Tutorial 2 - Visualization Methods
Tutorial 2 - Visualization Methods
@@ -41,7 +40,6 @@ Tutorials may be run in your browser using Google Colab
-
Tutorial 3 - LesMis Case Study
@@ -49,7 +47,6 @@ Tutorials may be run in your browser using Google Colab
-
Tutorial 4 - LesMis Visualizations-Book Tour
diff --git a/docs/build/.buildinfo b/docs/build/.buildinfo
index b088336c..7f8381d9 100644
--- a/docs/build/.buildinfo
+++ b/docs/build/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 100d5f0571659fa080bb0f6ef7eebc72
+config: 12513d66143dfa27e7a4e78bbb5b3696
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/.doctrees/algorithms/algorithms.doctree b/docs/build/.doctrees/algorithms/algorithms.doctree
index 174f4a48..8c352810 100644
Binary files a/docs/build/.doctrees/algorithms/algorithms.doctree and b/docs/build/.doctrees/algorithms/algorithms.doctree differ
diff --git a/docs/build/.doctrees/environment.pickle b/docs/build/.doctrees/environment.pickle
index cc52055e..ce4425f6 100644
Binary files a/docs/build/.doctrees/environment.pickle and b/docs/build/.doctrees/environment.pickle differ
diff --git a/docs/build/_modules/algorithms/homology_mod2.html b/docs/build/_modules/algorithms/homology_mod2.html
index e04f7a90..524dae71 100644
--- a/docs/build/_modules/algorithms/homology_mod2.html
+++ b/docs/build/_modules/algorithms/homology_mod2.html
@@ -8,7 +8,7 @@
-
# Copyright © 2018 Battelle Memorial Institute
# All rights reserved.
-# This module developed for PNNL's hyperbio LDRD project summer 2019
+
+"""
+
+S-Centrality Measures
+=====================
+We generalize graph metrics to s-metrics for a hypergraph by using its s-connected
+components. This is accomplished by computing the s edge-adjacency matrix and
+constructing the corresponding graph of the matrix. We then use existing graph metrics
+on this representation of the hypergraph. In essence we construct an *s*-line graph
+corresponding to the hypergraph on which to apply our methods.
+
+S-Metrics for hypergraphs are discussed in depth in:
+*Aksoy, S.G., Joslyn, C., Ortiz Marrero, C. et al. Hypernetwork science via high-order hypergraph walks.
+EPJ Data Sci. 9, 16 (2020). https://doi.org/10.1140/epjds/s13688-020-00231-0*
+
+"""
import numpy as np
from collections import defaultdict
@@ -193,10 +208,12 @@ Source code for algorithms.s_centrality_measures
A dictionary of s-betweenness centrality value of the edges.
'''
+
# Confirm there is at least 1 s edge for which we can compute the centrality
# Find all s-edges
#M,rdict,_ = H.incidence_matrix(index=True)
#A = M.transpose().dot(M)
+
A, coldict = H.edge_adjacency_matrix(s=s, index=True)
A.setdiag(0)
A = (A >= s) * 1
@@ -227,8 +244,10 @@ Source code for algorithms.s_centrality_measures
If edge then a single value is returned.
'''
+
# Confirm there is at least 1 s edge for which we can compute the centrality
# Find all s-edges
+
if edge and len(H.edges[edge]) < s:
return 0
@@ -250,6 +269,7 @@ Source code for algorithms.s_centrality_measures
# confirm there are at least 2 s-edges
# we follow the NX convention that the s-closeness centrality of a single edge Hypergraph is 0
+
output = {}
if not bool(Es) or len(Es) == 1:
output = {e: 0 for e in edges}
@@ -280,7 +300,11 @@ Source code for algorithms.s_centrality_measures
eccentricity[f] : float
else:
eccentricity_dict : dict
-
+ : dict or float
+ returns the s-eccentricity value of the edges, a floating point number
+ If edge=None a dictionary of values for each s-edge in H is returned.
+ If edge then a single value is returned.
