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Commit 3fedbb09 authored by Ale Abdo's avatar Ale Abdo
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Merge branch 'master' of... 

Merge branch 'master' of git://finn.forked.de/~count0/stuff/workspace/graph-tool into rewiring-merge
parents a76a512a 07be3fdc
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src/graph/graph.cc
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src/graph/graph.hh
View file @ 3fedbb09
......@@ -14,8 +14,7 @@
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#ifndef GRAPH_HH
#define GRAPH_HH
......@@ -33,11 +32,13 @@
namespace graph_tool
{
using namespace std;
using namespace boost;
//==============================================================================
// GraphInterface
// this structure is an interface to the internally kept graph
//==============================================================================
// this class is the main interface to the internally kept graph. This is how
// the external world will manipulate the graph. All the algorithms should be
// registered here. This class will be exported to python in graph_bind.hh
class GraphInterface
{
......@@ -54,52 +55,72 @@ public:
};
// histogram types
typedef std::tr1::unordered_map<double,double> hist_t;
typedef std::tr1::unordered_map<std::pair<double,double>,double, boost::hash<std::pair<double,double> > > hist2d_t;
typedef std::tr1::unordered_map<boost::tuple<double,double,double>,double, boost::hash<boost::tuple<double,double,double> > > hist3d_t;
typedef std::tr1::unordered_map<double,std::pair<double,double> > avg_corr_t;
typedef tr1::unordered_map<double,double> hist_t;
typedef tr1::unordered_map<pair<double,double>,double,
hash<pair<double,double> > > hist2d_t;
typedef tr1::unordered_map<tuple<double,double,double>,double,
hash<tuple<double,double,double> > > hist3d_t;
typedef tr1::unordered_map<double,pair<double,double> > avg_corr_t;
typedef boost::variant<degree_t,std::string> deg_t;
typedef variant<degree_t,string> deg_t;
//graph generation
typedef boost::function<double (size_t j, size_t k)> pjk_t;
typedef boost::function<std::pair<size_t,size_t> (double r1, double r2)> inv_ceil_t;
typedef boost::function<double (size_t jl, size_t kl, size_t j, size_t k)> corr_t;
typedef boost::function<std::pair<size_t,size_t> (double r1, double r2, size_t j, size_t k)> inv_corr_t;
void GenerateCorrelatedConfigurationalModel(size_t N, pjk_t p, pjk_t ceil, inv_ceil_t inv_ceil, double ceil_pjk_bound, corr_t corr, corr_t ceil_corr, inv_corr_t inv_ceil_corr, double ceil_corr_bound, bool undirected_corr, size_t seed, bool verbose);
typedef function<double (size_t j, size_t k)> pjk_t;
typedef function<pair<size_t,size_t> (double r1, double r2)> inv_ceil_t;
typedef function<double (size_t jl, size_t kl, size_t j, size_t k)> corr_t;
typedef function<pair<size_t,size_t>(double r1,
double r2,
size_t j,
size_t k)> inv_corr_t;
void GenerateCorrelatedConfigurationalModel(size_t N, pjk_t p, pjk_t ceil,
inv_ceil_t inv_ceil,
double ceil_pjk_bound,
corr_t corr, corr_t ceil_corr,
inv_corr_t inv_ceil_corr,
double ceil_corr_bound,
bool undirected_corr,
size_t seed, bool verbose);
// basic stats
size_t GetNumberOfVertices() const;
size_t GetNumberOfEdges() const;
hist_t GetVertexHistogram(deg_t degree) const;
hist_t GetEdgeHistogram(std::string property) const;
hist_t GetEdgeHistogram(string property) const;
//correlations
hist2d_t GetCombinedVertexHistogram(deg_t degree1, deg_t degree2) const;
avg_corr_t GetAverageCombinedVertexCorrelation(deg_t degree1, deg_t degree2) const;
hist2d_t GetVertexCorrelationHistogram(deg_t degree1, deg_t degree2, std::string weight) const;
