// version of grouped filter when contributions to ... come from several environment
DataFrame filter_grouped_multiple_env( const GroupedDataFrame& gdf, const List& args, const DataDots& dots){
const DataFrame& data = gdf.data() ;
CharacterVector names = data.names() ;
SymbolSet set ;
for( int i=0; i<names.size(); i++){
set.insert( Rf_install( names[i] ) ) ;
}
int nrows = data.nrows() ;
LogicalVector test(nrows, TRUE);
LogicalVector g_test ;
for( int k=0; k<args.size(); k++){
Call call( (SEXP)args[k] ) ;
GroupedCallProxy call_proxy( call, gdf, dots.envir(k) ) ;
int ngroups = gdf.ngroups() ;
GroupedDataFrame::group_iterator git = gdf.group_begin() ;
for( int i=0; i<ngroups; i++, ++git){
SlicingIndex indices = *git ;
int chunk_size = indices.size() ;
g_test = call_proxy.get( indices );
check_filter_result(g_test, chunk_size ) ;
for( int j=0; j<chunk_size; j++){
test[ indices[j] ] = test[ indices[j] ] & g_test[j] ;
}
}
}
DataFrame res = subset( data, test, names, classes_grouped() ) ;
res.attr( "vars") = data.attr("vars") ;
return res ;
}
DataFrame filter_grouped( const GroupedDataFrame& gdf, List args, Environment env){
// a, b, c -> a & b & c
Language call = and_calls( args ) ;
const DataFrame& data = gdf.data() ;
int nrows = data.nrows() ;
LogicalVector test = no_init(nrows);
LogicalVector g_test ;
GroupedCallProxy call_proxy( call, gdf, env ) ;
int ngroups = gdf.ngroups() ;
GroupedDataFrame::group_iterator git = gdf.group_begin() ;
for( int i=0; i<ngroups; i++, ++git){
SlicingIndex indices = *git ;
g_test = call_proxy.get( indices );
int chunk_size = indices.size() ;
for( int j=0; j<chunk_size; j++){
test[ indices[j] ] = g_test[j] ;
}
}
DataFrame res = subset( data, test, data.names(), classes_grouped() ) ;
res.attr( "vars") = data.attr("vars") ;
return res ;
}
DataFrame filter_grouped_single_env( const GroupedDataFrame& gdf, const List& args, const Environment& env){
const DataFrame& data = gdf.data() ;
CharacterVector names = data.names() ;
SymbolSet set ;
for( int i=0; i<names.size(); i++){
set.insert( Rf_install( names[i] ) ) ;
}
// a, b, c -> a & b & c
Call call( and_calls( args, set ) ) ;
int nrows = data.nrows() ;
LogicalVector test = no_init(nrows);
LogicalVector g_test ;
GroupedCallProxy call_proxy( call, gdf, env ) ;
int ngroups = gdf.ngroups() ;
GroupedDataFrame::group_iterator git = gdf.group_begin() ;
for( int i=0; i<ngroups; i++, ++git){
SlicingIndex indices = *git ;
int chunk_size = indices.size() ;
g_test = call_proxy.get( indices );
check_filter_result(g_test, chunk_size ) ;
for( int j=0; j<chunk_size; j++){
test[ indices[j] ] = g_test[j] ;
}
}
DataFrame res = subset( data, test, names, classes_grouped() ) ;
res.attr( "vars") = data.attr("vars") ;
return res ;
}
// [[Rcpp::export]]
IntegerVector grouped_indices_grouped_df_impl(GroupedDataFrame gdf) {
int n=gdf.nrows();
IntegerVector res = no_init(n);
int ngroups = gdf.ngroups();
GroupedDataFrameIndexIterator it = gdf.group_begin();
for (int i=0; i<ngroups; i++, ++it) {
SlicingIndex index = *it;
int n_index = index.size();
for (int j=0; j<n_index; j++) {
res[ index[j] ] = i + 1;
}
}
return res;
}
// version of grouped filter when contributions to ... come from several environment
DataFrame filter_grouped_multiple_env( const GroupedDataFrame& gdf, const LazyDots& dots){
const DataFrame& data = gdf.data() ;
CharacterVector names = data.names() ;
SymbolSet set ;
for( int i=0; i<names.size(); i++){
set.insert( Rf_install( names[i] ) ) ;
}
int nrows = data.nrows() ;
LogicalVector test(nrows, TRUE);
LogicalVector g_test ;
for( int k=0; k<dots.size(); k++){
Rcpp::checkUserInterrupt() ;
const Lazy& lazy = dots[k] ;
Call call( lazy.expr() ) ;
GroupedCallProxy<GroupedDataFrame> call_proxy( call, gdf, lazy.env() ) ;
int ngroups = gdf.ngroups() ;
GroupedDataFrame::group_iterator git = gdf.group_begin() ;
for( int i=0; i<ngroups; i++, ++git){
SlicingIndex indices = *git ;
int chunk_size = indices.size() ;
g_test = check_filter_logical_result(call_proxy.get( indices ));
if( g_test.size() == 1 ){
if( g_test[0] != TRUE ){
for( int j=0; j<chunk_size; j++){
test[indices[j]] = FALSE ;
}
}
} else {
check_filter_result(g_test, chunk_size ) ;
for( int j=0; j<chunk_size; j++){
if( g_test[j] != TRUE ){
test[ indices[j] ] = FALSE ;
}
}
}
}
}
