## Mercurial > repos > shellac > sam_consensus_v3

### view env/lib/python3.9/site-packages/networkx/algorithms/richclub.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |

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"""Functions for computing rich-club coefficients.""" import networkx as nx from itertools import accumulate from networkx.utils import not_implemented_for __all__ = ["rich_club_coefficient"] @not_implemented_for("directed") @not_implemented_for("multigraph") def rich_club_coefficient(G, normalized=True, Q=100, seed=None): r"""Returns the rich-club coefficient of the graph `G`. For each degree *k*, the *rich-club coefficient* is the ratio of the number of actual to the number of potential edges for nodes with degree greater than *k*: .. math:: \phi(k) = \frac{2 E_k}{N_k (N_k - 1)} where `N_k` is the number of nodes with degree larger than *k*, and `E_k` is the number of edges among those nodes. Parameters ---------- G : NetworkX graph Undirected graph with neither parallel edges nor self-loops. normalized : bool (optional) Normalize using randomized network as in [1]_ Q : float (optional, default=100) If `normalized` is True, perform `Q * m` double-edge swaps, where `m` is the number of edges in `G`, to use as a null-model for normalization. seed : integer, random_state, or None (default) Indicator of random number generation state. See :ref:`Randomness<randomness>`. Returns ------- rc : dictionary A dictionary, keyed by degree, with rich-club coefficient values. Examples -------- >>> G = nx.Graph([(0, 1), (0, 2), (1, 2), (1, 3), (1, 4), (4, 5)]) >>> rc = nx.rich_club_coefficient(G, normalized=False, seed=42) >>> rc[0] 0.4 Notes ----- The rich club definition and algorithm are found in [1]_. This algorithm ignores any edge weights and is not defined for directed graphs or graphs with parallel edges or self loops. Estimates for appropriate values of `Q` are found in [2]_. References ---------- .. [1] Julian J. McAuley, Luciano da Fontoura Costa, and TibĂ©rio S. Caetano, "The rich-club phenomenon across complex network hierarchies", Applied Physics Letters Vol 91 Issue 8, August 2007. https://arxiv.org/abs/physics/0701290 .. [2] R. Milo, N. Kashtan, S. Itzkovitz, M. E. J. Newman, U. Alon, "Uniform generation of random graphs with arbitrary degree sequences", 2006. https://arxiv.org/abs/cond-mat/0312028 """ if nx.number_of_selfloops(G) > 0: raise Exception( "rich_club_coefficient is not implemented for " "graphs with self loops." ) rc = _compute_rc(G) if normalized: # make R a copy of G, randomize with Q*|E| double edge swaps # and use rich_club coefficient of R to normalize R = G.copy() E = R.number_of_edges() nx.double_edge_swap(R, Q * E, max_tries=Q * E * 10, seed=seed) rcran = _compute_rc(R) rc = {k: v / rcran[k] for k, v in rc.items()} return rc def _compute_rc(G): """Returns the rich-club coefficient for each degree in the graph `G`. `G` is an undirected graph without multiedges. Returns a dictionary mapping degree to rich-club coefficient for that degree. """ deghist = nx.degree_histogram(G) total = sum(deghist) # Compute the number of nodes with degree greater than `k`, for each # degree `k` (omitting the last entry, which is zero). nks = (total - cs for cs in accumulate(deghist) if total - cs > 1) # Create a sorted list of pairs of edge endpoint degrees. # # The list is sorted in reverse order so that we can pop from the # right side of the list later, instead of popping from the left # side of the list, which would have a linear time cost. edge_degrees = sorted((sorted(map(G.degree, e)) for e in G.edges()), reverse=True) ek = G.number_of_edges() k1, k2 = edge_degrees.pop() rc = {} for d, nk in enumerate(nks): while k1 <= d: if len(edge_degrees) == 0: ek = 0 break k1, k2 = edge_degrees.pop() ek -= 1 rc[d] = 2 * ek / (nk * (nk - 1)) return rc