From b5b7876acc2fd95762800c6e47dc40fc4aed8fa0 Mon Sep 17 00:00:00 2001 From: fcphysics Date: Mon, 8 May 2023 09:33:04 -0400 Subject: [PATCH 01/12] Data cleanup --- .gitignore | 1 + 00-pre-process.py | 5 +- 01-calc-backbone.py | 10 +- 02-network-stats.py | 16 ++- 11-connected_components.py | 73 +++++++++++++ README.md | 4 +- networks.ini | 60 ++++++----- .../business/components-stats.csv | 7 ++ .../business/distortion-stats.csv | 12 +-- .../business/network-stats.csv | 14 +-- .../computer_science/components-stats.csv | 7 ++ .../computer_science/distortion-stats.csv | 12 +-- .../computer_science/network-stats.csv | 14 +-- .../history/components-stats.csv | 7 ++ .../history/distortion-stats.csv | 12 +-- .../academic_hiring/history/network-stats.csv | 14 +-- networks/bike-sharing/components-stats.csv | 7 ++ networks/bike-sharing/distortion-stats.csv | 2 +- networks/caviar_proj/components-stats.csv | 7 ++ networks/caviar_proj/distortion-stats.csv | 12 +-- networks/caviar_proj/network-stats.csv | 14 +-- networks/celegans/README.md | 1 - .../hermaphrodite/components-stats.csv | 7 ++ .../hermaphrodite/distortion-stats.csv | 12 +-- .../celegans/hermaphrodite/network-stats.csv | 14 +-- networks/celegans/male/components-stats.csv | 7 ++ networks/celegans/male/distortion-stats.csv | 12 +-- networks/celegans/male/network-stats.csv | 14 +-- .../calls/components-stats.csv | 7 ++ .../calls/distortion-stats.csv | 12 +-- .../colombia_social/calls/network-stats.csv | 14 +-- .../mobility/components-stats.csv | 7 ++ .../mobility/distortion-stats.csv | 12 +-- .../mobility/network-stats.csv | 14 +-- networks/comorbidity/components-stats.csv | 7 ++ networks/giraffe/components-stats.csv | 7 ++ networks/giraffe/distortion-stats.csv | 12 +-- networks/giraffe/network-stats.csv | 8 +- networks/host-pathogen/components-stats.csv | 7 ++ networks/host-pathogen/distortion-stats.csv | 12 +-- networks/host-pathogen/network-stats.csv | 14 +-- .../mobility/manizales/components-stats.csv | 7 ++ .../mobility/manizales/distortion-stats.csv | 12 +-- networks/mobility/manizales/network-stats.csv | 14 +-- .../mobility/medellin/components-stats.csv | 7 ++ .../mobility/medellin/distortion-stats.csv | 12 +-- networks/mobility/medellin/network-stats.csv | 14 +-- networks/phone-calls/README.md | 3 +- networks/phone-calls/components-stats.csv | 7 ++ networks/tennis_losses/components-stats.csv | 7 ++ networks/tennis_losses/distortion-stats.csv | 12 +-- networks/tennis_losses/network-stats.csv | 14 +-- .../us-airports-2006/components-stats.csv | 7 ++ .../us-airports-2006/distortion-stats.csv | 12 +-- networks/us-airports-2006/network-stats.csv | 14 +-- networks/water-pipes/README.md | 9 -- networks/water-pipes/distortion-stats.csv | 7 -- networks/water-pipes/network-stats.csv | 11 -- networks/weblinks_us/network-stats.csv | 11 ++ networks/yeast_grn/components-stats.csv | 7 ++ utils.py | 101 +++++++++++++++++- 61 files changed, 542 insertions(+), 256 deletions(-) create mode 100644 11-connected_components.py create mode 100644 networks/academic_hiring/business/components-stats.csv create mode 100644 networks/academic_hiring/computer_science/components-stats.csv create mode 100644 networks/academic_hiring/history/components-stats.csv create mode 100644 networks/bike-sharing/components-stats.csv create mode 100644 networks/caviar_proj/components-stats.csv create mode 100644 networks/celegans/hermaphrodite/components-stats.csv create mode 100644 networks/celegans/male/components-stats.csv create mode 100644 networks/colombia_social/calls/components-stats.csv create mode 100644 networks/colombia_social/mobility/components-stats.csv create mode 100644 networks/comorbidity/components-stats.csv create mode 100644 networks/giraffe/components-stats.csv create mode 100644 networks/host-pathogen/components-stats.csv create mode 100644 networks/mobility/manizales/components-stats.csv create mode 100644 networks/mobility/medellin/components-stats.csv create mode 100644 networks/phone-calls/components-stats.csv create mode 100644 networks/tennis_losses/components-stats.csv create mode 100644 networks/us-airports-2006/components-stats.csv delete mode 100644 networks/water-pipes/README.md delete mode 100644 networks/water-pipes/distortion-stats.csv delete mode 100644 networks/water-pipes/network-stats.csv create mode 100644 networks/weblinks_us/network-stats.csv create mode 100644 networks/yeast_grn/components-stats.csv diff --git a/.gitignore b/.gitignore index 4f40673..31de609 100644 --- a/.gitignore +++ b/.gitignore @@ -19,6 +19,7 @@ Summary/ # New stuff for now new_networks/ +Figures/ # Run scripts script* diff --git a/00-pre-process.py b/00-pre-process.py index fc6077a..bbe63cb 100644 --- a/00-pre-process.py +++ b/00-pre-process.py @@ -80,15 +80,16 @@ def read_gpickle(file_name): if weight_type in 'proximity': print('Prox -> Dist') - P_dict = nx.get_edge_attributes(G, weight_attr) + P_dict = dict(nx.get_edge_attributes(G, weight_attr)) D_dict = {key: prox2dist(value) for key, value in P_dict.items()} nx.set_edge_attributes(G, name='distance', values=D_dict) if weight_type == 'distance': - D_dict = nx.get_edge_attributes(G, name=weight_attr) + D_dict = dict(nx.get_edge_attributes(G, name=weight_attr)) P_dict = {key: dist2prox(value) for key, value in D_dict.items()} + print(P_dict.values()) if (min(P_dict.values()) < 0) or (max(P_dict.values()) > 1.0): raise TypeError("Proximity values not in [0,1]") diff --git a/01-calc-backbone.py b/01-calc-backbone.py index ee0e721..0468bd4 100644 --- a/01-calc-backbone.py +++ b/01-calc-backbone.py @@ -53,7 +53,7 @@ # Files wGgraphml = 'networks/{folder:s}/backbone.graphml'.format(folder=folder) wFdistortion = 'networks/{folder:s}/distortion.pickle'.format(folder=folder) - wFasymmetry = 'networks/{folder:s}/asymmetry.pickle'.format(folder=folder) + #wFasymmetry = 'networks/{folder:s}/asymmetry.pickle'.format(folder=folder) # Load Network rGfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) @@ -65,7 +65,7 @@ # # Asymmetry distribution # - alpha = get_asymmetry_distribution(G) + #alpha = get_asymmetry_distribution(G) # Dictionary of distortion distribution distortion_dist = dict() @@ -85,13 +85,13 @@ print('--- Exporting Formats ---') ensurePathExists(wGgraphml) ensurePathExists(wFdistortion) - ensurePathExists(wFasymmetry) + #ensurePathExists(wFasymmetry) print('> Backbone') nx.write_graphml(G, wGgraphml) print('> Distortion') pk.dump(distortion_dist, open(wFdistortion, 'wb')) - print('> Asymmetry') - pk.dump(alpha, open(wFasymmetry, 'wb')) + #print('> Asymmetry') + #pk.dump(alpha, open(wFasymmetry, 'wb')) print('\n\n') diff --git a/02-network-stats.py b/02-network-stats.py index 8d7c4ca..08fda3c 100644 --- a/02-network-stats.py +++ b/02-network-stats.py @@ -43,7 +43,7 @@ rGfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) rBfile = 'networks/{folder:s}/backbone.graphml'.format(folder=folder) wGstats = 'networks/{folder:s}/network-stats.csv'.format(folder=folder) - wFasymmetry = 'networks/{folder:s}/backbone_asymmetry.pickle'.format(folder=folder) + #wFasymmetry = 'networks/{folder:s}/backbone_asymmetry.pickle'.format(folder=folder) # Load graph G = nx.read_graphml(rGfile) @@ -60,13 +60,11 @@ n_edges_metric = G.number_of_edges() # New asymmetry dist - alpha = dict() - alpha['metric'] = get_asymmetry_distribution(G) + #alpha = dict() + #alpha['metric'] = get_asymmetry_distribution(G) # Ultrametric - edges2remove = [(i, j) for i, j, d in G.edges(data=True) if 'ultrametric' not in d] - G.remove_edges_from(edges2remove) - n_edges_ultrametric = G.number_of_edges() - alpha['ultrametric'] = get_asymmetry_distribution(G) + n_edges_ultrametric = sum([int(d) for _, _, d in G.edges(data='ultrametric')]) + #alpha['ultrametric'] = get_asymmetry_distribution(G) # to Result Series sR = pd.Series({ @@ -91,6 +89,6 @@ # Print print(sR) sR.to_csv(wGstats) - print('> Asymmetry') - pk.dump(alpha, open(wFasymmetry, 'wb')) + #print('> Asymmetry') + #pk.dump(alpha, open(wFasymmetry, 'wb')) print("\n\n") diff --git a/11-connected_components.py b/11-connected_components.py new file mode 100644 index 0000000..2daac6a --- /dev/null +++ b/11-connected_components.py @@ -0,0 +1,73 @@ +# coding=utf-8 +# Author: Felipe Xavier Costa +# Date: May 3, 2023 +# +# Description: Compare backbone inside and outside SCC. +# +# +import numpy as np +import pandas as pd +pd.set_option('display.max_rows', 100) +pd.set_option('display.max_columns', 500) +pd.set_option('display.width', 1000) +#pd.options.display.float_format = '{:.2%}'.format +import networkx as nx +import argparse +import configparser +from utils import get_asymmetry_distribution +import pickle as pk + + +if __name__ == '__main__': + + # + # Init + # + config = configparser.ConfigParser() + config.read('networks.ini') + networks = list(config.keys())[1:] + + # + # Args + # + parser = argparse.ArgumentParser() + parser.add_argument("--network", default='bike-sharing', type=str, choices=networks, help="Network name.") + args = parser.parse_args() + # + network = args.network + # + settings = config[network] + folder = settings.get('folder') + + # Files + rGfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) + rBfile = 'networks/{folder:s}/backbone.graphml'.format(folder=folder) + wGstats = 'networks/{folder:s}/components-stats.csv'.format(folder=folder) + + # Load graph + G = nx.read_graphml(rGfile) + + LSCC = G.subgraph(max(nx.strongly_connected_components(G), key=len)) + + # Load backbone + B = nx.read_graphml(rBfile) + + nEmLSCC = 0 + for u, v in B.edges(): + if LSCC.has_edge(u, v): + nEmLSCC += 1 + + # to Result Series + sR = pd.Series({ + 'n-nodes': G.number_of_nodes(), + 'n-edges': G.number_of_edges(), + # Metric + 'n-edges-metric': B.number_of_edges(), + # LSCC + 'n-nodes-lscc': LSCC.number_of_nodes(), + 'n-edges-lscc': LSCC.number_of_edges(), + # Metric + 'n-edges-metric-lscc': nEmLSCC, + }, name=network, dtype='object') + + sR.to_csv(wGstats) \ No newline at end of file diff --git a/README.md b/README.md index 8d73826..b4788c3 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,11 @@ Source codes for the Directed Distance Backbone project. +The considered networks have edge attributes 'distance' by construction. + ### Scripts functionalities: | Starts with | Functionality | |-------------|-------------------------| | 0 | Specific model measures | | 1 | All models analysis | -| 2 | Undirected analysis | \ No newline at end of file +| 2 | Undirected analysis | diff --git a/networks.ini b/networks.ini index 01bf385..640a1c8 100644 --- a/networks.ini +++ b/networks.ini @@ -2,80 +2,80 @@ [business-faculty] folder = academic_hiring/business -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [cs-faculty] folder = academic_hiring/computer_science -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [history-faculty] folder = academic_hiring/history -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [caviar-proj] folder = caviar_proj -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [celegans-her] folder = celegans/hermaphrodite -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [celegans-male] folder = celegans/male -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [colombia-calls] folder = colombia_social/calls -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [colombia-mobility] folder = colombia_social/mobility -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [mobility-manizales] folder = mobility/manizales -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [mobility-medellin] folder = mobility/medellin -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [tennis-loss] folder = tennis_losses -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [yeast-grn] folder = yeast_grn -weight-type = proximity -weight-attr = weight +weight-type = distance +weight-attr = distance [bike-sharing] folder = bike-sharing weight-type = distance -weight-attr = avg-trip-duration +weight-attr = distance [giraffe] @@ -93,7 +93,7 @@ weight-attr = distance [phone-calls] folder = phone-calls weight-type = distance -weight-attr = avg-call-duration +weight-attr = distance [us-airports] @@ -114,7 +114,9 @@ weight-type = distance weight-attr = distance -[water-pipes] -folder = water-pipes +[us-weblinks] +folder = weblinks_us weight-type = distance -weight-attr = distance \ No newline at end of file +weight-attr = distance + + diff --git a/networks/academic_hiring/business/components-stats.csv b/networks/academic_hiring/business/components-stats.csv