//' @export
// [[Rcpp::export]]
arma::vec th(Rcpp::StringVector strata_rsid, Rcpp::StringVector rsid, Rcpp::NumericVector r2){
// Inputs:
//
// strata_rsid is the overall index of rsid returned from stratify()
// rsid is the rsid column from LdList
// r2 is the r2 column from LdList
// Create the output vector of th numbers
arma::vec th(strata_rsid.size(), fill::zeros);
// Find the indices of where the rsid are in strata_rsid
for(int i = 0; i < rsid.size(); i++){
// Pull out each of the RSIDs successively
// std::string id = rsid(i);
// Find the index in strata_rsid where the RSID string is
// and fill it in with the r2 at the given id.
// th( arma::find( strata_rsid == rsid(i) ) ) = r2(i);
}
// Create duplicate vector to fill in discretized values
arma::vec out = th;
out.elem( find( th >= 0.2 ) ).fill(0.2);
out.elem( find( th >= 0.4 ) ).fill(0.4);
out.elem( find( th >= 0.6 ) ).fill(0.6);
out.elem( find( th >= 0.8 ) ).fill(0.8);
out.elem( find( th >= 0.9 ) ).fill(0.9);
out.elem( find( th >= 1 ) ).fill(1);
return out;
}
Rcpp::StringMatrix DataFrame_to_StringMatrix( Rcpp::DataFrame df ){
Rcpp::StringVector sv = df(0);
Rcpp::StringMatrix sm(sv.size(), df.size());
sm.attr("col.names") = df.attr("col.names");
sm.attr("row.names") = df.attr("row.names");
for(int i=0; i < df.size(); i++){
sv = df(i);
for(int j=0; j < sv.size(); j++){
sm(j, i) = sv(j);
}
}
return sm;
}
void TabEditor::displayEditor(RCore *rExe,std::string name, DataEditor *dataEditor, VariableEditor *variableEditor){
qDebug("Display Editor");
rExe->diplayData(name);
//----Update
dataEditor->setVarTypes(rExe->getVarTypes());
QStringList varNames;
Rcpp::StringVector sv = rExe->getColNames();
for(int i = 0; i < sv.size();i++){
varNames.push_back(QString(sv[i]));
}
dataEditor->setVarNames(varNames);
dataEditor->loadData(rExe->getDataFrame(),rExe->getColNames());
//---
variableEditor->loadVariable(rExe,rExe->getColNames());
addTab(dataEditor,"Data");
addTab(variableEditor, "Variable");
setTabPosition(West);
//Update 30 Juni
connect(this, SIGNAL(currentChanged(int)), variableEditor, SLOT(checkWidgetVisibility()));
}
// [[Rcpp::export]]
Rcpp::NumericMatrix infoContentMethod_cpp(
Rcpp::StringVector& id1_,
Rcpp::StringVector& id2_,
Rcpp::List& anc_,
Rcpp::NumericVector& ic_,
const std::string& method_,
const std::string& ont_
) {
go_dist_func_t* go_dist;
// Resnik does not consider how distant the terms are from their common ancestor.
// Lin and Jiang take that distance into account.
if (method_ == "Resnik") {
go_dist = &go_dist_Resnik;
}
else if (method_ == "Lin") {
go_dist = &go_dist_Lin;
}
else if (method_ == "Jiang") {
go_dist = &go_dist_Jiang;
}
else if (method_ == "Rel") {
go_dist = &go_dist_Rel;
}
else {
throw std::runtime_error( "Unknown GO distance method" );
}
typedef std::string term_id_t;
typedef std::set<term_id_t> term_set_t;
// calculate the maximum IC and build the map of normalized IC
typedef std::map<term_id_t, double> ic_map_t;
ic_map_t normIcMap;
// more specific term, larger IC value.
// Normalized, all divide the most informative IC.