hist3d_t GetEdgeVertexCorrelationHistogram(deg_t deg1, std::string scalar, deg_t deg2) const;
avg_corr_t GetAverageNearestNeighboursCorrelation(deg_t origin_degree, deg_t neighbour_degree, std::string weight) const;
avg_corr_t GetAverageCombinedVertexCorrelation(deg_t degree1,
deg_t degree2)const;
hist2d_t GetVertexCorrelationHistogram(deg_t degree1, deg_t degree2,
string weight) const;
hist3d_t GetEdgeVertexCorrelationHistogram(deg_t deg1, string scalar,
deg_t deg2) const;
avg_corr_t GetAverageNearestNeighboursCorrelation(deg_t origin_degree,
deg_t neighbour_degree,
string weight) const;
// mixing
std::pair<double,double> GetAssortativityCoefficient(deg_t deg) const;
std::pair<double,double> GetScalarAssortativityCoefficient(deg_t deg) const;
pair<double,double> GetAssortativityCoefficient(deg_t deg) const;
pair<double,double> GetScalarAssortativityCoefficient(deg_t deg) const;
//clustering
void SetLocalClusteringToProperty(std::string property);
std::pair<double,double> GetGlobalClustering();
void SetExtendedClusteringToProperty(std::string property_prefix, size_t max_depth);
void SetLocalClusteringToProperty(string property);
pair<double,double> GetGlobalClustering();
void SetExtendedClusteringToProperty(string property_prefix,
size_t max_depth);
// other
void LabelComponents(std::string property);
void LabelParallelEdges(std::string property);
hist_t GetDistanceHistogram(std::string weight) const;
hist_t GetSampledDistanceHistogram(std::string weight, size_t samples, size_t seed) const;
void LabelComponents(string property);
void LabelParallelEdges(string property);
hist_t GetDistanceHistogram(string weight) const;
hist_t GetSampledDistanceHistogram(string weight, size_t samples,
size_t seed) const;
double GetReciprocity() const;
void GetMinimumSpanningTree(std::string weight, std::string property);
void GetLineGraph(std::string out_file, std::string format);
void GetBetweenness(std::string weight, std::string edge_betweenness, std::string vertex_betweenness);
double GetCentralPointDominance(std::string vertex_betweenness);
void GetMinimumSpanningTree(string weight, string property);
void GetLineGraph(string out_file, string format);
void GetBetweenness(string weight, string edge_betweenness,
string vertex_betweenness);
double GetCentralPointDominance(string vertex_betweenness);
// community structure
enum comm_corr_t
......@@ -109,9 +130,13 @@ public:
CORRELATED
};
void GetCommunityStructure(double gamma, comm_corr_t corr, size_t n_iter, double Tmin, double Tmax, size_t Nseeds, size_t seed, bool verbose, std::string history_file, std::string weight, std::string property);
double GetModularity(std::string weight, std::string property);
void GetCommunityNetwork(std::string property, std::string size_property, std::string out_file, std::string format) const;
void GetCommunityStructure(double gamma, comm_corr_t corr, size_t n_iter,
double Tmin, double Tmax, size_t Nseeds,
size_t seed, bool verbose, string history_file,
string weight, string property);
double GetModularity(string weight, string property);
void GetCommunityNetwork(string property, string size_property,
string out_file, string format) const;
// graph random rewiring (shuffling)
enum rewire_strat_t
......@@ -129,121 +154,127 @@ public:
void SetReversed(bool reversed) {_reversed = reversed;}
bool GetReversed() const {return _reversed;}
void SetVertexFilterProperty(std::string property);
void SetVertexFilterRange(std::pair<double,double> allowed_range, std::pair<bool,bool> include, bool invert);
void SetVertexFilterProperty(string property);
void SetVertexFilterRange(pair<double,double> allowed_range,
pair<bool,bool> include, bool invert);
bool IsVertexFilterActive() const;