new file mode 100644 index 0000000..3af06de --- /dev/null +++ b/networks/academic_hiring/business/components-stats.csv @@ -0,0 +1,7 @@ +,business-faculty +n-nodes,113 +n-edges,3432 +n-edges-metric,1204 +n-nodes-lscc,94 +n-edges-lscc,2842 +n-edges-metric-lscc,1038 diff --git a/networks/academic_hiring/business/distortion-stats.csv b/networks/academic_hiring/business/distortion-stats.csv index 9b104f2..2ca9168 100644 --- a/networks/academic_hiring/business/distortion-stats.csv +++ b/networks/academic_hiring/business/distortion-stats.csv @@ -1,7 +1,7 @@ ,business-faculty -avg-metric-distrotion,1.8417604162738177 -std-metric-distrotion,0.8701525542567358 -med-metric-distrotion,1.5559188690842038 -avg-ultrametric-distrotion,1.8421666977235764 -std-ultrametric-distrotion,0.49975154308446146 -med-ultrametric-distrotion,1.7505810736026564 +avg-metric-distrotion,2.4711172793382956 +std-metric-distrotion,1.580389775275598 +med-metric-distrotion,1.9847995251912423 +avg-ultrametric-distrotion,1.8372344580535185 +std-ultrametric-distrotion,0.5361094982557445 +med-ultrametric-distrotion,1.7977272727272724 diff --git a/networks/academic_hiring/business/network-stats.csv b/networks/academic_hiring/business/network-stats.csv index ae7445d..799f588 100644 --- a/networks/academic_hiring/business/network-stats.csv +++ b/networks/academic_hiring/business/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,113 n-edges,3432 density,0.27117572692793934 -n-edges-metric,1565 -n-edges-ultrametric,638 -%-edges-metric,0.456002331002331 -%-edges-ultrametric,0.1858974358974359 -%-redundancy-metric,0.543997668997669 -%-redundancy-ultrametric,0.8141025641025641 -%-edges-ultrametric/metric,0.40766773162939296 +n-edges-metric,1204 +n-edges-ultrametric,335 +%-edges-metric,0.3508158508158508 +%-edges-ultrametric,0.09761072261072261 +%-redundancy-metric,0.6491841491841492 +%-redundancy-ultrametric,0.9023892773892774 +%-edges-ultrametric/metric,0.2782392026578073 diff --git a/networks/academic_hiring/computer_science/components-stats.csv b/networks/academic_hiring/computer_science/components-stats.csv new file mode 100644 index 0000000..17bf804 --- /dev/null +++ b/networks/academic_hiring/computer_science/components-stats.csv @@ -0,0 +1,7 @@ +,cs-faculty +n-nodes,206 +n-edges,2929 +n-edges-metric,1508 +n-nodes-lscc,167 +n-edges-lscc,2384 +n-edges-metric-lscc,1260 diff --git a/networks/academic_hiring/computer_science/distortion-stats.csv b/networks/academic_hiring/computer_science/distortion-stats.csv index 4135c63..3aebe35 100644 --- a/networks/academic_hiring/computer_science/distortion-stats.csv +++ b/networks/academic_hiring/computer_science/distortion-stats.csv @@ -1,7 +1,7 @@ ,cs-faculty -avg-metric-distrotion,1.4313423583624842 -std-metric-distrotion,0.5212111045943651 -med-metric-distrotion,1.2773205382146027 -avg-ultrametric-distrotion,1.919797245410675 -std-ultrametric-distrotion,0.3434775101932094 -med-ultrametric-distrotion,2.0004011231448056 +avg-metric-distrotion,2.2202344040987034 +std-metric-distrotion,1.4373428666614874 +med-metric-distrotion,1.74375 +avg-ultrametric-distrotion,1.9527656123892012 +std-ultrametric-distrotion,0.6084173541593506 +med-ultrametric-distrotion,1.9529346622369879 diff --git a/networks/academic_hiring/computer_science/network-stats.csv b/networks/academic_hiring/computer_science/network-stats.csv index 22a7653..8b25f79 100644 --- a/networks/academic_hiring/computer_science/network-stats.csv +++ b/networks/academic_hiring/computer_science/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,206 n-edges,2929 density,0.06935827610703292 -n-edges-metric,2149 -n-edges-ultrametric,1554 -%-edges-metric,0.7336975076818026 -%-edges-ultrametric,0.5305565039262546 -%-redundancy-metric,0.26630249231819736 -%-redundancy-ultrametric,0.46944349607374536 -%-edges-ultrametric/metric,0.7231270358306189 +n-edges-metric,1508 +n-edges-ultrametric,664 +%-edges-metric,0.5148514851485149 +%-edges-ultrametric,0.22669853192215772 +%-redundancy-metric,0.48514851485148514 +%-redundancy-ultrametric,0.7733014680778423 +%-edges-ultrametric/metric,0.4403183023872679 diff --git a/networks/academic_hiring/history/components-stats.csv b/networks/academic_hiring/history/components-stats.csv new file mode 100644 index 0000000..38ab415 --- /dev/null +++ b/networks/academic_hiring/history/components-stats.csv @@ -0,0 +1,7 @@ +,history-faculty +n-nodes,145 +n-edges,2428 +n-edges-metric,1006 +n-nodes-lscc,116 +n-edges-lscc,1897 +n-edges-metric-lscc,816 diff --git a/networks/academic_hiring/history/distortion-stats.csv b/networks/academic_hiring/history/distortion-stats.csv index 3b079be..945d967 100644 --- a/networks/academic_hiring/history/distortion-stats.csv +++ b/networks/academic_hiring/history/distortion-stats.csv @@ -1,7 +1,7 @@ ,history-faculty -avg-metric-distrotion,1.5559455725216669 -std-metric-distrotion,0.5811976176560245 -med-metric-distrotion,1.364675678928156 -avg-ultrametric-distrotion,1.701464140510005 -std-ultrametric-distrotion,0.36609771219019227 -med-ultrametric-distrotion,1.5003307607497243 +avg-metric-distrotion,2.47750378353155 +std-metric-distrotion,1.4141477302762964 +med-metric-distrotion,1.9434998587677366 +avg-ultrametric-distrotion,1.832526494252117 +std-ultrametric-distrotion,0.5194322232735079 +med-ultrametric-distrotion,1.7207792207792207 diff --git a/networks/academic_hiring/history/network-stats.csv b/networks/academic_hiring/history/network-stats.csv index 0e3ad35..8b72a06 100644 --- a/networks/academic_hiring/history/network-stats.csv +++ b/networks/academic_hiring/history/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,145 n-edges,2428 density,0.11628352490421456 -n-edges-metric,1473 -n-edges-ultrametric,1120 -%-edges-metric,0.60667215815486 -%-edges-ultrametric,0.4612850082372323 -%-redundancy-metric,0.39332784184514 -%-redundancy-ultrametric,0.5387149917627677 -%-edges-ultrametric/metric,0.7603530210454854 +n-edges-metric,1006 +n-edges-ultrametric,534 +%-edges-metric,0.414332784184514 +%-edges-ultrametric,0.21993410214168038 +%-redundancy-metric,0.585667215815486 +%-redundancy-ultrametric,0.7800658978583196 +%-edges-ultrametric/metric,0.5308151093439363 diff --git a/networks/bike-sharing/components-stats.csv b/networks/bike-sharing/components-stats.csv new file mode 100644 index 0000000..c9189a2 --- /dev/null +++ b/networks/bike-sharing/components-stats.csv @@ -0,0 +1,7 @@ +,bike-sharing +n-nodes,725 +n-edges,53118 +n-edges-metric,31622 +n-nodes-lscc,723 +n-edges-lscc,53115 +n-edges-metric-lscc,31619 diff --git a/networks/bike-sharing/distortion-stats.csv b/networks/bike-sharing/distortion-stats.csv index 9aa70a1..58936ae 100644 --- a/networks/bike-sharing/distortion-stats.csv +++ b/networks/bike-sharing/distortion-stats.csv @@ -3,5 +3,5 @@ avg-metric-distrotion,2.0641451556224766 std-metric-distrotion,5.746482376572031 med-metric-distrotion,1.2679001386170317 avg-ultrametric-distrotion,2.2656642639793887 -std-ultrametric-distrotion,0.8443258962297594 +std-ultrametric-distrotion,0.8443258962297593 med-ultrametric-distrotion,2.101589239008594 diff --git a/networks/caviar_proj/components-stats.csv b/networks/caviar_proj/components-stats.csv new file mode 100644 index 0000000..727b746 --- /dev/null +++ b/networks/caviar_proj/components-stats.csv @@ -0,0 +1,7 @@ +,caviar-proj +n-nodes,110 +n-edges,295 +n-edges-metric,208 +n-nodes-lscc,66 +n-edges-lscc,242 +n-edges-metric-lscc,160 diff --git a/networks/caviar_proj/distortion-stats.csv b/networks/caviar_proj/distortion-stats.csv index 3326164..0572657 100644 --- a/networks/caviar_proj/distortion-stats.csv +++ b/networks/caviar_proj/distortion-stats.csv @@ -1,7 +1,7 @@ ,caviar-proj -avg-metric-distrotion,12.303903201374151 -std-metric-distrotion,24.08885358639796 -med-metric-distrotion,5.1201119171412195 -avg-ultrametric-distrotion,1.1769867110300105 -std-ultrametric-distrotion,0.09952798505297794 -med-ultrametric-distrotion,1.1463308727746417 +avg-metric-distrotion,9.15718196706913 +std-metric-distrotion,11.72213843956718 +med-metric-distrotion,4.067175572519084 +avg-ultrametric-distrotion,1.4989875047551156 +std-ultrametric-distrotion,0.43815551328962954 +med-ultrametric-distrotion,1.4417112299465242 diff --git a/networks/caviar_proj/network-stats.csv b/networks/caviar_proj/network-stats.csv index 7295c80..880df61 100644 --- a/networks/caviar_proj/network-stats.csv +++ b/networks/caviar_proj/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,110 n-edges,295 density,0.024603836530442035 -n-edges-metric,197 -n-edges-ultrametric,192 -%-edges-metric,0.6677966101694915 -%-edges-ultrametric,0.6508474576271186 -%-redundancy-metric,0.33220338983050846 -%-redundancy-ultrametric,0.3491525423728814 -%-edges-ultrametric/metric,0.9746192893401014 +n-edges-metric,208 +n-edges-ultrametric,191 +%-edges-metric,0.7050847457627119 +%-edges-ultrametric,0.6474576271186441 +%-redundancy-metric,0.29491525423728815 +%-redundancy-ultrametric,0.3525423728813559 +%-edges-ultrametric/metric,0.9182692307692308 diff --git a/networks/celegans/README.md b/networks/celegans/README.md index fc9433b..49dba63 100644 --- a/networks/celegans/README.md +++ b/networks/celegans/README.md @@ -6,7 +6,6 @@ Reference: Cook et al., "Whole-animal connectomes of both Caenorhabditis elegans Files used: - `SI 2 Synapse adjacency matrices.xlsx`: data - The C. elegans connectome has two different types of connections. The gap junctions, which are symmetric, and the pre-post synapitc cell interactions, which are assymetric. Here we consider the former, and also distinguish the hermaphrodite and the male sex. Edge weight is the number of synapses between cells relative to the total number of synapses. Both networks contains multiple weakly connected components with the largest one comparising approximately 69% (64%) of the network in the case of the hermaphrodite (male) sex. diff --git a/networks/celegans/hermaphrodite/components-stats.csv b/networks/celegans/hermaphrodite/components-stats.csv new file mode 100644 index 0000000..3fc11d0 --- /dev/null +++ b/networks/celegans/hermaphrodite/components-stats.csv @@ -0,0 +1,7 @@ +,celegans-her +n-nodes,313 +n-edges,3500 +n-edges-metric,1949 +n-nodes-lscc,249 +n-edges-lscc,3046 +n-edges-metric-lscc,1685 diff --git a/networks/celegans/hermaphrodite/distortion-stats.csv b/networks/celegans/hermaphrodite/distortion-stats.csv index 22c4491..43efb30 100644 --- a/networks/celegans/hermaphrodite/distortion-stats.csv +++ b/networks/celegans/hermaphrodite/distortion-stats.csv @@ -1,7 +1,7 @@ ,celegans-her -avg-metric-distrotion,1.95588063043959 -std-metric-distrotion,1.1414160337694403 -med-metric-distrotion,1.614539364744017 -avg-ultrametric-distrotion,1.9689462272175715 -std-ultrametric-distrotion,0.6678309885158372 -med-ultrametric-distrotion,1.7150153217568949 +avg-metric-distrotion,2.1778130554853674 +std-metric-distrotion,1.488375519695493 +med-metric-distrotion,1.7408695652173913 +avg-ultrametric-distrotion,1.8737551458224337 +std-ultrametric-distrotion,0.7352574076141358 +med-ultrametric-distrotion,1.6490740740740741 diff --git a/networks/celegans/hermaphrodite/network-stats.csv b/networks/celegans/hermaphrodite/network-stats.csv index 083b61d..3ea6768 100644 --- a/networks/celegans/hermaphrodite/network-stats.csv +++ b/networks/celegans/hermaphrodite/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,313 n-edges,3500 density,0.03584009175063488 -n-edges-metric,2036 -n-edges-ultrametric,1153 -%-edges-metric,0.5817142857142857 -%-edges-ultrametric,0.3294285714285714 -%-redundancy-metric,0.41828571428571426 -%-redundancy-ultrametric,0.6705714285714286 -%-edges-ultrametric/metric,0.5663064833005893 +n-edges-metric,1949 +n-edges-ultrametric,937 +%-edges-metric,0.5568571428571428 +%-edges-ultrametric,0.26771428571428574 +%-redundancy-metric,0.44314285714285717 +%-redundancy-ultrametric,0.7322857142857142 +%-edges-ultrametric/metric,0.4807593637762956 diff --git a/networks/celegans/male/components-stats.csv b/networks/celegans/male/components-stats.csv new file mode 100644 index 0000000..5f8d8d8 --- /dev/null +++ b/networks/celegans/male/components-stats.csv @@ -0,0 +1,7 @@ +,celegans-male +n-nodes,328 +n-edges,3474 +n-edges-metric,1876 +n-nodes-lscc,289 +n-edges-lscc,3206 +n-edges-metric-lscc,1713 diff --git a/networks/celegans/male/distortion-stats.csv b/networks/celegans/male/distortion-stats.csv index 768bcb9..39fac76 100644 --- a/networks/celegans/male/distortion-stats.csv +++ b/networks/celegans/male/distortion-stats.csv @@ -1,7 +1,7 @@ ,celegans-male -avg-metric-distrotion,2.174823586114673 -std-metric-distrotion,1.2577969506447333 -med-metric-distrotion,1.7830454326057597 -avg-ultrametric-distrotion,2.0103309980406845 -std-ultrametric-distrotion,0.7861492489681112 -med-ultrametric-distrotion,2.0001587301587302 +avg-metric-distrotion,2.679056669037608 +std-metric-distrotion,1.977359626463165 +med-metric-distrotion,2.0560125342734037 +avg-ultrametric-distrotion,1.836252580334619 +std-ultrametric-distrotion,0.692744013193066 +med-ultrametric-distrotion,1.652475845410628 diff --git a/networks/celegans/male/network-stats.csv b/networks/celegans/male/network-stats.csv index 2bf9daa..6eb1e9b 100644 --- a/networks/celegans/male/network-stats.csv +++ b/networks/celegans/male/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,328 n-edges,3474 density,0.03238979637502797 -n-edges-metric,1908 -n-edges-ultrametric,1058 -%-edges-metric,0.5492227979274611 -%-edges-ultrametric,0.3045480713874496 -%-redundancy-metric,0.4507772020725389 -%-redundancy-ultrametric,0.6954519286125505 -%-edges-ultrametric/metric,0.5545073375262055 +n-edges-metric,1876 +n-edges-ultrametric,962 +%-edges-metric,0.5400115141047783 +%-edges-ultrametric,0.27691421991940124 +%-redundancy-metric,0.4599884858952217 +%-redundancy-ultrametric,0.7230857800805988 +%-edges-ultrametric/metric,0.5127931769722814 diff --git a/networks/colombia_social/calls/components-stats.csv b/networks/colombia_social/calls/components-stats.csv new file mode 100644 index 0000000..03d046a --- /dev/null +++ b/networks/colombia_social/calls/components-stats.csv @@ -0,0 +1,7 @@ +,colombia-calls +n-nodes,863 +n-edges,438484 +n-edges-metric,11407 +n-nodes-lscc,863 +n-edges-lscc,438484 +n-edges-metric-lscc,11407 diff --git a/networks/colombia_social/calls/distortion-stats.csv b/networks/colombia_social/calls/distortion-stats.csv index 01742de..828f3ef 100644 --- a/networks/colombia_social/calls/distortion-stats.csv +++ b/networks/colombia_social/calls/distortion-stats.csv @@ -1,7 +1,7 @@ ,colombia-calls -avg-metric-distrotion,301.0222927319763 -std-metric-distrotion,530.7021003980509 -med-metric-distrotion,120.82286357924608 -avg-ultrametric-distrotion,1.2770780163452997 -std-ultrametric-distrotion,0.2497648607723491 -med-ultrametric-distrotion,1.205631261877681 +avg-metric-distrotion,57.47057510114324 +std-metric-distrotion,145.37774293019044 +med-metric-distrotion,18.612675345787377 +avg-ultrametric-distrotion,1.6447399544714127 +std-ultrametric-distrotion,0.6065223885636564 +med-ultrametric-distrotion,1.472898064394248 diff --git a/networks/colombia_social/calls/network-stats.csv b/networks/colombia_social/calls/network-stats.csv index a561974..6b58b00 100644 --- a/networks/colombia_social/calls/network-stats.csv +++ b/networks/colombia_social/calls/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,863 n-edges,438484 density,0.5894346866405165 -n-edges-metric,2259 -n-edges-ultrametric,1746 -%-edges-metric,0.005151841344267978 -%-edges-ultrametric,0.003981901278039792 -%-redundancy-metric,0.9948481586557321 -%-redundancy-ultrametric,0.9960180987219602 -%-edges-ultrametric/metric,0.7729083665338646 +n-edges-metric,11407 +n-edges-ultrametric,3903 +%-edges-metric,0.026014632232875087 +%-edges-ultrametric,0.008901122960016786 +%-redundancy-metric,0.973985367767125 +%-redundancy-ultrametric,0.9910988770399832 +%-edges-ultrametric/metric,0.34215832383624095 diff --git a/networks/colombia_social/mobility/components-stats.csv b/networks/colombia_social/mobility/components-stats.csv new file mode 100644 index 0000000..e49a62a --- /dev/null +++ b/networks/colombia_social/mobility/components-stats.csv @@ -0,0 +1,7 @@ +,colombia-mobility +n-nodes,863 +n-edges,173857 +n-edges-metric,2971 +n-nodes-lscc,863 +n-edges-lscc,173857 +n-edges-metric-lscc,2971 diff --git a/networks/colombia_social/mobility/distortion-stats.csv b/networks/colombia_social/mobility/distortion-stats.csv index 4c42db3..ba0972f 100644 --- a/networks/colombia_social/mobility/distortion-stats.csv +++ b/networks/colombia_social/mobility/distortion-stats.csv @@ -1,7 +1,7 @@ ,colombia-mobility -avg-metric-distrotion,1820.2025896150562 -std-metric-distrotion,2472.0253138745315 -med-metric-distrotion,885.8200616884867 -avg-ultrametric-distrotion,1.4622926742178406 -std-ultrametric-distrotion,0.43348096030316424 -med-ultrametric-distrotion,1.325643948313469 +avg-metric-distrotion,893.4523910433584 +std-metric-distrotion,2534.0900110208036 +med-metric-distrotion,272.9416451435882 +avg-ultrametric-distrotion,1.6838892414737063 +std-ultrametric-distrotion,0.8659094276832128 +med-ultrametric-distrotion,1.408221397357254 diff --git a/networks/colombia_social/mobility/network-stats.csv b/networks/colombia_social/mobility/network-stats.csv index ff0de70..a5b2a6d 100644 --- a/networks/colombia_social/mobility/network-stats.csv +++ b/networks/colombia_social/mobility/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,863 n-edges,173857 density,0.23370829110129507 -n-edges-metric,2535 -n-edges-ultrametric,1727 -%-edges-metric,0.01458094871072203 -%-edges-ultrametric,0.009933451054602346 -%-redundancy-metric,0.985419051289278 -%-redundancy-ultrametric,0.9900665489453977 -%-edges-ultrametric/metric,0.6812623274161737 +n-edges-metric,2971 +n-edges-ultrametric,2115 +%-edges-metric,0.017088756851895523 +%-edges-ultrametric,0.012165170226105363 +%-redundancy-metric,0.9829112431481045 +%-redundancy-ultrametric,0.9878348297738946 +%-edges-ultrametric/metric,0.7118815213732751 diff --git a/networks/comorbidity/components-stats.csv b/networks/comorbidity/components-stats.csv new file mode 100644 index 0000000..eaad82a --- /dev/null +++ b/networks/comorbidity/components-stats.csv @@ -0,0 +1,7 @@ +,comorbidity +n-nodes,95 +n-edges,8930 +n-edges-metric,4236 +n-nodes-lscc,95 +n-edges-lscc,8930 +n-edges-metric-lscc,4236 diff --git a/networks/giraffe/components-stats.csv b/networks/giraffe/components-stats.csv new file mode 100644 index 0000000..7eff7dd --- /dev/null +++ b/networks/giraffe/components-stats.csv @@ -0,0 +1,7 @@ +,giraffe +n-nodes,6 +n-edges,30 +n-edges-metric,23 +n-nodes-lscc,6 +n-edges-lscc,30 +n-edges-metric-lscc,23 diff --git a/networks/giraffe/distortion-stats.csv b/networks/giraffe/distortion-stats.csv index 93298cf..c8c3ffa 100644 --- a/networks/giraffe/distortion-stats.csv +++ b/networks/giraffe/distortion-stats.csv @@ -1,7 +1,7 @@ ,giraffe -avg-metric-distrotion,1.465337597719577 -std-metric-distrotion,0.4390612512920237 -med-metric-distrotion,1.367236742904062 -avg-ultrametric-distrotion,1.3714221225553633 -std-ultrametric-distrotion,0.24759731942029223 -med-ultrametric-distrotion,1.3013617145913456 +avg-metric-distrotion,1.2960057452108402 +std-metric-distrotion,0.37148902016580027 +med-metric-distrotion,1.1218918698130869 +avg-ultrametric-distrotion,1.4646474300944707 +std-ultrametric-distrotion,0.3341136697792818 +med-ultrametric-distrotion,1.4018752160387138 diff --git a/networks/giraffe/network-stats.csv b/networks/giraffe/network-stats.csv index ab960ef..c3c3f82 100644 --- a/networks/giraffe/network-stats.csv +++ b/networks/giraffe/network-stats.csv @@ -3,9 +3,9 @@ n-nodes,6 n-edges,30 density,1.0 n-edges-metric,23 -n-edges-ultrametric,9 +n-edges-ultrametric,10 %-edges-metric,0.7666666666666667 -%-edges-ultrametric,0.3 +%-edges-ultrametric,0.3333333333333333 %-redundancy-metric,0.23333333333333328 -%-redundancy-ultrametric,0.7 -%-edges-ultrametric/metric,0.3913043478260869 +%-redundancy-ultrametric,0.6666666666666667 +%-edges-ultrametric/metric,0.4347826086956521 diff --git a/networks/host-pathogen/components-stats.csv b/networks/host-pathogen/components-stats.csv new file mode 100644 index 0000000..2480824 --- /dev/null +++ b/networks/host-pathogen/components-stats.csv @@ -0,0 +1,7 @@ +,host-pathogen +n-nodes,10578 +n-edges,18529 +n-edges-metric,18503 +n-nodes-lscc,1 +n-edges-lscc,0 +n-edges-metric-lscc,0 diff --git a/networks/host-pathogen/distortion-stats.csv b/networks/host-pathogen/distortion-stats.csv index 596638c..7843f84 100644 --- a/networks/host-pathogen/distortion-stats.csv +++ b/networks/host-pathogen/distortion-stats.csv @@ -1,7 +1,7 @@ ,host-pathogen -avg-metric-distrotion,15.746708631086898 -std-metric-distrotion,52.66714613659394 -med-metric-distrotion,3.754556157267433 -avg-ultrametric-distrotion,1.1836126570978225 -std-ultrametric-distrotion,0.21355185024850043 -med-ultrametric-distrotion,1.1836126570978225 +avg-metric-distrotion,7.006620804856615 +std-metric-distrotion,17.476809458728397 +med-metric-distrotion,2.044827586206897 +avg-ultrametric-distrotion,1.5556756756756756 +std-ultrametric-distrotion,0.2216555309882 +med-ultrametric-distrotion,1.6733333333333333 diff --git a/networks/host-pathogen/network-stats.csv b/networks/host-pathogen/network-stats.csv index a0bc58d..03af774 100644 --- a/networks/host-pathogen/network-stats.csv +++ b/networks/host-pathogen/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,10578 n-edges,18529 density,0.00016560975484625947 -n-edges-metric,18431 -n-edges-ultrametric,18429 -%-edges-metric,0.994710993577635 -%-edges-ultrametric,0.9946030546710561 -%-redundancy-metric,0.005289006422364961 -%-redundancy-ultrametric,0.0053969453289438585 -%-edges-ultrametric/metric,0.9998914871683576 +n-edges-metric,18503 +n-edges-ultrametric,18500 +%-edges-metric,0.9985967942144746 +%-edges-ultrametric,0.9984348858546063 +%-redundancy-metric,0.001403205785525441 +%-redundancy-ultrametric,0.0015651141453937312 +%-edges-ultrametric/metric,0.9998378641301411 diff --git a/networks/mobility/manizales/components-stats.csv b/networks/mobility/manizales/components-stats.csv new file mode 100644 index 0000000..c709fa0 --- /dev/null +++ b/networks/mobility/manizales/components-stats.csv @@ -0,0 +1,7 @@ +,mobility-manizales +n-nodes,57 +n-edges,2518 +n-edges-metric,671 +n-nodes-lscc,57 +n-edges-lscc,2518 +n-edges-metric-lscc,671 diff --git a/networks/mobility/manizales/distortion-stats.csv b/networks/mobility/manizales/distortion-stats.csv index 842963f..31ec7ef 100644 --- a/networks/mobility/manizales/distortion-stats.csv +++ b/networks/mobility/manizales/distortion-stats.csv @@ -1,7 +1,7 @@ ,mobility-manizales -avg-metric-distrotion,7.382533330580546 -std-metric-distrotion,6.4066607030629985 -med-metric-distrotion,5.044764455351957 -avg-ultrametric-distrotion,1.5196327721286316 -std-ultrametric-distrotion,0.39041882955255497 -med-ultrametric-distrotion,1.4449410090766284 +avg-metric-distrotion,3.10404732532493 +std-metric-distrotion,2.431873629408389 +med-metric-distrotion,2.285196874838309 +avg-ultrametric-distrotion,1.711458126647016 +std-ultrametric-distrotion,0.44409418888326574 +med-ultrametric-distrotion,1.6395005675368899 diff --git a/networks/mobility/manizales/network-stats.csv b/networks/mobility/manizales/network-stats.csv index 0fb288e..2f6ff9e 100644 --- a/networks/mobility/manizales/network-stats.csv +++ b/networks/mobility/manizales/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,57 n-edges,2518 density,0.7888471177944862 -n-edges-metric,213 -n-edges-ultrametric,118 -%-edges-metric,0.0845909451945989 -%-edges-ultrametric,0.04686258935663225 -%-redundancy-metric,0.9154090548054011 -%-redundancy-ultrametric,0.9531374106433678 -%-edges-ultrametric/metric,0.5539906103286385 +n-edges-metric,671 +n-edges-ultrametric,193 +%-edges-metric,0.2664813343923749 +%-edges-ultrametric,0.07664813343923749 +%-redundancy-metric,0.7335186656076251 +%-redundancy-ultrametric,0.9233518665607625 +%-edges-ultrametric/metric,0.2876304023845007 diff --git a/networks/mobility/medellin/components-stats.csv b/networks/mobility/medellin/components-stats.csv new file mode 100644 index 0000000..ba37486 --- /dev/null +++ b/networks/mobility/medellin/components-stats.csv @@ -0,0 +1,7 @@ +,mobility-medellin +n-nodes,413 +n-edges,33884 +n-edges-metric,8360 +n-nodes-lscc,413 +n-edges-lscc,33884 +n-edges-metric-lscc,8360 diff --git a/networks/mobility/medellin/distortion-stats.csv b/networks/mobility/medellin/distortion-stats.csv index 3d0605e..46b43ad 100644 --- a/networks/mobility/medellin/distortion-stats.csv +++ b/networks/mobility/medellin/distortion-stats.csv @@ -1,7 +1,7 @@ ,mobility-medellin -avg-metric-distrotion,3.7732374159991826 -std-metric-distrotion,2.58633322574124 -med-metric-distrotion,3.1537910562769813 -avg-ultrametric-distrotion,1.7624647721526723 -std-ultrametric-distrotion,0.5033429769462727 -med-ultrametric-distrotion,1.666692580988735 +avg-metric-distrotion,3.1622965882933673 +std-metric-distrotion,2.9929298281800114 +med-metric-distrotion,2.3756772882352553 +avg-ultrametric-distrotion,2.193308219577776 +std-ultrametric-distrotion,0.8543245553926707 +med-ultrametric-distrotion,2.0317460317460316 diff --git a/networks/mobility/medellin/network-stats.csv b/networks/mobility/medellin/network-stats.csv index e6f2a33..4e3fc75 100644 --- a/networks/mobility/medellin/network-stats.csv +++ b/networks/mobility/medellin/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,413 n-edges,33884 density,0.1991349114929829 -n-edges-metric,3362 -n-edges-ultrametric,1048 -%-edges-metric,0.09922087120764962 -%-edges-ultrametric,0.030929052059969306 -%-redundancy-metric,0.9007791287923503 -%-redundancy-ultrametric,0.9690709479400307 -%-edges-ultrametric/metric,0.31171921475312314 +n-edges-metric,8360 +n-edges-ultrametric,1844 +%-edges-metric,0.24672411757761775 +%-edges-ultrametric,0.05442096564750325 +%-redundancy-metric,0.7532758824223822 +%-redundancy-ultrametric,0.9455790343524968 +%-edges-ultrametric/metric,0.22057416267942584 diff --git a/networks/phone-calls/README.md b/networks/phone-calls/README.md index 298044c..a9e917a 100644 --- a/networks/phone-calls/README.md +++ b/networks/phone-calls/README.md @@ -5,4 +5,5 @@ Source: 0) and calculate the average call duration between users, from the caller to the callee. +This network measures the duration (in seconds) of phone calls collected during the Copenhagen Networks Study. +We consider only answered calls (duration >0) and calculate the average call duration between users, from the caller to the callee. diff --git a/networks/phone-calls/components-stats.csv b/networks/phone-calls/components-stats.csv new file mode 100644 index 0000000..1850044 --- /dev/null +++ b/networks/phone-calls/components-stats.csv @@ -0,0 +1,7 @@ +,phone-calls +n-nodes,322 +n-edges,609 +n-edges-metric,558 +n-nodes-lscc,114 +n-edges-lscc,274 +n-edges-metric-lscc,242 diff --git a/networks/tennis_losses/components-stats.csv b/networks/tennis_losses/components-stats.csv new file mode 100644 index 0000000..9cd3809 --- /dev/null +++ b/networks/tennis_losses/components-stats.csv @@ -0,0 +1,7 @@ +,tennis-loss +n-nodes,4245 +n-edges,101436 +n-edges-metric,60476 +n-nodes-lscc,2428 +n-edges-lscc,98102 +n-edges-metric-lscc,57142 diff --git a/networks/tennis_losses/distortion-stats.csv b/networks/tennis_losses/distortion-stats.csv index c3063be..8fe8eb3 100644 --- a/networks/tennis_losses/distortion-stats.csv +++ b/networks/tennis_losses/distortion-stats.csv @@ -1,7 +1,7 @@ ,tennis-loss -avg-metric-distrotion,1.603511869278301 -std-metric-distrotion,0.578379999534823 -med-metric-distrotion,1.440031508667256 -avg-ultrametric-distrotion,1.9112777254084488 -std-ultrametric-distrotion,0.41291702874323766 -med-ultrametric-distrotion,2.0000131811351594 +avg-metric-distrotion,1.657660299187473 +std-metric-distrotion,0.6365112324316072 +med-metric-distrotion,1.4749599996284433 +avg-ultrametric-distrotion,1.9961172719622648 +std-ultrametric-distrotion,0.7705697671646052 +med-ultrametric-distrotion,1.8181818181818181 diff --git a/networks/tennis_losses/network-stats.csv b/networks/tennis_losses/network-stats.csv index 90ffe84..e7da205 100644 --- a/networks/tennis_losses/network-stats.csv +++ b/networks/tennis_losses/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,4245 n-edges,101436 density,0.005630397351655049 -n-edges-metric,44772 -n-edges-ultrametric,21033 -%-edges-metric,0.44138175795575535 -%-edges-ultrametric,0.2073524192594345 -%-redundancy-metric,0.5586182420442447 -%-redundancy-ultrametric,0.7926475807405655 -%-edges-ultrametric/metric,0.4697802197802198 +n-edges-metric,60476 +n-edges-ultrametric,24118 +%-edges-metric,0.5961985882724082 +%-edges-ultrametric,0.23776568476674947 +%-redundancy-metric,0.40380141172759176 +%-redundancy-ultrametric,0.7622343152332505 +%-edges-ultrametric/metric,0.39880283087505786 diff --git a/networks/us-airports-2006/components-stats.csv b/networks/us-airports-2006/components-stats.csv new file mode 100644 index 0000000..3a149a0 --- /dev/null +++ b/networks/us-airports-2006/components-stats.csv @@ -0,0 +1,7 @@ +,us-airports +n-nodes,1075 +n-edges,18906 +n-edges-metric,5186 +n-nodes-lscc,995 +n-edges-lscc,18820 +n-edges-metric-lscc,5102 diff --git a/networks/us-airports-2006/distortion-stats.csv b/networks/us-airports-2006/distortion-stats.csv index eef3e69..36069ca 100644 --- a/networks/us-airports-2006/distortion-stats.csv +++ b/networks/us-airports-2006/distortion-stats.csv @@ -1,7 +1,7 @@ ,us-airports -avg-metric-distrotion,279.62369536587715 -std-metric-distrotion,2089.5648450053404 -med-metric-distrotion,17.74398880165022 -avg-ultrametric-distrotion,1.5860719422697427 -std-ultrametric-distrotion,0.48867596020871645 -med-ultrametric-distrotion,1.4736143472021324 +avg-metric-distrotion,325.7879369492816 +std-metric-distrotion,2785.479453072874 +med-metric-distrotion,24.801390651294934 +avg-ultrametric-distrotion,1.5869752815140707 +std-ultrametric-distrotion,0.5025409384862389 +med-ultrametric-distrotion,1.4674968591560829 diff --git a/networks/us-airports-2006/network-stats.csv b/networks/us-airports-2006/network-stats.csv index a40c518..27c41c5 100644 --- a/networks/us-airports-2006/network-stats.csv +++ b/networks/us-airports-2006/network-stats.csv @@ -2,10 +2,10 @@ n-nodes,1075 n-edges,18906 density,0.01637521112121606 -n-edges-metric,5217 -n-edges-ultrametric,3592 -%-edges-metric,0.2759441447159632 -%-edges-ultrametric,0.1899925949434042 -%-redundancy-metric,0.7240558552840368 -%-redundancy-ultrametric,0.8100074050565957 -%-edges-ultrametric/metric,0.6885183055395822 +n-edges-metric,5186 +n-edges-ultrametric,3589 +%-edges-metric,0.27430445361260974 +%-edges-ultrametric,0.18983391515920872 +%-redundancy-metric,0.7256955463873902 +%-redundancy-ultrametric,0.8101660848407912 +%-edges-ultrametric/metric,0.692055534130351 diff --git a/networks/water-pipes/README.md b/networks/water-pipes/README.md deleted file mode 100644 index 0e45e5f..0000000 --- a/networks/water-pipes/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Water Pipes Network - -Source: Farmani, R., Savic, D.A., Walters, G.A.: Exnet benchmark problem for multi-objective optimization of large water systems. Modelling and control for participatory planning and managing water systems (2004) - -Files used: -- `exnet_pipes.txt`: data -- `exnet_junct.txt`: metadata - -A graph with nodes being pipe junctions and edge weights are the pipe length $d_{ij}$ connecting the junctions. diff --git a/networks/water-pipes/distortion-stats.csv b/networks/water-pipes/distortion-stats.csv deleted file mode 100644 index 323a151..0000000 --- a/networks/water-pipes/distortion-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,water-pipes -avg-metric-distrotion,1.1686634712062107 -std-metric-distrotion,0.19395754201687038 -med-metric-distrotion,1.075268817204301 -avg-ultrametric-distrotion,1.4523543941158101 -std-ultrametric-distrotion,0.45166392882915574 -med-ultrametric-distrotion,1.3461538461538463 diff --git a/networks/water-pipes/network-stats.csv b/networks/water-pipes/network-stats.csv deleted file mode 100644 index 8854ec2..0000000 --- a/networks/water-pipes/network-stats.csv +++ /dev/null @@ -1,11 +0,0 @@ -,water-pipes -n-nodes,1836 -n-edges,2351 -density,0.0006978207571251328 -n-edges-metric,2342 -n-edges-ultrametric,2253 -%-edges-metric,0.9961718417694598 -%-edges-ultrametric,0.9583156103785623 -%-redundancy-metric,0.0038281582305401685 -%-redundancy-ultrametric,0.04168438962143772 -%-edges-ultrametric/metric,0.96199829205807 diff --git a/networks/weblinks_us/network-stats.csv b/networks/weblinks_us/network-stats.csv new file mode 100644 index 0000000..574c764 --- /dev/null +++ b/networks/weblinks_us/network-stats.csv @@ -0,0 +1,11 @@ +,us-weblinks +n-nodes,42800 +n-edges,505476 +density,0.0002759453939551824 +n-edges-metric,185919 +n-edges-ultrametric,128223 +%-edges-metric,0.36780974764380503 +%-edges-ultrametric,0.2536678299266434 +%-redundancy-metric,0.632190252356195 +%-redundancy-ultrametric,0.7463321700733566 +%-edges-ultrametric/metric,0.6896713084730447 diff --git a/networks/yeast_grn/components-stats.csv b/networks/yeast_grn/components-stats.csv new file mode 100644 index 0000000..91b9713 --- /dev/null +++ b/networks/yeast_grn/components-stats.csv @@ -0,0 +1,7 @@ +,yeast-grn +n-nodes,6216 +n-edges,1666106 +n-edges-metric,106160 +n-nodes-lscc,1229 +n-edges-lscc,367432 +n-edges-metric-lscc,24333 diff --git a/utils.py b/utils.py index acb51bb..97c46ff 100644 --- a/utils.py +++ b/utils.py @@ -95,4 +95,103 @@ def fuzzy_reciprocity(G, weight='proximity'): cov -= pbar*(G[u][v][weight] - pbar) stdev += (G[u][v][weight] - pbar)*(G[u][v][weight] - pbar) - return cov/stdev \ No newline at end of file + return cov/stdev + +def venn3_sqr_diagram(Ne, Nb, Nc, Nbc, width=0.1, title=None): + + import matplotlib.patches as mpatches + import matplotlib.pyplot as plt + import numpy as np + + fig, ax = plt.subplots(figsize=(5, 10)) + fig.set_facecolor('tab:gray') + ax.set_facecolor('tab:gray') + + L1 = Nb/Ne + L2 = Nc/Ne + L3 = Nbc/Ne + + artist = [mpatches.Rectangle((0.0, 0.0), width, 1.0, color='b'), + mpatches.Rectangle((0.0, 0.0), width, L1, color='g'), + mpatches.Rectangle((0.0, L1-L3), width, L2, color='r', alpha=0.5)] + + for art in artist: + ax.add_artist(art) + + ax.text(0.5*width, 0.5*(L1-L3), Nb-Nbc, verticalalignment='center', horizontalalignment='center', color='w') + ax.text(0.5*width, (L1-L3)+0.5*L3, Nbc, verticalalignment='center', horizontalalignment='center', color='w') + ax.text(0.5*width, L1+0.5*(L2-L3), Nc-Nbc, verticalalignment='center', horizontalalignment='center', color='w') + ax.text(0.5*width, 0.5*(1+L1+L2-L3), Ne-(Nb+Nc-Nbc), verticalalignment='center', horizontalalignment='center', color='w') + + ax.text(1.01*width, 0.5*(L1-L3), 'Backbone WCC', verticalalignment='center', horizontalalignment='left', color='k') + ax.text(1.01*width, (L1-L3)+0.5*L3, 'Backbone LSCC', verticalalignment='center', horizontalalignment='left', color='k') + ax.text(1.01*width, L1+0.5*(L2-L3), 'Semi-metric LSCC', verticalalignment='center', horizontalalignment='left', color='k') + ax.text(1.01*width, 0.5*(1+L1+L2-L3), 'Semi-Metric WCC', verticalalignment='center', horizontalalignment='left', color='k') + + ax.set_title(title) + ax.set_xlim((0.0, 1.3*width)) + #ax.set_ylim((-pad, 0.5+pad)) + ax.set_axis_off() + + #plt.show() + plt.savefig(f'Figures/Components/{title}.png') + + +def plot_s_dist(data, folder): + + import matplotlib.pyplot as plt + import powerlaw + import pandas as pd + + ss = pd.Series(list(data), name='s-value') + + # Select only s-values + dfs = ss.loc[(ss > 1.0)].sort_values(ascending=False).to_frame() + xmin = dfs['s-value'].min() + xmin = 1 + fit = powerlaw.Fit(dfs['s-value'], xmin=xmin, estimate_discrete=False) + + alpha = fit.power_law.alpha + sigma = fit.power_law.sigma + print('Powerlaw: alpha:', alpha) + print('sigma:', sigma) + + # Compare + R, p = fit.distribution_compare('power_law', 'lognormal_positive') + print("R:", R, 'p-value', p) + + fig, ax = plt.subplots(figsize=(5, 4)) + + fit.plot_pdf(color='#d62728', linewidth=2, label='Empirical data', ax=ax) + + # + Rp = '$R = {R:.2f}$; $p = {p:.3f}$'.format(R=R, p=p) + ax.annotate(Rp, xy=(.03, .13), xycoords='axes fraction', color='black') + + if R > 0: + pw_goodness = '$\sigma = {sigma:.3f}$'.format(sigma=fit.power_law.sigma) + ax.annotate(pw_goodness, xy=(.03, .05), xycoords='axes fraction', color='#1f77b4') + else: + ln_goodness = '$\mu = {mu:.2f}; \sigma = {sigma:.3f}$'.format(mu=fit.lognormal_positive.mu, sigma=fit.lognormal_positive.sigma) + ax.annotate(ln_goodness, xy=(.03, .05), xycoords='axes fraction', color='#2ca02c') + # + pw_label = r'Power law fit' + ln_label = r'Lognormal fit' + + fit.power_law.plot_pdf(color='#aec7e8', linewidth=1, linestyle='--', label=pw_label, ax=ax) + fit.lognormal_positive.plot_pdf(color='#98df8a', linewidth=1, linestyle='--', label=ln_label, ax=ax) + + # + ax.set_title(r'Semi-metric edges ($s_{{ij}}>1)$' '\n' '{source:s}'.format(source=folder)) + ax.set_ylabel(r'$P(s_{ij} \geq x)$') + ax.set_xlabel(r'$s_{ij}$ frequency') + + ax.grid() + + ax.legend(loc='best') + + plt.tight_layout() + # plt.subplots_adjust(left=0.09, right=0.98, bottom=0.07, top=0.90, wspace=0, hspace=0.0) + #plt.savefig(wImgFile, dpi=150, bbox_inches='tight') # , pad_inches=0.05) + plt.savefig(f'{folder}.pdf', dpi=150, bbox_inches='tight') + #plt.show() \ No newline at end of file From 7020a9f36b55c57d00395bdde92b6f973ea1b975 Mon Sep 17 00:00:00 2001 From: fcphysics Date: Wed, 10 May 2023 08:31:12 -0400 Subject: [PATCH 02/12] Undirected Distance Analysis --- .gitignore | 3 +- 20-undirected-version.py | 26 ++++--- 21-calc-backbone.py | 4 +- 22-backbone-comparison.py | 3 +- 22-network-stats.py | 71 +++++++++++++++++++ .../business/undirected_networks-stats.csv | 5 ++ .../undirected_networks-stats.csv | 5 ++ .../history/undirected_networks-stats.csv | 5 ++ .../undirected_networks-stats.csv | 5 ++ .../caviar_proj/undirected_networks-stats.csv | 5 ++ .../undirected_networks-stats.csv | 5 ++ .../male/undirected_networks-stats.csv | 5 ++ .../calls/undirected_networks-stats.csv | 5 ++ .../mobility/undirected_networks-stats.csv | 5 ++ .../comorbidity/undirected_networks-stats.csv | 5 ++ .../giraffe/undirected_networks-stats.csv | 5 ++ .../undirected_networks-stats.csv | 5 ++ .../manizales/undirected_networks-stats.csv | 5 ++ .../medellin/undirected_networks-stats.csv | 5 ++ .../phone-calls/undirected_networks-stats.csv | 5 ++ .../undirected_networks-stats.csv | 5 ++ .../undirected_networks-stats.csv | 5 ++ .../weblinks_us/undirected_networks-stats.csv | 5 ++ .../yeast_grn/undirected_networks-stats.csv | 5 ++ 24 files changed, 185 insertions(+), 17 deletions(-) create mode 100644 22-network-stats.py create mode 100644 networks/academic_hiring/business/undirected_networks-stats.csv create mode 100644 networks/academic_hiring/computer_science/undirected_networks-stats.csv create mode 100644 networks/academic_hiring/history/undirected_networks-stats.csv create mode 100644 networks/bike-sharing/undirected_networks-stats.csv create mode 100644 networks/caviar_proj/undirected_networks-stats.csv create mode 100644 networks/celegans/hermaphrodite/undirected_networks-stats.csv create mode 100644 networks/celegans/male/undirected_networks-stats.csv create mode 100644 networks/colombia_social/calls/undirected_networks-stats.csv create mode 100644 networks/colombia_social/mobility/undirected_networks-stats.csv create mode 100644 networks/comorbidity/undirected_networks-stats.csv create mode 100644 networks/giraffe/undirected_networks-stats.csv create mode 100644 networks/host-pathogen/undirected_networks-stats.csv create mode 100644 networks/mobility/manizales/undirected_networks-stats.csv create mode 100644 networks/mobility/medellin/undirected_networks-stats.csv create mode 100644 networks/phone-calls/undirected_networks-stats.csv create mode 100644 networks/tennis_losses/undirected_networks-stats.csv create mode 100644 networks/us-airports-2006/undirected_networks-stats.csv create mode 100644 networks/weblinks_us/undirected_networks-stats.csv create mode 100644 networks/yeast_grn/undirected_networks-stats.csv diff --git a/.gitignore b/.gitignore index 31de609..653d0f7 100644 --- a/.gitignore +++ b/.gitignore @@ -12,9 +12,8 @@ networks/weblinks LOCAL/ networks/example.py *old/ -sanity_checks.ipynb +*.ipynb nohup.out -undirect* Summary/ # New stuff for now diff --git a/20-undirected-version.py b/20-undirected-version.py index 8794bc8..5ff4ee5 100644 --- a/20-undirected-version.py +++ b/20-undirected-version.py @@ -49,27 +49,31 @@ nx.set_edge_attributes(G, values=None, name='alpha') - U = {'min': nx.Graph(), 'max': nx.Graph(), 'avg': nx.Graph()} + U = {'min': nx.Graph(), 'max': nx.Graph(), 'avg': nx.Graph(), 'harm': nx.Graph()} for g in U.values(): g.add_nodes_from(G.nodes()) for u, v, w in G.edges(data=True): if w['alpha'] == None: G[u][v]['alpha'] = 0.0 - pij = w['proximity'] + din = G[u][v]['distance'] if G.has_edge(v, u): G[v][u]['alpha'] = 0.0 - pji = G[v][u]['proximity'] - pmin = min(pij, pji) - U['min'].add_edge(u, v, distance=prox2dist(pmin)) + dout = G[v][u]['distance'] + + U['min'].add_edge(u, v, distance=min(din, dout)) + U['max'].add_edge(u, v, distance=max(din, dout)) + U['avg'].add_edge(u, v, distance=0.5*(din + dout)) + + if (din + dout) == 0.0: + U['harm'].add_edge(u, v, distance=0.0) + else: + U['harm'].add_edge(u, v, distance=2*din*dout/(din + dout)) + else: - pji = 0 + U['min'].add_edge(u, v, distance=din) + U['harm'].add_edge(u, v, distance=2*din) - pmax = max(pij, pji) - pavg = 0.5*(pij+pji) - - U['max'].add_edge(u, v, distance=prox2dist(pmax)) - U['avg'].add_edge(u, v, distance=prox2dist(pavg)) #nx.write_graphml(U, wGraphml) pk.dump(U, open(wGraphml, 'wb')) diff --git a/21-calc-backbone.py b/21-calc-backbone.py index d7561cc..36a0336 100644 --- a/21-calc-backbone.py +++ b/21-calc-backbone.py @@ -57,9 +57,9 @@ G = pk.load(open(rGfile, 'rb')) # Dictionary of distortion distribution - distortion_dist = {'min': dict(), 'max': dict(), 'avg': dict()} + distortion_dist = {'min': dict(), 'max': dict(), 'avg': dict(), 'harm': dict()} - for type in ['min', 'max', 'avg']: + for type in ['min', 'max', 'avg', 'harm']: print(type) # # Metric computation diff --git a/22-backbone-comparison.py b/22-backbone-comparison.py index ddccbd8..bb4c160 100644 --- a/22-backbone-comparison.py +++ b/22-backbone-comparison.py @@ -47,8 +47,7 @@ for idx, network in enumerate(networks): print(network) - settings = config[network] - folder = settings.get('folder') + folder = config[network].get('folder') dfM.loc[idx, 'name'] = network dfU.loc[idx, 'name'] = network diff --git a/22-network-stats.py b/22-network-stats.py new file mode 100644 index 0000000..4fe8ca6 --- /dev/null +++ b/22-network-stats.py @@ -0,0 +1,71 @@ +# coding=utf-8 +# Author: Rion B Correia & Felipe Xavier Costa +# Date: Feb 22, 2023 +# +# Description: Reads a network and computes backbone size statistics. +# +# +import numpy as np +import pandas as pd +pd.set_option('display.max_rows', 100) +pd.set_option('display.max_columns', 500) +pd.set_option('display.width', 1000) +#pd.options.display.float_format = '{:.2%}'.format +import networkx as nx +import argparse +import configparser +from utils import get_asymmetry_distribution +import pickle as pk + + +if __name__ == '__main__': + + # + # Init + # + config = configparser.ConfigParser() + config.read('networks.ini') + networks = list(config.keys())[1:] + + # + # Args + # + parser = argparse.ArgumentParser() + parser.add_argument("--network", default='bike-sharing', type=str, choices=networks, help="Network name.") + args = parser.parse_args() + # + network = args.network + # + settings = config[network] + folder = settings.get('folder') + + # Files + rGfile = 'networks/{folder:s}/undirected_networks.pickle'.format(folder=folder) + rBfile = 'networks/{folder:s}/undirected_backbones.pickle'.format(folder=folder) + wGstats = 'networks/{folder:s}/undirected_networks-stats.csv'.format(folder=folder) + #wFasymmetry = 'networks/{folder:s}/backbone_asymmetry.pickle'.format(folder=folder) + + # Load graph + G = pk.load(open(rGfile, 'rb')) + B = pk.load(open(rBfile, 'rb')) + + df = pd.DataFrame(columns=['n-nodes', 'n-edges', 'density', '%-edges-metric','%-edges-ultrametric'], + index=['min', 'max', 'avg', 'harm']) + + for type in ['min', 'max', 'avg', 'harm']: + print(type) + df['n-nodes'][type] = G[type].number_of_nodes() + df['n-edges'][type] = G[type].number_of_edges() + df['density'][type] = nx.density(G[type]) + + if df['n-edges'][type] > 0: + df['%-edges-metric'][type] = B[type].number_of_edges()/df['n-edges'][type] + df['%-edges-ultrametric'][type] = sum([int(d) for _, _, d in B[type].edges(data='ultrametric')])/df['n-edges'][type] + else: + df['%-edges-metric'][type] = 0.0 + df['%-edges-ultrametric'][type] = 0.0 + + # Print + print(df) + df.to_csv(wGstats) + print("\n\n") diff --git a/networks/academic_hiring/business/undirected_networks-stats.csv b/networks/academic_hiring/business/undirected_networks-stats.csv new file mode 100644 index 0000000..ed2f066 --- /dev/null +++ b/networks/academic_hiring/business/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,113,2944,0.46523388116308473,0.17459239130434784,0.043138586956521736 +max,113,488,0.07711757269279393,0.6290983606557377,0.1762295081967213 +avg,113,488,0.07711757269279393,0.6618852459016393,0.1721311475409836 +harm,113,2944,0.46523388116308473,0.18648097826086957,0.04076086956521739 diff --git a/networks/academic_hiring/computer_science/undirected_networks-stats.csv b/networks/academic_hiring/computer_science/undirected_networks-stats.csv new file mode 100644 index 0000000..0a90a11 --- /dev/null +++ b/networks/academic_hiring/computer_science/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,206,2741,0.12981292919725312,0.3349142648668369,0.11309740970448741 +max,206,188,0.008903623016812693,0.824468085106383,0.4787234042553192 +avg,206,188,0.008903623016812693,0.8776595744680851,0.4574468085106383 +harm,206,2741,0.12981292919725312,0.32834731849689897,0.09813936519518424 diff --git a/networks/academic_hiring/history/undirected_networks-stats.csv b/networks/academic_hiring/history/undirected_networks-stats.csv new file mode 100644 index 0000000..643823d --- /dev/null +++ b/networks/academic_hiring/history/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,145,2266,0.21704980842911878,0.2436010591350397,0.10326566637246248 +max,145,162,0.015517241379310345,0.7716049382716049,0.42592592592592593 +avg,145,162,0.015517241379310345,0.8148148148148148,0.36419753086419754 +harm,145,2266,0.21704980842911878,0.2471315092674316,0.09664607237422772 diff --git a/networks/bike-sharing/undirected_networks-stats.csv b/networks/bike-sharing/undirected_networks-stats.csv new file mode 100644 index 0000000..540ab8c --- /dev/null +++ b/networks/bike-sharing/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,725,35063,0.13359878072013717,0.5589367709551379,0.020762627270912357 +max,725,18055,0.0687940560106687,0.6353918582110218,0.04004430905566325 +avg,725,18055,0.0687940560106687,0.6767654389365827,0.03998892273608419 +harm,725,35063,0.13359878072013717,0.3849071670992214,0.02064854690129196 diff --git a/networks/caviar_proj/undirected_networks-stats.csv b/networks/caviar_proj/undirected_networks-stats.csv new file mode 100644 index 0000000..b1373aa --- /dev/null +++ b/networks/caviar_proj/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,110,205,0.03419516263552961,0.5902439024390244,0.5560975609756098 +max,110,90,0.015012510425354461,0.7555555555555555,0.6888888888888889 +avg,110,90,0.015012510425354461,0.7444444444444445,0.6888888888888889 +harm,110,205,0.03419516263552961,0.5951219512195122,0.5317073170731708 diff --git a/networks/celegans/hermaphrodite/undirected_networks-stats.csv b/networks/celegans/hermaphrodite/undirected_networks-stats.csv new file mode 100644 index 0000000..a77856c --- /dev/null +++ b/networks/celegans/hermaphrodite/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,313,2932,0.06004751372163513,0.32162346521145974,0.11425648021828104 +max,313,568,0.011632669779634636,0.823943661971831,0.43485915492957744 +avg,313,568,0.011632669779634636,0.8433098591549296,0.39436619718309857 +harm,313,2932,0.06004751372163513,0.3219645293315143,0.11050477489768076 diff --git a/networks/celegans/male/undirected_networks-stats.csv b/networks/celegans/male/undirected_networks-stats.csv new file mode 100644 index 0000000..fac2bf2 --- /dev/null +++ b/networks/celegans/male/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,328,2832,0.052808234504363394,0.330861581920904,0.1228813559322034 +max,328,642,0.01197135824569255,0.6947040498442367,0.397196261682243 +avg,328,642,0.01197135824569255,0.7305295950155763,0.38161993769470404 +harm,328,2832,0.052808234504363394,0.3343926553672316,0.1182909604519774 diff --git a/networks/colombia_social/calls/undirected_networks-stats.csv b/networks/colombia_social/calls/undirected_networks-stats.csv new file mode 100644 index 0000000..f0b922f --- /dev/null +++ b/networks/colombia_social/calls/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,863,238586,0.6414412573631615,0.009799401473682445,0.0036381011459180337 +max,863,199898,0.5374281159178713,0.01570300853435252,0.004317201772904181 +avg,863,199898,0.5374281159178713,0.01511771003211638,0.004312199221603017 +harm,863,238586,0.6414412573631615,0.009728148340640272,0.003612952981314914 diff --git a/networks/colombia_social/mobility/undirected_networks-stats.csv b/networks/colombia_social/mobility/undirected_networks-stats.csv new file mode 100644 index 0000000..4a39cb5 --- /dev/null +++ b/networks/colombia_social/mobility/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,863,106707,0.2868830201665264,0.013054438790332405,0.008087566888770183 +max,863,67150,0.1805335620360637,0.018183172002978407,0.012836932241250931 +avg,863,67150,0.1805335620360637,0.018093819806403573,0.012836932241250931 +harm,863,106707,0.2868830201665264,0.012857638205553525,0.008078195432352142 diff --git a/networks/comorbidity/undirected_networks-stats.csv b/networks/comorbidity/undirected_networks-stats.csv new file mode 100644 index 0000000..3fe254b --- /dev/null +++ b/networks/comorbidity/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,95,4465,1.0,0.3659574468085106,0.021052631578947368 +max,95,4465,1.0,0.5117581187010078,0.021052631578947368 +avg,95,4465,1.0,0.5068309070548712,0.021052631578947368 +harm,95,4465,1.0,0.4665173572228443,0.021052631578947368 diff --git a/networks/giraffe/undirected_networks-stats.csv b/networks/giraffe/undirected_networks-stats.csv new file mode 100644 index 0000000..bac8580 --- /dev/null +++ b/networks/giraffe/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,6,15,1.0,0.7333333333333333,0.3333333333333333 +max,6,15,1.0,0.8,0.3333333333333333 +avg,6,15,1.0,0.8666666666666667,0.3333333333333333 +harm,6,15,1.0,0.8,0.3333333333333333 diff --git a/networks/host-pathogen/undirected_networks-stats.csv b/networks/host-pathogen/undirected_networks-stats.csv new file mode 100644 index 0000000..c7d9634 --- /dev/null +++ b/networks/host-pathogen/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,10578,18529,0.00033121950969251893,0.6638242754600896,0.591451238598953 +max,10578,0,0,0.0,0.0 +avg,10578,0,0,0.0,0.0 +harm,10578,18529,0.00033121950969251893,0.6638242754600896,0.591451238598953 diff --git a/networks/mobility/manizales/undirected_networks-stats.csv b/networks/mobility/manizales/undirected_networks-stats.csv new file mode 100644 index 0000000..9dd00af --- /dev/null +++ b/networks/mobility/manizales/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,57,1281,0.8026315789473685,0.11943793911007025,0.04371584699453552 +max,57,1237,0.775062656641604,0.2651576394502829,0.04527081649151172 +avg,57,1237,0.775062656641604,0.2497978981406629,0.04527081649151172 +harm,57,1281,0.8026315789473685,0.14988290398126464,0.04371584699453552 diff --git a/networks/mobility/medellin/undirected_networks-stats.csv b/networks/mobility/medellin/undirected_networks-stats.csv new file mode 100644 index 0000000..8e36707 --- /dev/null +++ b/networks/mobility/medellin/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,413,18381,0.2160488022755589,0.15146074751101682,0.02459060986888635 +max,413,15503,0.1822210207104069,0.1897697219892924,0.02715603431593885 +avg,413,15503,0.1822210207104069,0.20537960394762303,0.026640005160291556 +harm,413,18381,0.2160488022755589,0.1702301289374898,0.022414449703498176 diff --git a/networks/phone-calls/undirected_networks-stats.csv b/networks/phone-calls/undirected_networks-stats.csv new file mode 100644 index 0000000..bf76cb0 --- /dev/null +++ b/networks/phone-calls/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,322,430,0.00832027244054875,0.8651162790697674,0.7465116279069768 +max,322,179,0.0034635552717633173,0.9497206703910615,0.9273743016759777 +avg,322,179,0.0034635552717633173,0.9553072625698324,0.9273743016759777 +harm,322,430,0.00832027244054875,0.8511627906976744,0.7465116279069768 diff --git a/networks/tennis_losses/undirected_networks-stats.csv b/networks/tennis_losses/undirected_networks-stats.csv new file mode 100644 index 0000000..1632cfe --- /dev/null +++ b/networks/tennis_losses/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,4245,85084,0.009445497225210344,0.15920737153871467,0.09086314700766301 +max,4245,16352,0.0018152974780997547,0.5377323874755382,0.0912426614481409 +avg,4245,16352,0.0018152974780997547,0.6114848336594912,0.07772749510763209 +harm,4245,85084,0.009445497225210344,0.16042969300926144,0.08662028113393823 diff --git a/networks/us-airports-2006/undirected_networks-stats.csv b/networks/us-airports-2006/undirected_networks-stats.csv new file mode 100644 index 0000000..eff8fd9 --- /dev/null +++ b/networks/us-airports-2006/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,1075,11973,0.02074054826555801,0.13822767894429133,0.09003591414014867 +max,1075,6933,0.012009873976874107,0.22717438338381654,0.1339968267705178 +avg,1075,6933,0.012009873976874107,0.243473243905957,0.13385258906678205 +harm,1075,11973,0.02074054826555801,0.1440741668754698,0.08978535037166958 diff --git a/networks/weblinks_us/undirected_networks-stats.csv b/networks/weblinks_us/undirected_networks-stats.csv new file mode 100644 index 0000000..e74ab27 --- /dev/null +++ b/networks/weblinks_us/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,42800,450539,0.0004919092572037996,0.16068975160862878,0.11274939572378861 +max,42800,54937,5.9981530706565113e-05,0.5996141034275625,0.44960591222673246 +avg,42800,54937,5.9981530706565113e-05,0.579208912026503,0.3865336658354115 +harm,42800,450539,0.0004919092572037996,0.16079407110150287,0.10819929018353572 diff --git a/networks/yeast_grn/undirected_networks-stats.csv b/networks/yeast_grn/undirected_networks-stats.csv new file mode 100644 index 0000000..1b9694d --- /dev/null +++ b/networks/yeast_grn/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +min,6216,1613628,0.08353746229852424,0.00934911887994011,0.003910442803421854 +max,6216,52478,0.0027167841327133363,0.09838408475932772,0.02519150882274477 +avg,6216,52478,0.0027167841327133363,0.09392507336407638,0.023324059605930102 +harm,6216,1613628,0.08353746229852424,0.009110526093994403,0.003893090600807621 From 4eb4499f4d4dbaf1b5fa0a7ac0028b0dae9c924d Mon Sep 17 00:00:00 2001 From: fcphysics Date: Tue, 16 May 2023 16:31:57 -0400 Subject: [PATCH 03/12] Organizing components backbone --- 02-network-stats.py | 55 +++++++++----- 11-connected_components.py | 73 ------------------- networks.ini | 10 +-- .../business/components-stats.csv | 7 -- .../business/network-stats.csv | 15 ++-- .../computer_science/components-stats.csv | 7 -- .../computer_science/network-stats.csv | 15 ++-- .../history/components-stats.csv | 7 -- .../academic_hiring/history/network-stats.csv | 15 ++-- networks/bike-sharing/components-stats.csv | 7 -- networks/bike-sharing/network-stats.csv | 15 ++-- networks/caviar_proj/components-stats.csv | 7 -- networks/caviar_proj/network-stats.csv | 15 ++-- .../hermaphrodite/components-stats.csv | 7 -- .../celegans/hermaphrodite/network-stats.csv | 15 ++-- networks/celegans/male/components-stats.csv | 7 -- networks/celegans/male/network-stats.csv | 15 ++-- .../calls/components-stats.csv | 7 -- .../colombia_social/calls/network-stats.csv | 15 ++-- .../mobility/components-stats.csv | 7 -- .../mobility/network-stats.csv | 15 ++-- networks/comorbidity/components-stats.csv | 7 -- networks/comorbidity/network-stats.csv | 15 ++-- networks/giraffe/components-stats.csv | 7 -- networks/giraffe/network-stats.csv | 15 ++-- networks/host-pathogen/network-stats.csv | 15 ++-- .../mobility/manizales/components-stats.csv | 7 -- networks/mobility/manizales/network-stats.csv | 15 ++-- .../mobility/medellin/components-stats.csv | 7 -- networks/mobility/medellin/network-stats.csv | 15 ++-- networks/phone-calls/components-stats.csv | 7 -- networks/phone-calls/network-stats.csv | 15 ++-- networks/tennis_losses/components-stats.csv | 7 -- networks/tennis_losses/network-stats.csv | 15 ++-- .../us-airports-2006/components-stats.csv | 7 -- networks/us-airports-2006/network-stats.csv | 15 ++-- networks/weblinks_us/network-stats.csv | 15 ++-- networks/yeast_grn/components-stats.csv | 7 -- networks/yeast_grn/network-stats.csv | 15 ++-- 39 files changed, 191 insertions(+), 351 deletions(-) delete mode 100644 11-connected_components.py delete mode 100644 networks/academic_hiring/business/components-stats.csv delete mode 100644 networks/academic_hiring/computer_science/components-stats.csv delete mode 100644 networks/academic_hiring/history/components-stats.csv delete mode 100644 networks/bike-sharing/components-stats.csv delete mode 100644 networks/caviar_proj/components-stats.csv delete mode 100644 networks/celegans/hermaphrodite/components-stats.csv delete mode 100644 networks/celegans/male/components-stats.csv delete mode 100644 networks/colombia_social/calls/components-stats.csv delete mode 100644 networks/colombia_social/mobility/components-stats.csv delete mode 100644 networks/comorbidity/components-stats.csv delete mode 100644 networks/giraffe/components-stats.csv delete mode 100644 networks/mobility/manizales/components-stats.csv delete mode 100644 networks/mobility/medellin/components-stats.csv delete mode 100644 networks/phone-calls/components-stats.csv delete mode 100644 networks/tennis_losses/components-stats.csv delete mode 100644 networks/us-airports-2006/components-stats.csv delete mode 100644 networks/yeast_grn/components-stats.csv diff --git a/02-network-stats.py b/02-network-stats.py index 08fda3c..3ff554a 100644 --- a/02-network-stats.py +++ b/02-network-stats.py @@ -49,40 +49,55 @@ G = nx.read_graphml(rGfile) # Calculate stats - n_nodes = G.number_of_nodes() - n_edges = G.number_of_edges() + wcc_nodes = G.number_of_nodes() + wcc_edges = G.number_of_edges() density = nx.density(G) + + LSCC = G.subgraph(max(nx.strongly_connected_components(G), key=len)) + + lscc_nodes = LSCC.number_of_nodes() + lscc_edges = LSCC.number_of_edges() # Load backbone - # Metric G = nx.read_graphml(rBfile) - n_edges_metric = G.number_of_edges() - - # New asymmetry dist - #alpha = dict() - #alpha['metric'] = get_asymmetry_distribution(G) - # Ultrametric - n_edges_ultrametric = sum([int(d) for _, _, d in G.edges(data='ultrametric')]) - #alpha['ultrametric'] = get_asymmetry_distribution(G) + # Metric + tau_wcc_metric = G.number_of_edges()/wcc_edges + # Ultrametric AND LSCC + tau_wcc_ultrametric = 0 #sum([int(d) for _, _, d in G.edges(data='ultrametric')])/wcc_edges + tau_lscc_metric = 0 + tau_lscc_ultrametric = 0 + for u, v, ultra in G.edges(data='ultrametric'): + if LSCC.has_edge(u, v): + tau_lscc_metric += 1 + if ultra: + tau_wcc_ultrametric += 1 + if LSCC.has_edge(u, v): + tau_lscc_ultrametric += 1 + + tau_wcc_ultrametric /= wcc_edges + if lscc_edges > 0.0: + tau_lscc_ultrametric /= lscc_edges + tau_lscc_metric /= lscc_edges # to Result Series sR = pd.Series({ - 'n-nodes': n_nodes, - 'n-edges': n_edges, + 'n-nodes': wcc_nodes, + 'n-edges': wcc_edges, # 'density': density, # - 'n-edges-metric': n_edges_metric, - 'n-edges-ultrametric': n_edges_ultrametric, + 'LSCC-nodes': lscc_nodes, + 'LSCC-edges': lscc_edges, # - '%-edges-metric': (n_edges_metric / n_edges), - '%-edges-ultrametric': (n_edges_ultrametric / n_edges), + 'tau-metric': tau_wcc_metric, + 'tau-ultrametric': tau_wcc_ultrametric, # - '%-redundancy-metric': 1 - (n_edges_metric / n_edges), - '%-redundancy-ultrametric': 1 - (n_edges_ultrametric / n_edges), + 'LSCC-tau-metric': tau_lscc_metric, + 'LSCC-tau-ultrametric': tau_lscc_ultrametric, # - '%-edges-ultrametric/metric': ((n_edges_ultrametric / n_edges) / (n_edges_metric / n_edges)), + 'ultrametric_metric_ratio': (tau_wcc_ultrametric/tau_wcc_metric), + 'LSCC-ultrametric_metric_ratio': (tau_lscc_ultrametric/tau_lscc_metric if tau_lscc_metric > 0 else 0), # }, name=network, dtype='object') diff --git a/11-connected_components.py b/11-connected_components.py deleted file mode 100644 index 2daac6a..0000000 --- a/11-connected_components.py +++ /dev/null @@ -1,73 +0,0 @@ -# coding=utf-8 -# Author: Felipe Xavier Costa -# Date: May 3, 2023 -# -# Description: Compare backbone inside and outside SCC. -# -# -import numpy as np -import pandas as pd -pd.set_option('display.max_rows', 100) -pd.set_option('display.max_columns', 500) -pd.set_option('display.width', 1000) -#pd.options.display.float_format = '{:.2%}'.format -import networkx as nx -import argparse -import configparser -from utils import get_asymmetry_distribution -import pickle as pk - - -if __name__ == '__main__': - - # - # Init - # - config = configparser.ConfigParser() - config.read('networks.ini') - networks = list(config.keys())[1:] - - # - # Args - # - parser = argparse.ArgumentParser() - parser.add_argument("--network", default='bike-sharing', type=str, choices=networks, help="Network name.") - args = parser.parse_args() - # - network = args.network - # - settings = config[network] - folder = settings.get('folder') - - # Files - rGfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) - rBfile = 'networks/{folder:s}/backbone.graphml'.format(folder=folder) - wGstats = 'networks/{folder:s}/components-stats.csv'.format(folder=folder) - - # Load graph - G = nx.read_graphml(rGfile) - - LSCC = G.subgraph(max(nx.strongly_connected_components(G), key=len)) - - # Load backbone - B = nx.read_graphml(rBfile) - - nEmLSCC = 0 - for u, v in B.edges(): - if LSCC.has_edge(u, v): - nEmLSCC += 1 - - # to Result Series - sR = pd.Series({ - 'n-nodes': G.number_of_nodes(), - 'n-edges': G.number_of_edges(), - # Metric - 'n-edges-metric': B.number_of_edges(), - # LSCC - 'n-nodes-lscc': LSCC.number_of_nodes(), - 'n-edges-lscc': LSCC.number_of_edges(), - # Metric - 'n-edges-metric-lscc': nEmLSCC, - }, name=network, dtype='object') - - sR.to_csv(wGstats) \ No newline at end of file diff --git a/networks.ini b/networks.ini index 640a1c8..4de991a 100644 --- a/networks.ini +++ b/networks.ini @@ -108,15 +108,13 @@ weight-type = distance weight-attr = distance -[host-pathogen] -folder = host-pathogen -weight-type = distance -weight-attr = distance - - [us-weblinks] folder = weblinks_us weight-type = distance weight-attr = distance +[host-pathogen] +folder = host-pathogen +weight-type = distance +weight-attr = distance \ No newline at end of file diff --git a/networks/academic_hiring/business/components-stats.csv b/networks/academic_hiring/business/components-stats.csv deleted file mode 100644 index 3af06de..0000000 --- a/networks/academic_hiring/business/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,business-faculty -n-nodes,113 -n-edges,3432 -n-edges-metric,1204 -n-nodes-lscc,94 -n-edges-lscc,2842 -n-edges-metric-lscc,1038 diff --git a/networks/academic_hiring/business/network-stats.csv b/networks/academic_hiring/business/network-stats.csv index 799f588..3643107 100644 --- a/networks/academic_hiring/business/network-stats.csv +++ b/networks/academic_hiring/business/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,113 n-edges,3432 density,0.27117572692793934 -n-edges-metric,1204 -n-edges-ultrametric,335 -%-edges-metric,0.3508158508158508 -%-edges-ultrametric,0.09761072261072261 -%-redundancy-metric,0.6491841491841492 -%-redundancy-ultrametric,0.9023892773892774 -%-edges-ultrametric/metric,0.2782392026578073 +LSCC-nodes,94 +LSCC-edges,2842 +tau-metric,0.3508158508158508 +tau-ultrametric,0.09761072261072261 +LSCC-tau-metric,0.36523574947220266 +LSCC-tau-ultrametric,0.09465165376495425 +ultrametric_metric_ratio,0.2782392026578073 +LSCC-ultrametric_metric_ratio,0.2591522157996146 diff --git a/networks/academic_hiring/computer_science/components-stats.csv b/networks/academic_hiring/computer_science/components-stats.csv deleted file mode 100644 index 17bf804..0000000 --- a/networks/academic_hiring/computer_science/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,cs-faculty -n-nodes,206 -n-edges,2929 -n-edges-metric,1508 -n-nodes-lscc,167 -n-edges-lscc,2384 -n-edges-metric-lscc,1260 diff --git a/networks/academic_hiring/computer_science/network-stats.csv b/networks/academic_hiring/computer_science/network-stats.csv index 8b25f79..407ff18 100644 --- a/networks/academic_hiring/computer_science/network-stats.csv +++ b/networks/academic_hiring/computer_science/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,206 n-edges,2929 density,0.06935827610703292 -n-edges-metric,1508 -n-edges-ultrametric,664 -%-edges-metric,0.5148514851485149 -%-edges-ultrametric,0.22669853192215772 -%-redundancy-metric,0.48514851485148514 -%-redundancy-ultrametric,0.7733014680778423 -%-edges-ultrametric/metric,0.4403183023872679 +LSCC-nodes,167 +LSCC-edges,2384 +tau-metric,0.5148514851485149 +tau-ultrametric,0.22669853192215772 +LSCC-tau-metric,0.5285234899328859 +LSCC-tau-ultrametric,0.22021812080536912 +ultrametric_metric_ratio,0.4403183023872679 +LSCC-ultrametric_metric_ratio,0.4166666666666667 diff --git a/networks/academic_hiring/history/components-stats.csv b/networks/academic_hiring/history/components-stats.csv deleted file mode 100644 index 38ab415..0000000 --- a/networks/academic_hiring/history/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,history-faculty -n-nodes,145 -n-edges,2428 -n-edges-metric,1006 -n-nodes-lscc,116 -n-edges-lscc,1897 -n-edges-metric-lscc,816 diff --git a/networks/academic_hiring/history/network-stats.csv b/networks/academic_hiring/history/network-stats.csv index 8b72a06..eb46f57 100644 --- a/networks/academic_hiring/history/network-stats.csv +++ b/networks/academic_hiring/history/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,145 n-edges,2428 density,0.11628352490421456 -n-edges-metric,1006 -n-edges-ultrametric,534 -%-edges-metric,0.414332784184514 -%-edges-ultrametric,0.21993410214168038 -%-redundancy-metric,0.585667215815486 -%-redundancy-ultrametric,0.7800658978583196 -%-edges-ultrametric/metric,0.5308151093439363 +LSCC-nodes,116 +LSCC-edges,1897 +tau-metric,0.414332784184514 +tau-ultrametric,0.21993410214168038 +LSCC-tau-metric,0.430152872957301 +LSCC-tau-ultrametric,0.2087506589351608 +ultrametric_metric_ratio,0.5308151093439363 +LSCC-ultrametric_metric_ratio,0.4852941176470589 diff --git a/networks/bike-sharing/components-stats.csv b/networks/bike-sharing/components-stats.csv deleted file mode 100644 index c9189a2..0000000 --- a/networks/bike-sharing/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,bike-sharing -n-nodes,725 -n-edges,53118 -n-edges-metric,31622 -n-nodes-lscc,723 -n-edges-lscc,53115 -n-edges-metric-lscc,31619 diff --git a/networks/bike-sharing/network-stats.csv b/networks/bike-sharing/network-stats.csv index 7beb8f8..855e272 100644 --- a/networks/bike-sharing/network-stats.csv +++ b/networks/bike-sharing/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,725 n-edges,53118 density,0.10119641836540294 -n-edges-metric,31622 -n-edges-ultrametric,1462 -%-edges-metric,0.5953160887081592 -%-edges-ultrametric,0.027523626642569375 -%-redundancy-metric,0.4046839112918408 -%-redundancy-ultrametric,0.9724763733574306 -%-edges-ultrametric/metric,0.04623363481120739 +LSCC-nodes,723 +LSCC-edges,53115 +tau-metric,0.5953160887081592 +tau-ultrametric,0.027523626642569375 +LSCC-tau-metric,0.5952932316671373 +LSCC-tau-ultrametric,0.027487527063917914 +ultrametric_metric_ratio,0.04623363481120739 +LSCC-ultrametric_metric_ratio,0.046174768335494484 diff --git a/networks/caviar_proj/components-stats.csv b/networks/caviar_proj/components-stats.csv deleted file mode 100644 index 727b746..0000000 --- a/networks/caviar_proj/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,caviar-proj -n-nodes,110 -n-edges,295 -n-edges-metric,208 -n-nodes-lscc,66 -n-edges-lscc,242 -n-edges-metric-lscc,160 diff --git a/networks/caviar_proj/network-stats.csv b/networks/caviar_proj/network-stats.csv index 880df61..284545c 100644 --- a/networks/caviar_proj/network-stats.csv +++ b/networks/caviar_proj/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,110 n-edges,295 density,0.024603836530442035 -n-edges-metric,208 -n-edges-ultrametric,191 -%-edges-metric,0.7050847457627119 -%-edges-ultrametric,0.6474576271186441 -%-redundancy-metric,0.29491525423728815 -%-redundancy-ultrametric,0.3525423728813559 -%-edges-ultrametric/metric,0.9182692307692308 +LSCC-nodes,66 +LSCC-edges,242 +tau-metric,0.7050847457627119 +tau-ultrametric,0.6474576271186441 +LSCC-tau-metric,0.6611570247933884 +LSCC-tau-ultrametric,0.5991735537190083 +ultrametric_metric_ratio,0.9182692307692308 +LSCC-ultrametric_metric_ratio,0.90625 diff --git a/networks/celegans/hermaphrodite/components-stats.csv b/networks/celegans/hermaphrodite/components-stats.csv deleted file mode 100644 index 3fc11d0..0000000 --- a/networks/celegans/hermaphrodite/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,celegans-her -n-nodes,313 -n-edges,3500 -n-edges-metric,1949 -n-nodes-lscc,249 -n-edges-lscc,3046 -n-edges-metric-lscc,1685 diff --git a/networks/celegans/hermaphrodite/network-stats.csv b/networks/celegans/hermaphrodite/network-stats.csv index 3ea6768..299e8c2 100644 --- a/networks/celegans/hermaphrodite/network-stats.csv +++ b/networks/celegans/hermaphrodite/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,313 n-edges,3500 density,0.03584009175063488 -n-edges-metric,1949 -n-edges-ultrametric,937 -%-edges-metric,0.5568571428571428 -%-edges-ultrametric,0.26771428571428574 -%-redundancy-metric,0.44314285714285717 -%-redundancy-ultrametric,0.7322857142857142 -%-edges-ultrametric/metric,0.4807593637762956 +LSCC-nodes,249 +LSCC-edges,3046 +tau-metric,0.5568571428571428 +tau-ultrametric,0.26771428571428574 +LSCC-tau-metric,0.5531845042678923 +LSCC-tau-ultrametric,0.25673013788575183 +ultrametric_metric_ratio,0.4807593637762956 +LSCC-ultrametric_metric_ratio,0.46409495548961427 diff --git a/networks/celegans/male/components-stats.csv b/networks/celegans/male/components-stats.csv deleted file mode 100644 index 5f8d8d8..0000000 --- a/networks/celegans/male/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,celegans-male -n-nodes,328 -n-edges,3474 -n-edges-metric,1876 -n-nodes-lscc,289 -n-edges-lscc,3206 -n-edges-metric-lscc,1713 diff --git a/networks/celegans/male/network-stats.csv b/networks/celegans/male/network-stats.csv index 6eb1e9b..a266b58 100644 --- a/networks/celegans/male/network-stats.csv +++ b/networks/celegans/male/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,328 n-edges,3474 density,0.03238979637502797 -n-edges-metric,1876 -n-edges-ultrametric,962 -%-edges-metric,0.5400115141047783 -%-edges-ultrametric,0.27691421991940124 -%-redundancy-metric,0.4599884858952217 -%-redundancy-ultrametric,0.7230857800805988 -%-edges-ultrametric/metric,0.5127931769722814 +LSCC-nodes,289 +LSCC-edges,3206 +tau-metric,0.5400115141047783 +tau-ultrametric,0.27691421991940124 +LSCC-tau-metric,0.5343106674984405 +LSCC-tau-ultrametric,0.26824703680598877 +ultrametric_metric_ratio,0.5127931769722814 +LSCC-ultrametric_metric_ratio,0.5020431990659661 diff --git a/networks/colombia_social/calls/components-stats.csv b/networks/colombia_social/calls/components-stats.csv deleted file mode 100644 index 03d046a..0000000 --- a/networks/colombia_social/calls/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,colombia-calls -n-nodes,863 -n-edges,438484 -n-edges-metric,11407 -n-nodes-lscc,863 -n-edges-lscc,438484 -n-edges-metric-lscc,11407 diff --git a/networks/colombia_social/calls/network-stats.csv b/networks/colombia_social/calls/network-stats.csv index 6b58b00..d30453c 100644 --- a/networks/colombia_social/calls/network-stats.csv +++ b/networks/colombia_social/calls/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,863 n-edges,438484 density,0.5894346866405165 -n-edges-metric,11407 -n-edges-ultrametric,3903 -%-edges-metric,0.026014632232875087 -%-edges-ultrametric,0.008901122960016786 -%-redundancy-metric,0.973985367767125 -%-redundancy-ultrametric,0.9910988770399832 -%-edges-ultrametric/metric,0.34215832383624095 +LSCC-nodes,863 +LSCC-edges,438484 +tau-metric,0.026014632232875087 +tau-ultrametric,0.008901122960016786 +LSCC-tau-metric,0.026014632232875087 +LSCC-tau-ultrametric,0.008901122960016786 +ultrametric_metric_ratio,0.34215832383624095 +LSCC-ultrametric_metric_ratio,0.34215832383624095 diff --git a/networks/colombia_social/mobility/components-stats.csv b/networks/colombia_social/mobility/components-stats.csv deleted file mode 100644 index e49a62a..0000000 --- a/networks/colombia_social/mobility/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,colombia-mobility -n-nodes,863 -n-edges,173857 -n-edges-metric,2971 -n-nodes-lscc,863 -n-edges-lscc,173857 -n-edges-metric-lscc,2971 diff --git a/networks/colombia_social/mobility/network-stats.csv b/networks/colombia_social/mobility/network-stats.csv index a5b2a6d..1e78cad 100644 --- a/networks/colombia_social/mobility/network-stats.csv +++ b/networks/colombia_social/mobility/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,863 n-edges,173857 density,0.23370829110129507 -n-edges-metric,2971 -n-edges-ultrametric,2115 -%-edges-metric,0.017088756851895523 -%-edges-ultrametric,0.012165170226105363 -%-redundancy-metric,0.9829112431481045 -%-redundancy-ultrametric,0.9878348297738946 -%-edges-ultrametric/metric,0.7118815213732751 +LSCC-nodes,863 +LSCC-edges,173857 +tau-metric,0.017088756851895523 +tau-ultrametric,0.012165170226105363 +LSCC-tau-metric,0.017088756851895523 +LSCC-tau-ultrametric,0.012165170226105363 +ultrametric_metric_ratio,0.7118815213732751 +LSCC-ultrametric_metric_ratio,0.7118815213732751 diff --git