DataFrame res = subset( data, test, names, classes_grouped<GroupedDataFrame>() ) ;
res.attr( "vars") = data.attr("vars") ;
return res ;
}
DataFrame filter_grouped_single_env( const GroupedDataFrame& gdf, const LazyDots& dots){
typedef GroupedCallProxy<GroupedDataFrame, LazyGroupedSubsets> Proxy ;
Environment env = dots[0].env() ;
const DataFrame& data = gdf.data() ;
CharacterVector names = data.names() ;
SymbolSet set ;
for( int i=0; i<names.size(); i++){
set.insert( Rf_install( names[i] ) ) ;
}
// a, b, c -> a & b & c
Call call( and_calls( dots, set, env ) ) ;
int nrows = data.nrows() ;
LogicalVector test(nrows, TRUE);
LogicalVector g_test ;
Proxy call_proxy( call, gdf, env ) ;
int ngroups = gdf.ngroups() ;
GroupedDataFrame::group_iterator git = gdf.group_begin() ;
for( int i=0; i<ngroups; i++, ++git){
SlicingIndex indices = *git ;
int chunk_size = indices.size() ;
g_test = check_filter_logical_result( call_proxy.get( indices ) ) ;
if( g_test.size() == 1 ){
int val = g_test[0] == TRUE ;
for( int j=0; j<chunk_size; j++){
test[ indices[j] ] = val ;
}
} else {
check_filter_result(g_test, chunk_size ) ;
for( int j=0; j<chunk_size; j++){
if( g_test[j] != TRUE ) test[ indices[j] ] = FALSE ;
}
}
}
DataFrame res = subset( data, test, names, classes_grouped<GroupedDataFrame>() ) ;
res.attr( "vars") = data.attr("vars") ;
return res ;
}
SEXP slice_grouped(GroupedDataFrame gdf, const LazyDots& dots) {
typedef GroupedCallProxy<GroupedDataFrame, LazyGroupedSubsets> Proxy;
const DataFrame& data = gdf.data();
const Lazy& lazy = dots[0];
Environment env = lazy.env();
SymbolVector names = data.names();
// we already checked that we have only one expression
Call call(lazy.expr());
std::vector<int> indx;
indx.reserve(1000);
IntegerVector g_test;
Proxy call_proxy(call, gdf, env);
int ngroups = gdf.ngroups();
GroupedDataFrame::group_iterator git = gdf.group_begin();
for (int i=0; i<ngroups; i++, ++git) {
const SlicingIndex& indices = *git;
int nr = indices.size();
g_test = check_filter_integer_result(call_proxy.get(indices));
CountIndices counter(indices.size(), g_test);
if (counter.is_positive()) {
// positive indexing
int ntest = g_test.size();
for (int j=0; j<ntest; j++) {
if (!(g_test[j] > nr || g_test[j] == NA_INTEGER)) {
indx.push_back(indices[g_test[j]-1]);
}
}
} else if (counter.get_n_negative() != 0) {
// negative indexing
std::set<int> drop;
int n = g_test.size();
for (int j=0; j<n; j++) {
if (g_test[j] != NA_INTEGER)
drop.insert(-g_test[j]);
}
int n_drop = drop.size();
std::set<int>::const_iterator drop_it = drop.begin();
int k = 0, j = 0;
while (drop_it != drop.end()) {
int next_drop = *drop_it - 1;
while (j < next_drop) {
indx.push_back(indices[j++]);
k++;
}
j++;
++drop_it;
}
while (k < nr - n_drop) {
indx.push_back(indices[j++]);
k++;
}
}
}
DataFrame res = subset(data, indx, names, classes_grouped<GroupedDataFrame>());
set_vars(res, get_vars(data));
strip_index(res);
return GroupedDataFrame(res).data();
}
//[[Rcpp::export]]
DataFrame complement_impl(GroupedDataFrame gdf, DataFrame genome) {
genome_map_t chrom_sizes = makeChromSizes(genome) ;
DataFrame df = gdf.data() ;
IntegerVector starts = df["start"] ;
IntegerVector ends = df["end"] ;
CharacterVector chroms = df["chrom"] ;
std::vector<std::string> chroms_out ;
std::vector<int> starts_out ;
std::vector<int> ends_out ;
int ngroups = gdf.ngroups() ;
GroupedDataFrame::group_iterator git = gdf.group_begin() ;
for (int i = 0; i < ngroups; ++i, ++git) {
SlicingIndex indices = *git ;
int ni = indices.size() ;
int start, end ;
int last_end = 1 ;
// get chrom from first index
auto chrom = as<std::string>(chroms[indices[0]]) ;
for (int j = 0; j < ni; ++j) {
start = starts[indices[j]] ;
end = ends[indices[j]] ;
if (j == 0) {
if (start == 1) {
last_end = end ;
continue ;
} else {
chroms_out.push_back(chrom) ;
starts_out.push_back(1) ;
ends_out.push_back(start) ;
}
} else {
chroms_out.push_back(chrom) ;
starts_out.push_back(last_end) ;
ends_out.push_back(start) ;
}
last_end = end;
}
auto chrom_size = chrom_sizes[chrom] ;
if (last_end < chrom_size) {
chroms_out.push_back(chrom) ;
starts_out.push_back(last_end) ;
ends_out.push_back(chrom_size) ;
}
}
return DataFrame::create(_("chrom") = chroms_out,
_("start") = starts_out,
_("end") = ends_out,
_("stringsAsFactors") = false) ;
}