void SetEdgeFilterProperty(std::string property);
void SetEdgeFilterRange(std::pair<double,double> allowed_range, std::pair<bool,bool> include, bool invert);
void SetEdgeFilterProperty(string property);
void SetEdgeFilterRange(pair<double,double> allowed_range,
pair<bool,bool> include, bool invert);
bool IsEdgeFilterActive() const;
// modification
void RemoveVertexProperty(std::string property);
void RemoveEdgeProperty(std::string property);
void RemoveGraphProperty(std::string property);
void InsertEdgeIndexProperty(std::string property);
void InsertVertexIndexProperty(std::string property);
void EditVertexProperty(std::string property, std::string type, boost::python::object op);
void EditEdgeProperty(std::string property, std::string type, boost::python::object op);
void EditGraphProperty(std::string property, std::string type, boost::python::object op);
void RemoveVertexProperty(string property);
void RemoveEdgeProperty(string property);
void RemoveGraphProperty(string property);
void InsertEdgeIndexProperty(string property);
void InsertVertexIndexProperty(string property);
void EditVertexProperty(string property, string type, python::object op);
void EditEdgeProperty(string property, string type, python::object op);
void EditGraphProperty(string property, string type, python::object op);
void ListProperties() const;
void PurgeVertices();
void PurgeEdges();
// layout
void ComputeGraphLayoutGursoy(std::string prop, std::string weight, std::string topology, size_t iter = 0, size_t seed = 4357);
void ComputeGraphLayoutSpringBlock(std::string prop, std::string weight, std::string type, size_t iter = 0, size_t seed = 4357);
void ComputeGraphLayoutGursoy(string prop, string weight, string topology,
size_t iter = 0, size_t seed = 4357);
void ComputeGraphLayoutSpringBlock(string prop, string weight, string type,
size_t iter = 0, size_t seed = 4357);
// i/o
void WriteToFile(std::string s);
void WriteToFile(std::string s, std::string format);
void ReadFromFile(std::string s);
void ReadFromFile(std::string s, std::string format);
void WriteToFile(string s);
void WriteToFile(string s, string format);
void ReadFromFile(string s);
void ReadFromFile(string s, string format);
// signal handling
void InitSignalHandling();
// the following defines the edges' internal properties
typedef boost::property<boost::edge_index_t, size_t> EdgeProperty;
typedef property<edge_index_t, size_t> EdgeProperty;
// this is the main graph type
typedef boost::adjacency_list <boost::vecS, // edges
boost::vecS, // vertices
boost::bidirectionalS,
boost::no_property,
EdgeProperty > multigraph_t;
typedef adjacency_list <vecS, // edges
vecS, // vertices
bidirectionalS,
no_property,
EdgeProperty> multigraph_t;
typedef graph_traits<multigraph_t>::vertex_descriptor vertex_t;
typedef graph_traits<multigraph_t>::edge_descriptor edge_t;
private:
template <class Action, class ReverseCheck, class DirectedCheck>
friend void check_filter(const GraphInterface &g, Action a, ReverseCheck, DirectedCheck);
template <class Graph, class Action, class ReverseCheck, class DirectedCheck>
friend void check_python_filter(const Graph& g, const GraphInterface &gi, Action a, bool& found, ReverseCheck, DirectedCheck);
friend void check_filter(const GraphInterface &g, Action a,
ReverseCheck, DirectedCheck);
friend class scalarS;
// this is the main graph
multigraph_t _mg;
bool _reversed;
bool _directed;
// vertex index map
typedef boost::property_map<multigraph_t, boost::vertex_index_t>::type vertex_index_map_t;
typedef property_map<multigraph_t,vertex_index_t>::type vertex_index_map_t;
vertex_index_map_t _vertex_index;
// edge index map
typedef boost::property_map<multigraph_t, boost::edge_index_t>::type edge_index_map_t;