+
'''
if f:
if isinstance(f, Entity):
diff --git a/docs/build/_modules/classes/entity.html b/docs/build/_modules/classes/entity.html
index b8bb3fd5..79c7c5ba 100644
--- a/docs/build/_modules/classes/entity.html
+++ b/docs/build/_modules/classes/entity.html
@@ -8,7 +8,7 @@
- classes.entity — HyperNetX 0.3.4 documentation
+ classes.entity — HyperNetX 0.3.5 documentation
diff --git a/docs/build/_modules/classes/hypergraph.html b/docs/build/_modules/classes/hypergraph.html
index 98df0572..d35cec2e 100644
--- a/docs/build/_modules/classes/hypergraph.html
+++ b/docs/build/_modules/classes/hypergraph.html
@@ -8,7 +8,7 @@
- classes.hypergraph — HyperNetX 0.3.4 documentation
+ classes.hypergraph — HyperNetX 0.3.5 documentation
diff --git a/docs/build/_modules/drawing/rubber_band.html b/docs/build/_modules/drawing/rubber_band.html
index ea2b8369..11b98e95 100644
--- a/docs/build/_modules/drawing/rubber_band.html
+++ b/docs/build/_modules/drawing/rubber_band.html
@@ -8,7 +8,7 @@
- drawing.rubber_band — HyperNetX 0.3.4 documentation
+ drawing.rubber_band — HyperNetX 0.3.5 documentation
diff --git a/docs/build/_modules/drawing/two_column.html b/docs/build/_modules/drawing/two_column.html
index 7c977043..352a2116 100644
--- a/docs/build/_modules/drawing/two_column.html
+++ b/docs/build/_modules/drawing/two_column.html
@@ -8,7 +8,7 @@
- drawing.two_column — HyperNetX 0.3.4 documentation
+ drawing.two_column — HyperNetX 0.3.5 documentation
diff --git a/docs/build/_modules/drawing/util.html b/docs/build/_modules/drawing/util.html
index 0e71704e..50b7a36f 100644
--- a/docs/build/_modules/drawing/util.html
+++ b/docs/build/_modules/drawing/util.html
@@ -8,7 +8,7 @@
- drawing.util — HyperNetX 0.3.4 documentation
+ drawing.util — HyperNetX 0.3.5 documentation
diff --git a/docs/build/_modules/index.html b/docs/build/_modules/index.html
index ff8e508d..9a56bc17 100644
--- a/docs/build/_modules/index.html
+++ b/docs/build/_modules/index.html
@@ -8,7 +8,7 @@
- Overview: module code — HyperNetX 0.3.4 documentation
+ Overview: module code — HyperNetX 0.3.5 documentation
diff --git a/docs/build/_modules/reports/descriptive_stats.html b/docs/build/_modules/reports/descriptive_stats.html
index bf2ab790..099b33f3 100644
--- a/docs/build/_modules/reports/descriptive_stats.html
+++ b/docs/build/_modules/reports/descriptive_stats.html
@@ -8,7 +8,7 @@
- reports.descriptive_stats — HyperNetX 0.3.4 documentation
+ reports.descriptive_stats — HyperNetX 0.3.5 documentation
diff --git a/docs/build/_static/documentation_options.js b/docs/build/_static/documentation_options.js
index 6e4da6fd..883b606f 100644
--- a/docs/build/_static/documentation_options.js
+++ b/docs/build/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '0.3.4',
+ VERSION: '0.3.5',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/docs/build/algorithms/algorithms.html b/docs/build/algorithms/algorithms.html
index 96106adb..228bd9e3 100644
--- a/docs/build/algorithms/algorithms.html
+++ b/docs/build/algorithms/algorithms.html
@@ -8,7 +8,7 @@
- algorithms package — HyperNetX 0.3.4 documentation
+ algorithms package — HyperNetX 0.3.5 documentation
@@ -101,7 +101,10 @@
Homology and Smith Normal Form
-algorithms.s_centrality_measures module
+algorithms.s_centrality_measures module
+
Module contents
@@ -599,6 +602,16 @@ Homology Mod2
algorithms.s_centrality_measures module¶
+
+S-Centrality Measures¶
+We generalize graph metrics to s-metrics for a hypergraph by using its s-connected
+components. This is accomplished by computing the s edge-adjacency matrix and
+constructing the corresponding graph of the matrix. We then use existing graph metrics
+on this representation of the hypergraph. In essence we construct an s-line graph
+corresponding to the hypergraph on which to apply our methods.
+S-Metrics for hypergraphs are discussed in depth in:
+Aksoy, S.G., Joslyn, C., Ortiz Marrero, C. et al. Hypernetwork science via high-order hypergraph walks.
