
#endif
  if(density.size())
    opts.density(std::string(density.at(0)).c_str());
  if(depth.size())
    opts.depth(depth.at(0));
  for(int i = 0; i < paths.size(); i++)
    Magick::readImages(image.get(), std::string(paths[i]), opts);
#else
  for(int i = 0; i < paths.size(); i++)
    Magick::readImages(image.get(), std::string(paths[i]));
#endif
  if(strip)
    for_each (image->begin(), image->end(), Magick::stripImage());
  return image;
}

// [[Rcpp::export]]
Rcpp::CharacterVector icd9MajMinToShort(const Rcpp::CharacterVector major,
		const Rcpp::CharacterVector minor) {
#ifdef ICD9_DEBUG_TRACE
  Rcpp::Rcout << "icd9MajMinToShort: major.size() = " << major.size()
			<< " and minor.size() = " << minor.size() << "\n";
#endif
	if ((major.size() != 1 && major.size() != minor.size())
			|| (major.size() == 1 && minor.size() == 0)) {
		Rcpp::stop(
				"icd9MajMinToShort, length of majors and minors must be equal, unless majors length is one.");
	}
	if (major.size() == 1) {
#ifdef ICD9_DEBUG_TRACE
	  Rcpp::Rcout << "icd9MajMinToShort: major.size() = 1\n";
#endif
		Rcpp::CharacterVector newmajor(minor.size(), major[0]);
		return icd9MajMinToCode(newmajor, minor, true);
	}
	return icd9MajMinToCode(major, minor, true);
}

SEXP constructDissimilarityMatrix(SEXP object, SEXP clusters_)
{
BEGIN_RCPP
	Rcpp::S4 rawSymmetric = object;
	Rcpp::NumericVector levels = Rcpp::as<Rcpp::NumericVector>(rawSymmetric.slot("levels"));
	Rcpp::CharacterVector markers = Rcpp::as<Rcpp::CharacterVector>(rawSymmetric.slot("markers"));
	Rcpp::RawVector data = Rcpp::as<Rcpp::RawVector>(rawSymmetric.slot("data"));
	int nMarkers = markers.size();
	std::vector<double> levelsCopied = Rcpp::as<std::vector<double> >(levels);
	
	std::vector<int> permutation(nMarkers);
	for(int i = 0; i < nMarkers; i++) permutation[i] = i;
	return constructDissimilarityMatrixInternal(&(data(0)), levelsCopied, nMarkers, clusters_, 0, permutation);
END_RCPP
}

// [[Rcpp::export]]
XPtrImage magick_image_readbin(Rcpp::RawVector x, Rcpp::CharacterVector density, Rcpp::IntegerVector depth, bool strip = false){
  XPtrImage image = create();
#if MagickLibVersion >= 0x689
  Magick::ReadOptions opts = Magick::ReadOptions();
#if MagickLibVersion >= 0x690
  opts.quiet(1);
#endif
  if(density.size())
    opts.density(std::string(density.at(0)).c_str());
  if(depth.size())
    opts.depth(depth.at(0));
  Magick::readImages(image.get(), Magick::Blob(x.begin(), x.length()), opts);
#else
  Magick::readImages(image.get(), Magick::Blob(x.begin(), x.length()));
#endif
  if(strip)
    for_each (image->begin(), image->end(), Magick::stripImage());
  return image;
}

    DataFrameSubsetVisitors::DataFrameSubsetVisitors( const Rcpp::DataFrame& data_, const Rcpp::CharacterVector& names ) :
        data(data_),
        visitors(),
        visitor_names(names),
        nvisitors(visitor_names.size())
    {

        std::string name ;
        int n = names.size() ;
        IntegerVector indices  = Language( "match", names,  RCPP_GET_NAMES(data)  ).fast_eval() ;

        for( int i=0; i<n; i++){
            int pos = indices[i] ;
            if( pos == NA_INTEGER ){
                name = (String)names[i] ;
                stop( "unknown column '%s' ", name ) ;
            }
            visitors.push_back(subset_visitor( data[pos-1] )) ;
        }
    }

