graph_tool.correlations - Correlations

Summary

assortativity

Obtain the assortativity coefficient for the given graph.

scalar_assortativity

Obtain the scalar assortativity coefficient for the given graph.

corr_hist

Obtain the correlation histogram for the given graph.

combined_corr_hist

Obtain the single-vertex combined correlation histogram for the given graph.

avg_neighbor_corr

Obtain the average neighbor-neighbor correlation for the given graph.

avg_combined_corr

Obtain the single-vertex combined correlation histogram for the given graph.

Contents

graph_tool.correlations.assortativity(g, deg, eweight=None)[source]

Obtain the assortativity coefficient for the given graph.

Parameters
gGraph

Graph to be used.

degstring or VertexPropertyMap

Degree type (“in”, “out” or “total”) or vertex property map, which specifies the vertex types.

eweightEdgePropertyMap (optional, default: None)

If given, this will specify the edge weights, otherwise a constant value of one will be used.

Returns
assortativity coefficienttuple of two floats

The assortativity coefficient, and its variance.

See also

assortativity

assortativity coefficient

scalar_assortativity

scalar assortativity coefficient

corr_hist

vertex-vertex correlation histogram

combined_corr_hist

combined single-vertex correlation histogram

avg_neighbor_corr

average nearest-neighbor correlation

avg_combined_corr

average combined single-vertex correlation

Notes

The assortativity coefficient [newman-mixing-2003] tells in a concise fashion how vertices of different types are preferentially connected amongst themselves, and is defined by

\[r = \frac{\sum_i e_{ii} - \sum_i a_i b_i}{1-\sum_i a_i b_i}\]

where \(a_i=\sum_je_{ij}\) and \(b_j=\sum_ie_{ij}\), and \(e_{ij}\) is the fraction of edges from a vertex of type i to a vertex of type j.

The variance is obtained with the jackknife method.

If enabled during compilation, this algorithm runs in parallel.

References

newman-mixing-2003

M. E. J. Newman, “Mixing patterns in networks”, Phys. Rev. E 67, 026126 (2003), DOI: 10.1103/PhysRevE.67.026126 [sci-hub, @tor]

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g = gt.GraphView(g, directed=False)
>>> gt.assortativity(g, "out")
(0.0240578552..., 0.0003272847...)
graph_tool.correlations.scalar_assortativity(g, deg, eweight=None)[source]

Obtain the scalar assortativity coefficient for the given graph.

Parameters
gGraph

Graph to be used.

degstring or VertexPropertyMap

Degree type (“in”, “out” or “total”) or vertex property map, which specifies the vertex scalar values.

eweightEdgePropertyMap (optional, default: None)

If given, this will specify the edge weights, otherwise a constant value of one will be used.

Returns
scalar assortativity coefficienttuple of two floats

The scalar assortativity coefficient, and its variance.

See also

assortativity

assortativity coefficient

scalar_assortativity

scalar assortativity coefficient

corr_hist

vertex-vertex correlation histogram

combined_corr_hist

combined single-vertex correlation histogram

avg_neighbor_corr

average nearest-neighbor correlation

avg_combined_corr

average combined single-vertex correlation

Notes

The scalar assortativity coefficient [newman-mixing-2003] tells in a concise fashion how vertices of different types are preferentially connected amongst themselves, and is defined by

\[r = \frac{\sum_{xy} xy(e_{xy} - a_x b_y)}{\sigma_a\sigma_b}\]

where \(a_x=\sum_ye_{xy}\) and \(b_y=\sum_xe_{xy}\), and \(e_{xy}\) is the fraction of edges from a vertex of type x to a vertex of type y.

The variance is obtained with the jackknife method.

If enabled during compilation, this algorithm runs in parallel.