+EPJ Data Sci. 9, 16 (2020). https://doi.org/10.1140/epjds/s13688-020-00231-0
-
algorithms.s_centrality_measures.s_betweenness_centrality(H, s=1, normalized=True)[source]¶
@@ -630,10 +643,18 @@ Homology Mod2
+
- if f:
eccentricity[f] : float
- else:
eccentricity_dict : dict
+- else:
+eccentricity_dict : dict
+
+
+- : dict or float
returns the s-eccentricity value of the edges, a floating point number
+If edge=None a dictionary of values for each s-edge in H is returned.
+If edge then a single value is returned.
+
@@ -664,6 +685,7 @@ Homology Mod2
Module contents¶
diff --git a/docs/build/algorithms/modules.html b/docs/build/algorithms/modules.html
index 3c3fbb74..e96b072a 100644
--- a/docs/build/algorithms/modules.html
+++ b/docs/build/algorithms/modules.html
@@ -8,7 +8,7 @@
- algorithms — HyperNetX 0.3.4 documentation
+ algorithms — HyperNetX 0.3.5 documentation
@@ -178,7 +178,10 @@ algorithmsalgorithms.s_centrality_measures module
+
algorithms.s_centrality_measures module
+
Module contents
diff --git a/docs/build/classes/classes.html b/docs/build/classes/classes.html
index 6519bcfd..0d765a01 100644
--- a/docs/build/classes/classes.html
+++ b/docs/build/classes/classes.html
@@ -8,7 +8,7 @@
- classes package — HyperNetX 0.3.4 documentation
+ classes package — HyperNetX 0.3.5 documentation
diff --git a/docs/build/classes/modules.html b/docs/build/classes/modules.html
index 9913da1a..bdd51296 100644
--- a/docs/build/classes/modules.html
+++ b/docs/build/classes/modules.html
@@ -8,7 +8,7 @@
- classes — HyperNetX 0.3.4 documentation
+ classes — HyperNetX 0.3.5 documentation
diff --git a/docs/build/drawing/drawing.html b/docs/build/drawing/drawing.html
index f0a41b20..2923aa73 100644
--- a/docs/build/drawing/drawing.html
+++ b/docs/build/drawing/drawing.html
@@ -8,7 +8,7 @@
- drawing package — HyperNetX 0.3.4 documentation
+ drawing package — HyperNetX 0.3.5 documentation
diff --git a/docs/build/drawing/modules.html b/docs/build/drawing/modules.html
index 82eedc21..9b1ca2e8 100644
--- a/docs/build/drawing/modules.html
+++ b/docs/build/drawing/modules.html
@@ -8,7 +8,7 @@
- drawing — HyperNetX 0.3.4 documentation
+ drawing — HyperNetX 0.3.5 documentation
diff --git a/docs/build/genindex.html b/docs/build/genindex.html
index f6432d5e..d72a5c80 100644
--- a/docs/build/genindex.html
+++ b/docs/build/genindex.html
@@ -9,7 +9,7 @@
- Index — HyperNetX 0.3.4 documentation
+ Index — HyperNetX 0.3.5 documentation
diff --git a/docs/build/glossary.html b/docs/build/glossary.html
index 8a412121..48f4fc33 100644
--- a/docs/build/glossary.html
+++ b/docs/build/glossary.html
@@ -8,7 +8,7 @@
- Glossary of HNX terms — HyperNetX 0.3.4 documentation
+ Glossary of HNX terms — HyperNetX 0.3.5 documentation
diff --git a/docs/build/index.html b/docs/build/index.html
index 0cbbfe5a..255ddf92 100644
--- a/docs/build/index.html
+++ b/docs/build/index.html
@@ -8,7 +8,7 @@
- HyperNetX (HNX) — HyperNetX 0.3.4 documentation
+ HyperNetX (HNX) — HyperNetX 0.3.5 documentation
diff --git a/docs/build/install.html b/docs/build/install.html
index 890dd8a3..9e26fadc 100644
--- a/docs/build/install.html
+++ b/docs/build/install.html
@@ -8,7 +8,7 @@
- Installing HyperNetX — HyperNetX 0.3.4 documentation
+ Installing HyperNetX — HyperNetX 0.3.5 documentation
diff --git a/docs/build/license.html b/docs/build/license.html
index ab054128..20805e71 100644
--- a/docs/build/license.html
+++ b/docs/build/license.html
@@ -8,7 +8,7 @@
- License — HyperNetX 0.3.4 documentation
+ License — HyperNetX 0.3.5 documentation