typedef property_map<multigraph_t,edge_index_t>::type edge_index_map_t;
edge_index_map_t _edge_index;
// graph properties
boost::dynamic_properties _properties;
dynamic_properties _properties;
// vertex filter
std::string _vertex_filter_property;
typedef boost::variant<boost::vector_property_map<double, vertex_index_map_t>,
HashedDescriptorMap<vertex_index_map_t,double>,
boost::vector_property_map<size_t, vertex_index_map_t>,
HashedDescriptorMap<vertex_index_map_t, size_t>,
vertex_index_map_t,
DynamicPropertyMapWrap<double, boost::graph_traits<multigraph_t>::vertex_descriptor> > vertex_filter_map_t;
string _vertex_filter_property;
typedef variant<vector_property_map<double,vertex_index_map_t>,
HashedDescriptorMap<vertex_index_map_t,double>,
vector_property_map<size_t,vertex_index_map_t>,
HashedDescriptorMap<vertex_index_map_t,size_t>,
vertex_index_map_t,
DynamicPropertyMapWrap<double,vertex_t> >
vertex_filter_map_t;
vertex_filter_map_t _vertex_filter_map;
std::pair<double,double> _vertex_range;
std::pair<bool,bool> _vertex_range_include;
pair<double,double> _vertex_range;
pair<bool,bool> _vertex_range_include;
bool _vertex_range_invert;
// edge filter
std::string _edge_filter_property;
typedef boost::variant<boost::vector_property_map<double, edge_index_map_t>,
HashedDescriptorMap<edge_index_map_t, double>,
boost::vector_property_map<size_t, edge_index_map_t>,
HashedDescriptorMap<edge_index_map_t, size_t>,
edge_index_map_t,
DynamicPropertyMapWrap<double, boost::graph_traits<multigraph_t>::edge_descriptor> > edge_filter_map_t;
string _edge_filter_property;
typedef variant<vector_property_map<double, edge_index_map_t>,
HashedDescriptorMap<edge_index_map_t, double>,
vector_property_map<size_t, edge_index_map_t>,
HashedDescriptorMap<edge_index_map_t, size_t>,
edge_index_map_t,
DynamicPropertyMapWrap<double,edge_t> >
edge_filter_map_t;
edge_filter_map_t _edge_filter_map;
std::pair<double,double> _edge_range;
std::pair<bool,bool> _edge_range_include;
pair<double,double> _edge_range;
pair<bool,bool> _edge_range_include;
bool _edge_range_invert;
};
std::pair<GraphInterface::degree_t,std::string> get_degree_type(GraphInterface::deg_t degree);
pair<GraphInterface::degree_t,string>
get_degree_type(GraphInterface::deg_t degree);
//==============================================================================
// GraphException
//==============================================================================
// GraphException
// This is the main exception which will be thrown the outside world, when
// things go wrong
class GraphException : public std::exception
class GraphException : public exception
{
std::string _error;
string _error;
public:
GraphException(std::string error) {_error = error;}
GraphException(string error) {_error = error;}
virtual ~GraphException() throw () {}
virtual const char * what () const throw () {return _error.c_str();}
};
} //namespace graph_tool
//#include "node_graph_io.hh"
#endif
......
src/graph/graph_adaptor.hh
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src/graph/graph_assortativity.cc
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......@@ -13,8 +13,8 @@
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#include <algorithm>
#include <tr1/unordered_set>
......@@ -34,16 +34,14 @@ using namespace boost;
using namespace boost::lambda;
using namespace graph_tool;
//==============================================================================
// GetAssortativityCoefficient(type)
//==============================================================================
// this will calculate the assortativity coefficient, based on the property
// pointed by 'deg'
template <class DegreeSelector>