References

newman-mixing-2003

M. E. J. Newman, “Mixing patterns in networks”, Phys. Rev. E 67, 026126 (2003), DOI: 10.1103/PhysRevE.67.026126 [sci-hub, @tor]

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g = gt.GraphView(g, directed=False)
>>> gt.scalar_assortativity(g, "out")
(0.026384932418..., 0.001213444270...)
graph_tool.correlations.corr_hist(g, deg_source, deg_target, bins=[[0, 1], [0, 1]], weight=None, float_count=True)[source]

Obtain the correlation histogram for the given graph.

Parameters
gGraph

Graph to be used.

deg_sourcestring or VertexPropertyMap

degree type (“in”, “out” or “total”) or vertex property map for the source vertex.

deg_targetstring or VertexPropertyMap

degree type (“in”, “out” or “total”) or vertex property map for the target vertex.

binslist of lists (optional, default: [[0, 1], [0, 1]])

A list of bin edges to be used for the source and target degrees. If any list has size 2, it is used to create an automatically generated bin range starting from the first value, and with constant bin width given by the second value.

weightedge property map (optional, default: None)

Weight (multiplicative factor) to be used on each edge.

float_countbool (optional, default: True)

If True, the bin counts are converted float variables, which is useful for normalization, and other processing. It False, the bin counts will be unsigned integers.

Returns
bin_countsnumpy.ndarray

Two-dimensional array with the bin counts.

source_binsnumpy.ndarray

Source degree bins

target_binsnumpy.ndarray

Target degree bins

See also

assortativity

assortativity coefficient

scalar_assortativity

scalar assortativity coefficient

corr_hist

vertex-vertex correlation histogram

combined_corr_hist

combined single-vertex correlation histogram

avg_neighbor_corr

average nearest-neighbor correlation

avg_combined_corr

average combined single-vertex correlation

Notes

The correlation histogram counts, for every vertex with degree (or scalar property) ‘source_deg’, the number of out-neighbors with degree (or scalar property) ‘target_deg’.

If enabled during compilation, this algorithm runs in parallel.

Examples

>>> def sample_k(max):
...     accept = False
...     while not accept:
...         k = np.random.randint(1,max+1)
...         accept = np.random.random() < 1.0/k
...     return k
...
>>> g = gt.random_graph(10000, lambda: sample_k(40),
...                     model="probabilistic-configuration",
...                     edge_probs=lambda i, j: (sin(i / pi) * sin(j / pi) + 1) / 2,
...                     directed=False, n_iter=100)
>>> h = gt.corr_hist(g, "out", "out")
>>> clf()
>>> xlabel("Source out-degree")
Text(...)
>>> ylabel("Target out-degree")
Text(...)
>>> imshow(h[0].T, interpolation="nearest", origin="lower")
<...>
>>> colorbar()
<...>
>>> savefig("corr.svg")
_images/corr.svg

Out/out-degree correlation histogram.

graph_tool.correlations.combined_corr_hist(g, deg1, deg2, bins=[[0, 1], [0, 1]], float_count=True)[source]

Obtain the single-vertex combined correlation histogram for the given graph.

Parameters
gGraph

Graph to be used.

deg1string or VertexPropertyMap

first degree type (“in”, “out” or “total”) or vertex property map.

deg2string or VertexPropertyMap

second degree type (“in”, “out” or “total”) or vertex property map.

binslist of lists (optional, default: [[0, 1], [0, 1]])

A list of bin edges to be used for the first and second degrees. If any list has size 2, it is used to create an automatically generated bin range starting from the first value, and with constant bin width given by the second value.

float_countbool (optional, default: True)

If True, the bin counts are converted float variables, which is useful for normalization, and other processing. It False, the bin counts will be unsigned integers.

Returns
bin_countsnumpy.ndarray

Two-dimensional array with the bin counts.

first_binsnumpy.ndarray

First degree bins

second_binsnumpy.ndarray

Second degree bins

See also

assortativity

assortativity coefficient

scalar_assortativity

scalar assortativity coefficient

corr_hist

vertex-vertex correlation histogram

combined_corr_hist

combined single-vertex correlation histogram

avg_neighbor_corr

average nearest-neighbor correlation

avg_combined_corr

average combined single-vertex correlation

Notes

If enabled during compilation, this algorithm runs in parallel.