// all IC values range from 0(root node) to 1(most specific node)
double mic = NA_REAL;
{
Rcpp::StringVector icNames( ic_.names() );
for (std::size_t i=0; i < ic_.size(); i++ ) {
const double cic = ic_[i];
if ( Rcpp::NumericVector::is_na( cic ) || cic == R_PosInf ) continue;
if ( Rcpp::NumericVector::is_na( mic ) || mic < cic ) mic = cic;
}
LOG_DEBUG( "mic=" << mic );
for (std::size_t i=0; i < ic_.size(); i++ ) {
const double cic = ic_[i];
if ( Rcpp::NumericVector::is_na( cic ) || cic == R_PosInf ) continue;
normIcMap.insert( std::make_pair( (std::string) icNames[i], cic / mic ) );
}
}
// set root node IC to 0
if(ont_ == "DO") {
normIcMap["DOID:4"] = 0;
} else {
normIcMap["all"] = 0;
}
// convert anc_ into map of sets
typedef std::map<term_id_t, term_set_t> anc_map_t;
anc_map_t ancMap;
{
Rcpp::StringVector goTerms( anc_.names() );
for (std::size_t i=0; i < anc_.size(); i++ ) {
const std::vector<std::string> ancVec = Rcpp::as<std::vector<std::string> >( anc_[i] );
term_set_t ancestors( ancVec.begin(), ancVec.end() );
// term itself is also considered an ancestor
ancestors.insert( (std::string)goTerms[i] );
ancMap.insert( std::make_pair( (std::string) goTerms[i], ancestors ) );
}
}
Rcpp::NumericMatrix res( id1_.size(), id2_.size() );
res.attr("dimnames") = Rcpp::Rcpp_list2( id1_, id2_ );
for ( std::size_t i = 0; i < id1_.size(); i++ ) {
const std::string id1_term = (std::string)id1_[i];
const ic_map_t::const_iterator iIcIt = normIcMap.find( id1_term );
if ( iIcIt != normIcMap.end() && iIcIt->second != 0 ) {
const double iIc = iIcIt->second;
LOG_DEBUG( "ic[" << id1_term << "]=" << iIc );
const anc_map_t::const_iterator iAncsIt = ancMap.find( id1_term );
for ( std::size_t j = 0; j < id2_.size(); j++ ) {
const std::string id2_term = (std::string)id2_[j];
const ic_map_t::const_iterator jIcIt = normIcMap.find( id2_term );
if ( jIcIt != normIcMap.end() && jIcIt->second != 0 ) {
const anc_map_t::const_iterator jAncsIt = ancMap.find( id2_term );
// find common ancestors
term_set_t commonAncs;
if ( iAncsIt != ancMap.end() && jAncsIt != ancMap.end() ) {
std::set_intersection( iAncsIt->second.begin(), iAncsIt->second.end(),
jAncsIt->second.begin(), jAncsIt->second.end(),
std::inserter( commonAncs, commonAncs.end() ) );
}
LOG_DEBUG( "n(commonAncs(" << id1_term << "," << id2_term << "))=" << commonAncs.size() );
// Information Content of the most informative common ancestor (MICA)
double mica = 0;
for ( term_set_t::const_iterator termIt = commonAncs.begin(); termIt != commonAncs.end(); ++termIt ) {
ic_map_t::const_iterator ancIcIt = normIcMap.find( *termIt );
if ( ancIcIt != normIcMap.end() && mica < ancIcIt->second ) mica = ancIcIt->second;
}
LOG_DEBUG( "mica(" << id1_term << "," << id2_term << ")=" << mica );
res(i,j) = go_dist( mica, iIc, jIcIt->second, mic );
} else {
res(i,j) = NA_REAL;
}
}
} else {
for ( std::size_t j = 0; j < id2_.size(); j++ ) {
res(i,j) = NA_REAL;
}
}
}
return ( res );
}
// [[Rcpp::export]]
void write_vcf_body_gz( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) {
// http://stackoverflow.com/a/5649224
// fix DataFrame
Rcpp::StringVector chrom = fix["CHROM"];
Rcpp::StringVector pos = fix["POS"];
Rcpp::StringVector id = fix["ID"];
Rcpp::StringVector ref = fix["REF"];
Rcpp::StringVector alt = fix["ALT"];
Rcpp::StringVector qual = fix["QUAL"];
Rcpp::StringVector filter = fix["FILTER"];
Rcpp::StringVector info = fix["INFO"];
// gt DataFrame
Rcpp::StringMatrix gt_cm = DataFrame_to_StringMatrix(gt);
Rcpp::StringVector column_names(gt.size());
column_names = gt.attr("names");
int i = 0;
int j = 0;
gzFile *fi = (gzFile *)gzopen(filename.c_str(),"ab");
// gzFile *fi = (gzFile *)gzopen(filename.c_str(),"abw");
for(i=0; i<chrom.size(); i++){
Rcpp::checkUserInterrupt();
if(mask == 1 && filter(i) != "PASS" ){
// Don't print variant.