    DataFrameJoinVisitors::DataFrameJoinVisitors(const Rcpp::DataFrame& left_, const Rcpp::DataFrame& right_, Rcpp::CharacterVector names_left, Rcpp::CharacterVector names_right, bool warn_ ) :
        left(left_), right(right_),
        visitor_names_left(names_left),
        visitor_names_right(names_right),
        nvisitors(names_left.size()),
        visitors(nvisitors),
        warn(warn_)
    {
        std::string name_left, name_right ;
        for( int i=0; i<nvisitors; i++){
            name_left  = names_left[i] ;
            name_right = names_right[i] ;

            try{
                visitors[i] = join_visitor( left[name_left], right[name_right], name_left, name_right, warn ) ;
            } catch( const std::exception& ex ){
                stop( "cannot join on columns '%s' x '%s': %s ", name_left, name_right, ex.what() ) ;
            } catch( ... ){
                stop( "cannot join on columns '%s' x '%s'", name_left, name_right ) ;
            }
        }
    }

SEXP hclustCombinedMatrix(SEXP mpcrossRF_, SEXP preClusterResults_)
{
BEGIN_RCPP
	bool noDuplicates;
	R_xlen_t preClusterMarkers = countPreClusterMarkers(preClusterResults_, noDuplicates);
	if(!noDuplicates)
	{
		throw std::runtime_error("Duplicate marker indices in call to hclustThetaMatrix");
	}

	Rcpp::List preClusterResults = preClusterResults_;
	Rcpp::S4 mpcrossRF = mpcrossRF_;
	Rcpp::S4 rf = mpcrossRF.slot("rf");

	Rcpp::RObject lodObject = rf.slot("lod");
	if(lodObject.isNULL())
	{
		throw std::runtime_error("Slot [email protected]@lod cannot be NULL if clusterBy is equal to \"combined\"");
	}
	Rcpp::S4 lod = Rcpp::as<Rcpp::S4>(lodObject);
	Rcpp::S4 theta = rf.slot("theta");
	Rcpp::RawVector data = theta.slot("data");
	Rcpp::NumericVector levels = theta.slot("levels");
	Rcpp::CharacterVector markers = theta.slot("markers");
	Rcpp::NumericVector lodData = lod.slot("x");
	if(markers.size() != preClusterMarkers || lodData.size() != (preClusterMarkers*(preClusterMarkers+(R_xlen_t)1))/(R_xlen_t)2)
	{
		throw std::runtime_error("Number of markers in precluster object was inconsistent with number of markers in mpcrossRF object");
	}
	R_xlen_t resultDimension = preClusterResults.size();
	//Work out minimum difference between recombination levels
	double minDifference = 1;
	for(int i = 0; i < levels.size()-1; i++)
	{
		minDifference = std::min(minDifference, levels[i+1] - levels[i]);
	}
	double maxLod = *std::max_element(lodData.begin(), lodData.end());
	double lodMultiplier = minDifference/maxLod;
	//Allocate enough storage. This symmetric matrix stores the *LOWER* triangular part, in column-major storage. Excluding the diagonal. 
	Rcpp::NumericVector result(((resultDimension-(R_xlen_t)1)*resultDimension)/(R_xlen_t)2);
	for(R_xlen_t column = 0; column < resultDimension; column++)
	{
		Rcpp::IntegerVector columnMarkers = preClusterResults(column);
		for(R_xlen_t row = column + (R_xlen_t)1; row < resultDimension; row++)
		{
			Rcpp::IntegerVector rowMarkers = preClusterResults(row);
			double total = 0;
			R_xlen_t counter = 0;
			for(int columnMarkerCounter = 0; columnMarkerCounter < columnMarkers.size(); columnMarkerCounter++)
			{
				R_xlen_t marker1 = columnMarkers[columnMarkerCounter]-(R_xlen_t)1;
				for(int rowMarkerCounter = 0; rowMarkerCounter < rowMarkers.size(); rowMarkerCounter++)
				{
					R_xlen_t marker2 = rowMarkers[rowMarkerCounter]-(R_xlen_t)1;
					R_xlen_t column = std::max(marker1, marker2);
					R_xlen_t row = std::min(marker1, marker2);
					Rbyte thetaDataValue = data((column*(column+(R_xlen_t)1))/(R_xlen_t)2 + row);
					double currentLodDataValue = lodData((column*(column+(R_xlen_t)1))/(R_xlen_t)2 + row);
					if(thetaDataValue != 0xFF && currentLodDataValue != NA_REAL && currentLodDataValue == currentLodDataValue)
					{
						total += levels(thetaDataValue) + (maxLod - currentLodDataValue) *lodMultiplier;
						counter++;
					}
				}
			}
			if(counter == 0) total = 0.5 + minDifference;
			else total /= counter;
			result(((resultDimension-1)*resultDimension)/(R_xlen_t)2 - ((resultDimension - column)*(resultDimension-column-(R_xlen_t)1))/(R_xlen_t)2 + row-column-(R_xlen_t)1) = total;
		}
	}
	return result;
END_RCPP
}