Examples

>>> def sample_k(max):
...     accept = False
...     while not accept:
...         i = np.random.randint(1, max + 1)
...         j = np.random.randint(1, max + 1)
...         accept = np.random.random() < (sin(i / pi) * sin(j / pi) + 1) / 2
...     return i,j
...
>>> g = gt.random_graph(10000, lambda: sample_k(40))
>>> h = gt.combined_corr_hist(g, "in", "out")
>>> clf()
>>> xlabel("In-degree")
Text(...)
>>> ylabel("Out-degree")
Text(...)
>>> imshow(h[0].T, interpolation="nearest", origin="lower")
<...>
>>> colorbar()
<...>
>>> savefig("combined_corr.svg")
_images/combined_corr.svg

Combined in/out-degree correlation histogram.

graph_tool.correlations.avg_neighbor_corr(g, deg_source, deg_target, bins=[0, 1], weight=None)[source]

Obtain the average neighbor-neighbor correlation for the given graph.

Parameters
gGraph

Graph to be used.

deg_sourcestring or VertexPropertyMap

degree type (“in”, “out” or “total”) or vertex property map for the source vertex.

deg_targetstring or VertexPropertyMap

degree type (“in”, “out” or “total”) or vertex property map for the target vertex.

binslist (optional, default: [0, 1])

Bins to be used for the source degrees. If the list has size 2, it is used as the constant width of an automatically generated bin range, starting from the first value.

weightedge property map (optional, default: None)

Weight (multiplicative factor) to be used on each edge.

Returns
bin_avgnumpy.ndarray

Array with the deg_target average for the get_source bins.

bin_devnumpy.ndarray

Array with the standard deviation of the deg_target average for the get_source bins.

binsnumpy.ndarray

Source degree bins,

See also

assortativity

assortativity coefficient

scalar_assortativity

scalar assortativity coefficient

corr_hist

vertex-vertex correlation histogram

combined_corr_hist

combined single-vertex correlation histogram

avg_neighbor_corr

average nearest-neighbor correlation

avg_combined_corr

average combined single-vertex correlation

Notes

The average correlation is the average, for every vertex with degree (or scalar property) ‘source_deg’, the of the ‘target_deg’ degree (or scalar property) of its neighbors.

If enabled during compilation, this algorithm runs in parallel.

Examples

>>> def sample_k(max):
...     accept = False
...     while not accept:
...         k = np.random.randint(1,max+1)
...         accept = np.random.random() < 1.0 / k
...     return k
...
>>> g = gt.random_graph(10000, lambda: sample_k(40),
...                     model="probabilistic-configuration",
...                     edge_probs=lambda i, j: (sin(i / pi) * sin(j / pi) + 1) / 2,
...                     directed=False, n_iter=100)
>>> h = gt.avg_neighbor_corr(g, "out", "out")
>>> clf()
>>> xlabel("Source out-degree")
Text(...)
>>> ylabel("Target out-degree")
Text(...)
>>> errorbar(h[2][:-1], h[0], yerr=h[1], fmt="o")
<...>
>>> savefig("avg_corr.svg")
_images/avg_corr.svg

Average out/out degree correlation.

graph_tool.correlations.avg_neighbour_corr(g, deg_source, deg_target, bins=[0, 1], weight=None)

Obtain the average neighbor-neighbor correlation for the given graph.