} else {
std::string tmpstring;
tmpstring = chrom(i);
tmpstring = tmpstring + "\t" + pos(i) + "\t";
if(id(i) == NA_STRING){
tmpstring = tmpstring + ".";
} else {
tmpstring = tmpstring + id(i);
}
tmpstring = tmpstring + "\t" + ref(i) + "\t" + alt(i) + "\t";
if(qual(i) == NA_STRING){
tmpstring = tmpstring + "." + "\t";
} else {
tmpstring = tmpstring + qual(i) + "\t";
}
if(filter(i) == NA_STRING){
tmpstring = tmpstring + "." + "\t";
} else {
tmpstring = tmpstring + filter(i) + "\t";
}
tmpstring = tmpstring + info(i);
// gt portion
for(j=0; j<column_names.size(); j++){
if(gt_cm(i, j) == NA_STRING){
tmpstring = tmpstring + "\t" + "./.";
} else {
tmpstring = tmpstring + "\t" + gt_cm(i, j);
}
}
// gzwrite(fi,"my decompressed data",strlen("my decompressed data"));
// gzwrite(fi,"\n",strlen("\n"));
// std::string tmpstring = "test string\n";
gzwrite(fi, (char *)tmpstring.c_str(), tmpstring.size());
gzwrite(fi,"\n",strlen("\n"));
}
}
gzclose(fi);
return;
}
// [[Rcpp::export]]
void write_vcf_body( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) {
//int write_vcf_body( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) {
// fix DataFrame
Rcpp::StringVector chrom = fix["CHROM"];
Rcpp::StringVector pos = fix["POS"];
Rcpp::StringVector id = fix["ID"];
Rcpp::StringVector ref = fix["REF"];
Rcpp::StringVector alt = fix["ALT"];
Rcpp::StringVector qual = fix["QUAL"];
Rcpp::StringVector filter = fix["FILTER"];
Rcpp::StringVector info = fix["INFO"];
// gt DataFrame
Rcpp::StringMatrix gt_cm = DataFrame_to_StringMatrix(gt);
Rcpp::StringVector column_names(gt.size());
column_names = gt.attr("names");
// column_names = gt_cm.attr("col.names");
// delete gt;
int i = 0;
int j = 0;
// Uncompressed.
std::ofstream myfile;
myfile.open (filename.c_str(), std::ios::out | std::ios::app | std::ios::binary);
// gzFile *fi = (gzFile *)gzopen("file.gz","wb");
for(i=0; i<chrom.size(); i++){
Rcpp::checkUserInterrupt();
if(mask == 1 && filter(i) == "PASS" ){
// Don't print variant.
} else {
myfile << chrom(i);
myfile << "\t";
myfile << pos(i);
myfile << "\t";
if(id(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << id(i);
myfile << "\t";
}
myfile << ref(i);
myfile << "\t";
myfile << alt(i);
myfile << "\t";
if(qual(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << qual(i);
myfile << "\t";
}
if(filter(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << filter(i);
myfile << "\t";
}
if(info(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << info(i);
}
// gt region.