struct get_assortativity_coefficient
{
get_assortativity_coefficient(DegreeSelector& deg): _deg(deg) {}
template <class Graph>
void operator()(const Graph& g, double& r, double& r_err) const
{
......@@ -53,7 +51,8 @@ struct get_assortativity_coefficient
SharedMap<tr1::unordered_map<double,int> > sa(a), sb(b);
int i, N = num_vertices(g);
#pragma omp parallel for default(shared) private(i) firstprivate(sa,sb) schedule(dynamic) reduction(+:e_kk, n_edges)
#pragma omp parallel for default(shared) private(i) firstprivate(sa,sb)\
schedule(dynamic) reduction(+:e_kk, n_edges)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
......@@ -77,17 +76,18 @@ struct get_assortativity_coefficient
sb.Gather();
double t1=double(e_kk)/n_edges, t2=0.0;
for (typeof(a.begin()) iter = a.begin(); iter != a.end(); ++iter)
if (b.find(iter->second) != b.end())
t2 += double(iter->second * b[iter->first]);
t2 /= n_edges*n_edges;
r = (t1 - t2)/(1.0 - t2);
// "jackknife" variance
double err = 0.0;
#pragma omp parallel for default(shared) private(i) schedule(dynamic) reduction(+:err)
#pragma omp parallel for default(shared) private(i) schedule(dynamic)\
reduction(+:err)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
......@@ -98,8 +98,9 @@ struct get_assortativity_coefficient
typename graph_traits<Graph>::out_edge_iterator e, e_end;
for (tie(e,e_end) = out_edges(v, g); e != e_end; ++e)
{
double k2 = _deg(target(*e,g),g);
double tl2 = (t2*(n_edges*n_edges) - b[k1] - a[k2])/((n_edges-1)*(n_edges-1));
double k2 = _deg(target(*e,g),g);
double tl2 = (t2*(n_edges*n_edges) - b[k1] - a[k2])/
((n_edges-1)*(n_edges-1));
double tl1 = t1*n_edges;
if (k1 == k2)
tl1 -= 1;
......@@ -110,31 +111,34 @@ struct get_assortativity_coefficient
}
r_err = sqrt(err);
}
DegreeSelector& _deg;
};
struct choose_assortativity_coefficient
{
choose_assortativity_coefficient(const GraphInterface& g, GraphInterface::deg_t deg, double& a, double& a_err)
: _g(g), _a(a), _a_err(a_err)
choose_assortativity_coefficient(const GraphInterface& g,
GraphInterface::deg_t deg,
double& a, double& a_err)
: _g(g), _a(a), _a_err(a_err)
{
tie(_deg, _deg_name) = get_degree_type(deg);
}
template <class DegreeSelector>
void operator()(DegreeSelector)
{
{
if (mpl::at<degree_selector_index, DegreeSelector>::type::value == _deg)
{
DegreeSelector deg(_deg_name, _g, true);
check_filter(_g, bind<void>(get_assortativity_coefficient<DegreeSelector>(deg), _1, var(_a), var(_a_err)),
check_filter(_g, bind<void>(get_assortativity_coefficient
<DegreeSelector>(deg),
_1, var(_a), var(_a_err)),
reverse_check(),directed_check());
}
};
const GraphInterface& _g;
double& _a;
double& _a_err;
......@@ -149,21 +153,22 @@ GraphInterface::GetAssortativityCoefficient(GraphInterface::deg_t deg) const
double a, a_err;
try
{
typedef mpl::vector<in_degreeS, out_degreeS, total_degreeS, scalarS> degrees;
mpl::for_each<degrees>(choose_assortativity_coefficient(*this, deg, a, a_err));
typedef mpl::vector<in_degreeS, out_degreeS, total_degreeS, scalarS>
degrees;
mpl::for_each<degrees>(choose_assortativity_coefficient(*this, deg, a,
a_err));
}
catch (dynamic_get_failure &e)
{
throw GraphException("error getting scalar property: " + string(e.what()));
throw GraphException("error getting scalar property: " +
string(e.what()));
}
return make_pair(a, a_err);
}
//==============================================================================
// GetScalarAssortativityCoefficient(type)
//==============================================================================
// this will calculate the _scalar_ assortativity coefficient, based on the
// scalar property pointed by 'deg'
template <class DegreeSelector>
struct get_scalar_assortativity_coefficient