Parameters
gGraph

Graph to be used.

deg_sourcestring or VertexPropertyMap

degree type (“in”, “out” or “total”) or vertex property map for the source vertex.

deg_targetstring or VertexPropertyMap

degree type (“in”, “out” or “total”) or vertex property map for the target vertex.

binslist (optional, default: [0, 1])

Bins to be used for the source degrees. If the list has size 2, it is used as the constant width of an automatically generated bin range, starting from the first value.

weightedge property map (optional, default: None)

Weight (multiplicative factor) to be used on each edge.

Returns
bin_avgnumpy.ndarray

Array with the deg_target average for the get_source bins.

bin_devnumpy.ndarray

Array with the standard deviation of the deg_target average for the get_source bins.

binsnumpy.ndarray

Source degree bins,

See also

assortativity

assortativity coefficient

scalar_assortativity

scalar assortativity coefficient

corr_hist

vertex-vertex correlation histogram

combined_corr_hist

combined single-vertex correlation histogram

avg_neighbor_corr

average nearest-neighbor correlation

avg_combined_corr

average combined single-vertex correlation

Notes

The average correlation is the average, for every vertex with degree (or scalar property) ‘source_deg’, the of the ‘target_deg’ degree (or scalar property) of its neighbors.

If enabled during compilation, this algorithm runs in parallel.

Examples

>>> def sample_k(max):
...     accept = False
...     while not accept:
...         k = np.random.randint(1,max+1)
...         accept = np.random.random() < 1.0 / k
...     return k
...
>>> g = gt.random_graph(10000, lambda: sample_k(40),
...                     model="probabilistic-configuration",
...                     edge_probs=lambda i, j: (sin(i / pi) * sin(j / pi) + 1) / 2,
...                     directed=False, n_iter=100)
>>> h = gt.avg_neighbor_corr(g, "out", "out")
>>> clf()
>>> xlabel("Source out-degree")
Text(...)
>>> ylabel("Target out-degree")
Text(...)
>>> errorbar(h[2][:-1], h[0], yerr=h[1], fmt="o")
<...>
>>> savefig("avg_corr.svg")
_images/avg_corr.svg

Average out/out degree correlation.

graph_tool.correlations.avg_combined_corr(g, deg1, deg2, bins=[0, 1])[source]

Obtain the single-vertex combined correlation histogram for the given graph.

Parameters
gGraph

Graph to be used.

deg1string or VertexPropertyMap

first degree type (“in”, “out” or “total”) or vertex property map.

deg2string or VertexPropertyMap

second degree type (“in”, “out” or “total”) or vertex property map.

binslist (optional, default: [0, 1])

Bins to be used for the first degrees. If the list has size 2, it is used as the constant width of an automatically generated bin range, starting from the first value.

Returns
bin_avgnumpy.ndarray

Array with the deg2 average for the deg1 bins.

bin_devnumpy.ndarray

Array with the standard deviation of the deg2 average for the deg1 bins.

binsnumpy.ndarray

The deg1 bins.

See also

assortativity

assortativity coefficient

scalar_assortativity

scalar assortativity coefficient

corr_hist

vertex-vertex correlation histogram

combined_corr_hist

combined single-vertex correlation histogram

avg_neighbor_corr

average nearest-neighbor correlation

avg_combined_corr

average combined single-vertex correlation

Notes

If enabled during compilation, this algorithm runs in parallel.

Examples

>>> def sample_k(max):
...     accept = False
...     while not accept:
...         i = np.random.randint(1,max+1)
...         j = np.random.randint(1,max+1)
...         accept = np.random.random() < (sin(i/pi)*sin(j/pi)+1)/2
...     return i,j
...
>>> g = gt.random_graph(10000, lambda: sample_k(40))
>>> h = gt.avg_combined_corr(g, "in", "out")
>>> clf()
>>> xlabel("In-degree")
Text(...)
>>> ylabel("Out-degree")
Text(...)
>>> errorbar(h[2][:-1], h[0], yerr=h[1], fmt="o")
<...>
>>> savefig("combined_avg_corr.svg")
_images/combined_avg_corr.svg

Average combined in/out-degree correlation.