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annotate planemo/lib/python3.7/site-packages/networkx/algorithms/reciprocity.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1 # -*- coding: utf-8 -*-
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2 # Copyright (C) 2015-2019 by
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3 # Aric Hagberg <hagberg@lanl.gov>
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4 # Dan Schult <dschult@colgate.edu>
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5 # Pieter Swart <swart@lanl.gov>
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6 # All rights reserved.
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7 # BSD license.
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8 #
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9 # Authors: Haochen Wu (wuhaochen42@gmail.com)
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10 """Algorithms to calculate reciprocity in a directed graph."""
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11 from networkx import NetworkXError
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12 from ..utils import not_implemented_for
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13
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14 __all__ = ['reciprocity', 'overall_reciprocity']
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15
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16
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17 @not_implemented_for('undirected', 'multigraph')
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18 def reciprocity(G, nodes=None):
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19 r"""Compute the reciprocity in a directed graph.
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20
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21 The reciprocity of a directed graph is defined as the ratio
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22 of the number of edges pointing in both directions to the total
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23 number of edges in the graph.
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24 Formally, $r = |{(u,v) \in G|(v,u) \in G}| / |{(u,v) \in G}|$.
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25
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26 The reciprocity of a single node u is defined similarly,
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27 it is the ratio of the number of edges in both directions to
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28 the total number of edges attached to node u.
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29
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30 Parameters
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31 ----------
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32 G : graph
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33 A networkx directed graph
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34 nodes : container of nodes, optional (default=whole graph)
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35 Compute reciprocity for nodes in this container.
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36
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37 Returns
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38 -------
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39 out : dictionary
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40 Reciprocity keyed by node label.
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41
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42 Notes
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43 -----
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44 The reciprocity is not defined for isolated nodes.
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45 In such cases this function will return None.
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46
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47 """
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48 # If `nodes` is not specified, calculate the reciprocity of the graph.
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49 if nodes is None:
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50 return overall_reciprocity(G)
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51
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52 # If `nodes` represents a single node in the graph, return only its
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53 # reciprocity.
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54 if nodes in G:
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55 reciprocity = next(_reciprocity_iter(G, nodes))[1]
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56 if reciprocity is None:
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57 raise NetworkXError('Not defined for isolated nodes.')
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58 else:
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59 return reciprocity
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60
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61 # Otherwise, `nodes` represents an iterable of nodes, so return a
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62 # dictionary mapping node to its reciprocity.
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63 return dict(_reciprocity_iter(G, nodes))
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64
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65
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66 def _reciprocity_iter(G, nodes):
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67 """ Return an iterator of (node, reciprocity).
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68 """
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69 n = G.nbunch_iter(nodes)
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70 for node in n:
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71 pred = set(G.predecessors(node))
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72 succ = set(G.successors(node))
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73 overlap = pred & succ
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74 n_total = len(pred) + len(succ)
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75
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76 # Reciprocity is not defined for isolated nodes.
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77 # Return None.
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78 if n_total == 0:
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79 yield (node, None)
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80 else:
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81 reciprocity = 2.0 * float(len(overlap)) / float(n_total)
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82 yield (node, reciprocity)
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83
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84
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85 @not_implemented_for('undirected', 'multigraph')
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86 def overall_reciprocity(G):
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87 """Compute the reciprocity for the whole graph.
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88
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89 See the doc of reciprocity for the definition.
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90
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91 Parameters
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92 ----------
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93 G : graph
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94 A networkx graph
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95
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96 """
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97 n_all_edge = G.number_of_edges()
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98 n_overlap_edge = (n_all_edge - G.to_undirected().number_of_edges()) * 2
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99
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100 if n_all_edge == 0:
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101 raise NetworkXError("Not defined for empty graphs")
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102
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103 return float(n_overlap_edge) / float(n_all_edge)