diff --git a/docs/build/overview/index.html b/docs/build/overview/index.html
index 1dda0f8e..e1dcae6f 100644
--- a/docs/build/overview/index.html
+++ b/docs/build/overview/index.html
@@ -8,7 +8,7 @@
- Overview — HyperNetX 0.3.4 documentation
+ Overview — HyperNetX 0.3.5 documentation
diff --git a/docs/build/py-modindex.html b/docs/build/py-modindex.html
index ce4e9d6c..c6528fe6 100644
--- a/docs/build/py-modindex.html
+++ b/docs/build/py-modindex.html
@@ -8,7 +8,7 @@
- Python Module Index — HyperNetX 0.3.4 documentation
+ Python Module Index — HyperNetX 0.3.5 documentation
diff --git a/docs/build/reports/modules.html b/docs/build/reports/modules.html
index f13a1467..ec4413f1 100644
--- a/docs/build/reports/modules.html
+++ b/docs/build/reports/modules.html
@@ -8,7 +8,7 @@
- reports — HyperNetX 0.3.4 documentation
+ reports — HyperNetX 0.3.5 documentation
diff --git a/docs/build/reports/reports.html b/docs/build/reports/reports.html
index a9c0d014..6436b5e2 100644
--- a/docs/build/reports/reports.html
+++ b/docs/build/reports/reports.html
@@ -8,7 +8,7 @@
- reports package — HyperNetX 0.3.4 documentation
+ reports package — HyperNetX 0.3.5 documentation
diff --git a/docs/build/search.html b/docs/build/search.html
index 90bdd44d..b330fd4e 100644
--- a/docs/build/search.html
+++ b/docs/build/search.html
@@ -8,7 +8,7 @@
- Search — HyperNetX 0.3.4 documentation
+ Search — HyperNetX 0.3.5 documentation
diff --git a/docs/build/searchindex.js b/docs/build/searchindex.js
index b981cdc7..c4f8af3b 100644
--- a/docs/build/searchindex.js
+++ b/docs/build/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 3d3a9527..705f508d 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -19,7 +19,7 @@
import os
import shlex
-__version__ = "0.3.4"
+__version__ = "0.3.5"
# If extensions (or modules to document with autodoc) are in another directory,
diff --git a/hypernetx/algorithms/s_centrality_measures.py b/hypernetx/algorithms/s_centrality_measures.py
index fd3d5ec6..a4c61792 100644
--- a/hypernetx/algorithms/s_centrality_measures.py
+++ b/hypernetx/algorithms/s_centrality_measures.py
@@ -1,6 +1,21 @@
# Copyright © 2018 Battelle Memorial Institute
# All rights reserved.
-# This module developed for PNNL's hyperbio LDRD project summer 2019
+
+"""
+
+S-Centrality Measures
+=====================
+We generalize graph metrics to s-metrics for a hypergraph by using its s-connected
+components. This is accomplished by computing the s edge-adjacency matrix and
+constructing the corresponding graph of the matrix. We then use existing graph metrics
+on this representation of the hypergraph. In essence we construct an *s*-line graph
+corresponding to the hypergraph on which to apply our methods.
+
+S-Metrics for hypergraphs are discussed in depth in:
+*Aksoy, S.G., Joslyn, C., Ortiz Marrero, C. et al. Hypernetwork science via high-order hypergraph walks.
+EPJ Data Sci. 9, 16 (2020). https://doi.org/10.1140/epjds/s13688-020-00231-0*
+
+"""
import numpy as np
from collections import defaultdict
@@ -32,10 +47,12 @@ def s_betweenness_centrality(H, s=1, normalized=True):
A dictionary of s-betweenness centrality value of the edges.
'''
+
# Confirm there is at least 1 s edge for which we can compute the centrality
# Find all s-edges
#M,rdict,_ = H.incidence_matrix(index=True)
#A = M.transpose().dot(M)
+
A, coldict = H.edge_adjacency_matrix(s=s, index=True)
A.setdiag(0)
A = (A >= s) * 1
@@ -66,8 +83,10 @@ def s_harmonic_closeness_centrality(H, edge=None, s=1):
If edge then a single value is returned.