......@@ -179,7 +184,8 @@ struct get_scalar_assortativity_coefficient
SharedMap<tr1::unordered_map<double,int> > sa(a), sb(b);
int i, N = num_vertices(g);
#pragma omp parallel for default(shared) private(i) firstprivate(sa,sb) schedule(dynamic) reduction(+:e_xy, n_edges)
#pragma omp parallel for default(shared) private(i) firstprivate(sa,sb)\
schedule(dynamic) reduction(+:e_xy, n_edges)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
......@@ -201,11 +207,11 @@ struct get_scalar_assortativity_coefficient
sa.Gather();
sb.Gather();
double t1 = e_xy/n_edges;
double avg_a = GetHistogramMean(a), avg_b = GetHistogramMean(b);
double da = GetHistogramDeviation(a,avg_a), db = GetHistogramDeviation(b,avg_b);
double da = GetHistogramDeviation(a,avg_a), db =
GetHistogramDeviation(b,avg_b);
if (da*db > 0)
r = (t1 - avg_a*avg_b)/(da*db);
else
......@@ -218,9 +224,10 @@ struct get_scalar_assortativity_coefficient
diff_a += (iter->first - avg_a)*iter->second;
for (typeof(b.begin()) iter = b.begin(); iter != b.end(); ++iter)
diff_b += (iter->first - avg_b)*iter->second;
double err = 0.0;
#pragma omp parallel for default(shared) private(i) schedule(dynamic) reduction(+:err)
#pragma omp parallel for default(shared) private(i) schedule(dynamic)\
reduction(+:err)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
......@@ -231,11 +238,14 @@ struct get_scalar_assortativity_coefficient
typename graph_traits<Graph>::out_edge_iterator e, e_end;
for (tie(e,e_end) = out_edges(v, g); e != e_end; ++e)
{
double k2 = _deg(target(*e, g), g);
double k2 = _deg(target(*e, g), g);
double t1l = (e_xy - k1*k2)/(n_edges-1);
double avg_al = (avg_a*n_edges - k1)/(n_edges-1), avg_bl = (avg_b*n_edges - k2)/(n_edges-1);
double dal = da - 2*diff_a*(avg_al-avg_a) + (avg_al-avg_a)*(avg_al-avg_a);
double dbl = db - 2*diff_b*(avg_bl-avg_b) + (avg_bl-avg_b)*(avg_bl-avg_b);
double avg_al = (avg_a*n_edges - k1)/(n_edges-1);
double avg_bl = (avg_b*n_edges - k2)/(n_edges-1);
double dal = da - 2*diff_a*(avg_al-avg_a) +
(avg_al-avg_a)*(avg_al-avg_a);
double dbl = db - 2*diff_b*(avg_bl-avg_b) +
(avg_bl-avg_b)*(avg_bl-avg_b);
double rl;
if (dal*dbl > 0)
rl = (t1l - avg_al*avg_bl)/(dal*dbl);
......@@ -246,31 +256,34 @@ struct get_scalar_assortativity_coefficient
}
r_err = sqrt(err);
}
DegreeSelector& _deg;
};
struct choose_scalar_assortativity_coefficient
{
choose_scalar_assortativity_coefficient(const GraphInterface& g, GraphInterface::deg_t deg, double& a, double& a_err)
: _g(g), _a(a), _a_err(a_err)
choose_scalar_assortativity_coefficient(const GraphInterface& g,
GraphInterface::deg_t deg,
double& a, double& a_err)
: _g(g), _a(a), _a_err(a_err)
{
tie(_deg, _deg_name) = get_degree_type(deg);
}
template <class DegreeSelector>
void operator()(DegreeSelector)
{
{
if (mpl::at<degree_selector_index, DegreeSelector>::type::value == _deg)
{
DegreeSelector deg(_deg_name, _g, true);
check_filter(_g, bind<void>(get_scalar_assortativity_coefficient<DegreeSelector>(deg), _1, var(_a), var(_a_err)),
check_filter(_g, bind<void>(get_scalar_assortativity_coefficient
<DegreeSelector>(deg),
_1, var(_a), var(_a_err)),
reverse_check(),directed_check());
}
};
const GraphInterface& _g;
double& _a;
double& _a_err;
......@@ -280,17 +293,21 @@ struct choose_scalar_assortativity_coefficient
pair<double,double>
GraphInterface::GetScalarAssortativityCoefficient(GraphInterface::deg_t deg) const
GraphInterface::GetScalarAssortativityCoefficient(GraphInterface::deg_t deg)
const
{
double a, a_err;
try
{
typedef mpl::vector<in_degreeS, out_degreeS, total_degreeS, scalarS> degrees;
mpl::for_each<degrees>(choose_scalar_assortativity_coefficient(*this, deg, a, a_err));
typedef mpl::vector<in_degreeS, out_degreeS, total_degreeS, scalarS>