myfile << "\t";
myfile << gt_cm(i, 0);
for(j=1; j<column_names.size(); j++){
myfile << "\t";
myfile << gt_cm(i, j);
}
myfile << "\n";
}
}
myfile.close();
return;
}
//' rcpp_lines_as_network
//'
//' Return OSM data in Simple Features format
//'
//' @param sf_lines An sf collection of LINESTRING objects
//' @param pr Rcpp::DataFrame containing the weighting profile
//'
//' @return Rcpp::List objects of OSM data
//'
//' @noRd
// [[Rcpp::export]]
Rcpp::List rcpp_lines_as_network (const Rcpp::List &sf_lines,
Rcpp::DataFrame pr)
{
std::map <std::string, float> profile;
Rcpp::StringVector hw = pr [1];
Rcpp::NumericVector val = pr [2];
for (int i = 0; i != hw.size (); i ++)
profile.insert (std::make_pair (std::string (hw [i]), val [i]));
Rcpp::CharacterVector nms = sf_lines.attr ("names");
if (nms [nms.size () - 1] != "geometry")
throw std::runtime_error ("sf_lines have no geometry component");
if (nms [0] != "osm_id")
throw std::runtime_error ("sf_lines have no osm_id component");
int one_way_index = -1;
int one_way_bicycle_index = -1;
int highway_index = -1;
for (int i = 0; i < nms.size (); i++)
{
if (nms [i] == "oneway")
one_way_index = i;
if (nms [i] == "oneway.bicycle")
one_way_bicycle_index = i;
if (nms [i] == "highway")
highway_index = i;
}
Rcpp::CharacterVector ow = NULL;
Rcpp::CharacterVector owb = NULL;
Rcpp::CharacterVector highway = NULL;
if (one_way_index >= 0)
ow = sf_lines [one_way_index];
if (one_way_bicycle_index >= 0)
owb = sf_lines [one_way_bicycle_index];
if (highway_index >= 0)
highway = sf_lines [highway_index];
if (ow.size () > 0)
{
if (ow.size () == owb.size ())
{
for (unsigned i = 0; i != ow.size (); ++ i)
if (ow [i] == "NA" && owb [i] != "NA")
ow [i] = owb [i];
} else if (owb.size () > ow.size ())
ow = owb;
}
Rcpp::List geoms = sf_lines [nms.size () - 1];
std::vector<bool> isOneWay (geoms.length ());
std::fill (isOneWay.begin (), isOneWay.end (), false);
// Get dimension of matrix
size_t nrows = 0;
int ngeoms = 0;
for (auto g = geoms.begin (); g != geoms.end (); ++g)
{
// Rcpp uses an internal proxy iterator here, NOT a direct copy
Rcpp::NumericMatrix gi = (*g);
int rows = gi.nrow () - 1;
nrows += rows;
if (ngeoms < ow.size ())
{
if (!(ow [ngeoms] == "yes" || ow [ngeoms] == "-1"))
{
nrows += rows;
isOneWay [ngeoms] = true;
}
}
ngeoms ++;
}
Rcpp::NumericMatrix nmat = Rcpp::NumericMatrix (Rcpp::Dimension (nrows, 6));
Rcpp::CharacterMatrix idmat = Rcpp::CharacterMatrix (Rcpp::Dimension (nrows,
3));
nrows = 0;
ngeoms = 0;
int fake_id = 0;
for (auto g = geoms.begin (); g != geoms.end (); ++ g)
{
Rcpp::NumericMatrix gi = (*g);
std::string hway = std::string (highway [ngeoms]);
float hw_factor = profile [hway];
if (hw_factor == 0.0) hw_factor = 1e-5;
hw_factor = 1.0 / hw_factor;
Rcpp::List ginames = gi.attr ("dimnames");
Rcpp::CharacterVector rnms;
if (ginames.length () > 0)
rnms = ginames [0];
else
{
rnms = Rcpp::CharacterVector (gi.nrow ());
for (int i = 0; i < gi.nrow (); i ++)
rnms [i] = fake_id ++;
}
if (rnms.size () != gi.nrow ())
throw std::runtime_error ("geom size differs from rownames");
for (int i = 1; i < gi.nrow (); i ++)
{
float d = haversine (gi (i-1, 0), gi (i-1, 1), gi (i, 0),
gi (i, 1));
nmat (nrows, 0) = gi (i-1, 0);
nmat (nrows, 1) = gi (i-1, 1);
nmat (nrows, 2) = gi (i, 0);
nmat (nrows, 3) = gi (i, 1);
nmat (nrows, 4) = d;
nmat (nrows, 5) = d * hw_factor;
idmat (nrows, 0) = rnms (i-1);
idmat (nrows, 1) = rnms (i);
idmat (nrows, 2) = hway;
nrows ++;
if (isOneWay [ngeoms])
{
nmat (nrows, 0) = gi (i, 0);
nmat (nrows, 1) = gi (i, 1);
nmat (nrows, 2) = gi (i-1, 0);
nmat (nrows, 3) = gi (i-1, 1);
nmat (nrows, 4) = d;
nmat (nrows, 5) = d * hw_factor;
idmat (nrows, 0) = rnms (i);
idmat (nrows, 1) = rnms (i-1);
idmat (nrows, 2) = hway;
nrows ++;
}
}
ngeoms ++;
}
Rcpp::List res (2);
res [0] = nmat;
res [1] = idmat;
return res;
}