'''
+
# Confirm there is at least 1 s edge for which we can compute the centrality
# Find all s-edges
+
if edge and len(H.edges[edge]) < s:
return 0
@@ -89,6 +108,7 @@ def temp(e, f):
# confirm there are at least 2 s-edges
# we follow the NX convention that the s-closeness centrality of a single edge Hypergraph is 0
+
output = {}
if not bool(Es) or len(Es) == 1:
output = {e: 0 for e in edges}
@@ -123,6 +143,7 @@ def s_eccentricity(H, f=None, s=1):
returns the s-eccentricity value of the edges, a floating point number
If edge=None a dictionary of values for each s-edge in H is returned.
If edge then a single value is returned.
+
'''
if f:
if isinstance(f, Entity):
diff --git a/setup.py b/setup.py
index 06a8c0ac..f5759121 100644
--- a/setup.py
+++ b/setup.py
@@ -1,15 +1,16 @@
-from setuptools import setup
-import sys, os.path
+from setuptools import setup
+import sys
+import os.path
-__version__ = '0.3.4'
+__version__ = '0.3.5'
-if sys.version_info < (3,6):
+if sys.version_info < (3, 6):
sys.exit('HyperNetX requires Python 3.6 or later.')
setup(
name='hypernetx',
packages=['hypernetx',
- 'hypernetx.algorithms',
+ 'hypernetx.algorithms',
'hypernetx.classes',
'hypernetx.drawing',
'hypernetx.reports'],
@@ -18,28 +19,26 @@
author_email="hypernetx@pnnl.gov",
url='https://github.com/pnnl/HyperNetX',
description='HyperNetX is a Python library for the creation and study of hypergraphs.',
- install_requires=['networkx>=2.2,<3.0','numpy>=1.15.0,<2.0','scipy>=1.1.0,<2.0','matplotlib>3.0','scikit-learn>=0.20.0'],
+ install_requires=['networkx>=2.2,<3.0', 'numpy>=1.15.0,<2.0', 'scipy>=1.1.0,<2.0', 'matplotlib>3.0', 'scikit-learn>=0.20.0'],
license='3-Clause BSD license',
long_description='''
- The HyperNetX library provides classes and methods for complex network data.
- HyperNetX uses data structures designed to represent set systems containing
- nested data and/or multi-way relationships. The library generalizes traditional
- graph metrics to hypergraphs.
+ The HyperNetX library provides classes and methods for complex network data.
+ HyperNetX uses data structures designed to represent set systems containing
+ nested data and/or multi-way relationships. The library generalizes traditional
+ graph metrics to hypergraphs.
- The current version is preliminary. We are actively testing and would be grateful
- for comments and suggestions. Expect changes in both class names and methods as
+ The current version is preliminary. We are actively testing and would be grateful
+ for comments and suggestions. Expect changes in both class names and methods as
many of the requirements demanded of the library are worked out.
''',
extras_require={
- 'testing':['pytest>=4.0'],
- 'notebooks':['jupyter>=1.0','pandas>=0.23'],
- 'tutorials':['jupyter>=1.0','pandas>=0.23'],
- 'documentation':['sphinx>=1.8.2','nb2plots>=0.6','sphinx-rtd-theme>=0.4.2'],
- 'all':['sphinx>=1.8.2','nb2plots>=0.6','sphinx-rtd-theme>=0.4.2','pytest>=4.0','jupyter>=1.0','pandas>=0.23']
+ 'testing': ['pytest>=4.0'],
+ 'notebooks': ['jupyter>=1.0', 'pandas>=0.23'],
+ 'tutorials': ['jupyter>=1.0', 'pandas>=0.23'],
+ 'documentation': ['sphinx>=1.8.2', 'nb2plots>=0.6', 'sphinx-rtd-theme>=0.4.2'],
+ 'all': ['sphinx>=1.8.2', 'nb2plots>=0.6', 'sphinx-rtd-theme>=0.4.2', 'pytest>=4.0', 'jupyter>=1.0', 'pandas>=0.23']
}
)
-### Since this package is still in development, please install in a virtualenv or conda environment.
-### See README for installations instructions
-
-
+# Since this package is still in development, please install in a virtualenv or conda environment.
+# See README for installations instructions