a/networks/comorbidity/components-stats.csv b/networks/comorbidity/components-stats.csv deleted file mode 100644 index eaad82a..0000000 --- a/networks/comorbidity/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,comorbidity -n-nodes,95 -n-edges,8930 -n-edges-metric,4236 -n-nodes-lscc,95 -n-edges-lscc,8930 -n-edges-metric-lscc,4236 diff --git a/networks/comorbidity/network-stats.csv b/networks/comorbidity/network-stats.csv index dedffba..c1dd436 100644 --- a/networks/comorbidity/network-stats.csv +++ b/networks/comorbidity/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,95 n-edges,8930 density,1.0 -n-edges-metric,4236 -n-edges-ultrametric,194 -%-edges-metric,0.4743561030235162 -%-edges-ultrametric,0.021724524076147816 -%-redundancy-metric,0.5256438969764838 -%-redundancy-ultrametric,0.9782754759238522 -%-edges-ultrametric/metric,0.04579792256846081 +LSCC-nodes,95 +LSCC-edges,8930 +tau-metric,0.4743561030235162 +tau-ultrametric,0.021724524076147816 +LSCC-tau-metric,0.4743561030235162 +LSCC-tau-ultrametric,0.021724524076147816 +ultrametric_metric_ratio,0.04579792256846081 +LSCC-ultrametric_metric_ratio,0.04579792256846081 diff --git a/networks/giraffe/components-stats.csv b/networks/giraffe/components-stats.csv deleted file mode 100644 index 7eff7dd..0000000 --- a/networks/giraffe/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,giraffe -n-nodes,6 -n-edges,30 -n-edges-metric,23 -n-nodes-lscc,6 -n-edges-lscc,30 -n-edges-metric-lscc,23 diff --git a/networks/giraffe/network-stats.csv b/networks/giraffe/network-stats.csv index c3c3f82..c0e8a3a 100644 --- a/networks/giraffe/network-stats.csv +++ b/networks/giraffe/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,6 n-edges,30 density,1.0 -n-edges-metric,23 -n-edges-ultrametric,10 -%-edges-metric,0.7666666666666667 -%-edges-ultrametric,0.3333333333333333 -%-redundancy-metric,0.23333333333333328 -%-redundancy-ultrametric,0.6666666666666667 -%-edges-ultrametric/metric,0.4347826086956521 +LSCC-nodes,6 +LSCC-edges,30 +tau-metric,0.7666666666666667 +tau-ultrametric,0.3333333333333333 +LSCC-tau-metric,0.7666666666666667 +LSCC-tau-ultrametric,0.3333333333333333 +ultrametric_metric_ratio,0.4347826086956521 +LSCC-ultrametric_metric_ratio,0.4347826086956521 diff --git a/networks/host-pathogen/network-stats.csv b/networks/host-pathogen/network-stats.csv index 03af774..42be838 100644 --- a/networks/host-pathogen/network-stats.csv +++ b/networks/host-pathogen/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,10578 n-edges,18529 density,0.00016560975484625947 -n-edges-metric,18503 -n-edges-ultrametric,18500 -%-edges-metric,0.9985967942144746 -%-edges-ultrametric,0.9984348858546063 -%-redundancy-metric,0.001403205785525441 -%-redundancy-ultrametric,0.0015651141453937312 -%-edges-ultrametric/metric,0.9998378641301411 +LSCC-nodes,1 +LSCC-edges,0 +tau-metric,0.9985967942144746 +tau-ultrametric,0.9984348858546063 +LSCC-tau-metric,0 +LSCC-tau-ultrametric,0 +ultrametric_metric_ratio,0.9998378641301411 +LSCC-ultrametric_metric_ratio,0 diff --git a/networks/mobility/manizales/components-stats.csv b/networks/mobility/manizales/components-stats.csv deleted file mode 100644 index c709fa0..0000000 --- a/networks/mobility/manizales/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,mobility-manizales -n-nodes,57 -n-edges,2518 -n-edges-metric,671 -n-nodes-lscc,57 -n-edges-lscc,2518 -n-edges-metric-lscc,671 diff --git a/networks/mobility/manizales/network-stats.csv b/networks/mobility/manizales/network-stats.csv index 2f6ff9e..c8a56f8 100644 --- a/networks/mobility/manizales/network-stats.csv +++ b/networks/mobility/manizales/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,57 n-edges,2518 density,0.7888471177944862 -n-edges-metric,671 -n-edges-ultrametric,193 -%-edges-metric,0.2664813343923749 -%-edges-ultrametric,0.07664813343923749 -%-redundancy-metric,0.7335186656076251 -%-redundancy-ultrametric,0.9233518665607625 -%-edges-ultrametric/metric,0.2876304023845007 +LSCC-nodes,57 +LSCC-edges,2518 +tau-metric,0.2664813343923749 +tau-ultrametric,0.07664813343923749 +LSCC-tau-metric,0.2664813343923749 +LSCC-tau-ultrametric,0.07664813343923749 +ultrametric_metric_ratio,0.2876304023845007 +LSCC-ultrametric_metric_ratio,0.2876304023845007 diff --git a/networks/mobility/medellin/components-stats.csv b/networks/mobility/medellin/components-stats.csv deleted file mode 100644 index ba37486..0000000 --- a/networks/mobility/medellin/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,mobility-medellin -n-nodes,413 -n-edges,33884 -n-edges-metric,8360 -n-nodes-lscc,413 -n-edges-lscc,33884 -n-edges-metric-lscc,8360 diff --git a/networks/mobility/medellin/network-stats.csv b/networks/mobility/medellin/network-stats.csv index 4e3fc75..872a869 100644 --- a/networks/mobility/medellin/network-stats.csv +++ b/networks/mobility/medellin/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,413 n-edges,33884 density,0.1991349114929829 -n-edges-metric,8360 -n-edges-ultrametric,1844 -%-edges-metric,0.24672411757761775 -%-edges-ultrametric,0.05442096564750325 -%-redundancy-metric,0.7532758824223822 -%-redundancy-ultrametric,0.9455790343524968 -%-edges-ultrametric/metric,0.22057416267942584 +LSCC-nodes,413 +LSCC-edges,33884 +tau-metric,0.24672411757761775 +tau-ultrametric,0.05442096564750325 +LSCC-tau-metric,0.24672411757761775 +LSCC-tau-ultrametric,0.05442096564750325 +ultrametric_metric_ratio,0.22057416267942584 +LSCC-ultrametric_metric_ratio,0.22057416267942584 diff --git a/networks/phone-calls/components-stats.csv b/networks/phone-calls/components-stats.csv deleted file mode 100644 index 1850044..0000000 --- a/networks/phone-calls/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,phone-calls -n-nodes,322 -n-edges,609 -n-edges-metric,558 -n-nodes-lscc,114 -n-edges-lscc,274 -n-edges-metric-lscc,242 diff --git a/networks/phone-calls/network-stats.csv b/networks/phone-calls/network-stats.csv index 087dcf6..18a1848 100644 --- a/networks/phone-calls/network-stats.csv +++ b/networks/phone-calls/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,322 n-edges,609 density,0.0058919138561560344 -n-edges-metric,558 -n-edges-ultrametric,517 -%-edges-metric,0.916256157635468 -%-edges-ultrametric,0.8489326765188834 -%-redundancy-metric,0.08374384236453203 -%-redundancy-ultrametric,0.15106732348111662 -%-edges-ultrametric/metric,0.9265232974910393 +LSCC-nodes,114 +LSCC-edges,274 +tau-metric,0.916256157635468 +tau-ultrametric,0.8489326765188834 +LSCC-tau-metric,0.8832116788321168 +LSCC-tau-ultrametric,0.7737226277372263 +ultrametric_metric_ratio,0.9265232974910393 +LSCC-ultrametric_metric_ratio,0.8760330578512397 diff --git a/networks/tennis_losses/components-stats.csv b/networks/tennis_losses/components-stats.csv deleted file mode 100644 index 9cd3809..0000000 --- a/networks/tennis_losses/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,tennis-loss -n-nodes,4245 -n-edges,101436 -n-edges-metric,60476 -n-nodes-lscc,2428 -n-edges-lscc,98102 -n-edges-metric-lscc,57142 diff --git a/networks/tennis_losses/network-stats.csv b/networks/tennis_losses/network-stats.csv index e7da205..963c2db 100644 --- a/networks/tennis_losses/network-stats.csv +++ b/networks/tennis_losses/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,4245 n-edges,101436 density,0.005630397351655049 -n-edges-metric,60476 -n-edges-ultrametric,24118 -%-edges-metric,0.5961985882724082 -%-edges-ultrametric,0.23776568476674947 -%-redundancy-metric,0.40380141172759176 -%-redundancy-ultrametric,0.7622343152332505 -%-edges-ultrametric/metric,0.39880283087505786 +LSCC-nodes,2428 +LSCC-edges,98102 +tau-metric,0.5961985882724082 +tau-ultrametric,0.23776568476674947 +LSCC-tau-metric,0.5824753827648774 +LSCC-tau-ultrametric,0.21186112413610325 +ultrametric_metric_ratio,0.39880283087505786 +LSCC-ultrametric_metric_ratio,0.3637254558818382 diff --git a/networks/us-airports-2006/components-stats.csv b/networks/us-airports-2006/components-stats.csv deleted file mode 100644 index 3a149a0..0000000 --- a/networks/us-airports-2006/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,us-airports -n-nodes,1075 -n-edges,18906 -n-edges-metric,5186 -n-nodes-lscc,995 -n-edges-lscc,18820 -n-edges-metric-lscc,5102 diff --git a/networks/us-airports-2006/network-stats.csv b/networks/us-airports-2006/network-stats.csv index 27c41c5..ef83c30 100644 --- a/networks/us-airports-2006/network-stats.csv +++ b/networks/us-airports-2006/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,1075 n-edges,18906 density,0.01637521112121606 -n-edges-metric,5186 -n-edges-ultrametric,3589 -%-edges-metric,0.27430445361260974 -%-edges-ultrametric,0.18983391515920872 -%-redundancy-metric,0.7256955463873902 -%-redundancy-ultrametric,0.8101660848407912 -%-edges-ultrametric/metric,0.692055534130351 +LSCC-nodes,995 +LSCC-edges,18820 +tau-metric,0.27430445361260974 +tau-ultrametric,0.18983391515920872 +LSCC-tau-metric,0.27109458023379385 +LSCC-tau-ultrametric,0.18629117959617428 +ultrametric_metric_ratio,0.692055534130351 +LSCC-ultrametric_metric_ratio,0.6871814974519795 diff --git a/networks/weblinks_us/network-stats.csv b/networks/weblinks_us/network-stats.csv index 574c764..30e91f1 100644 --- a/networks/weblinks_us/network-stats.csv +++ b/networks/weblinks_us/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,42800 n-edges,505476 density,0.0002759453939551824 -n-edges-metric,185919 -n-edges-ultrametric,128223 -%-edges-metric,0.36780974764380503 -%-edges-ultrametric,0.2536678299266434 -%-redundancy-metric,0.632190252356195 -%-redundancy-ultrametric,0.7463321700733566 -%-edges-ultrametric/metric,0.6896713084730447 +LSCC-nodes,27725 +LSCC-edges,372626 +tau-metric,0.36780974764380503 +tau-ultrametric,0.2536678299266434 +LSCC-tau-metric,0.3800352095666969 +LSCC-tau-ultrametric,0.2562837805198778 +ultrametric_metric_ratio,0.6896713084730447 +LSCC-ultrametric_metric_ratio,0.6743685165700404 diff --git a/networks/yeast_grn/components-stats.csv b/networks/yeast_grn/components-stats.csv deleted file mode 100644 index 91b9713..0000000 --- a/networks/yeast_grn/components-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,yeast-grn -n-nodes,6216 -n-edges,1666106 -n-edges-metric,106160 -n-nodes-lscc,1229 -n-edges-lscc,367432 -n-edges-metric-lscc,24333 diff --git a/networks/yeast_grn/network-stats.csv b/networks/yeast_grn/network-stats.csv index 286d7c1..3fba1c4 100644 --- a/networks/yeast_grn/network-stats.csv +++ b/networks/yeast_grn/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,6216 n-edges,1666106 density,0.04312712321561879 -n-edges-metric,106160 -n-edges-ultrametric,22963 -%-edges-metric,0.06371743454498092 -%-edges-ultrametric,0.013782436411608865 -%-redundancy-metric,0.9362825654550191 -%-redundancy-ultrametric,0.9862175635883912 -%-edges-ultrametric/metric,0.21630557648831955 +LSCC-nodes,1229 +LSCC-edges,367432 +tau-metric,0.06371743454498092 +tau-ultrametric,0.013782436411608865 +LSCC-tau-metric,0.06622449868274946 +LSCC-tau-ultrametric,0.015491301791896188 +ultrametric_metric_ratio,0.21630557648831955 +LSCC-ultrametric_metric_ratio,0.2339210126166112 From 578f6d7e6095fa974eee7914d610a32733b22808 Mon Sep 17 00:00:00 2001 From: fcphysics Date: Thu, 18 May 2023 14:49:37 -0400 Subject: [PATCH 04/12] Adjust variables name --- 22-network-stats.py | 10 +++++----- .../business/undirected_networks-stats.csv | 2 +- .../computer_science/undirected_networks-stats.csv | 2 +- .../history/undirected_networks-stats.csv | 2 +- networks/bike-sharing/undirected_networks-stats.csv | 2 +- networks/caviar_proj/undirected_networks-stats.csv | 2 +- .../hermaphrodite/undirected_networks-stats.csv | 2 +- networks/celegans/male/undirected_networks-stats.csv | 2 +- .../calls/undirected_networks-stats.csv | 2 +- .../mobility/undirected_networks-stats.csv | 2 +- networks/comorbidity/undirected_networks-stats.csv | 2 +- networks/giraffe/undirected_networks-stats.csv | 2 +- networks/host-pathogen/undirected_networks-stats.csv | 2 +- .../mobility/manizales/undirected_networks-stats.csv | 2 +- .../mobility/medellin/undirected_networks-stats.csv | 2 +- networks/phone-calls/undirected_networks-stats.csv | 2 +- networks/tennis_losses/undirected_networks-stats.csv | 2 +- .../us-airports-2006/undirected_networks-stats.csv | 2 +- networks/weblinks_us/undirected_networks-stats.csv | 2 +- networks/yeast_grn/undirected_networks-stats.csv | 2 +- 20 files changed, 24 insertions(+), 24 deletions(-) diff --git a/22-network-stats.py b/22-network-stats.py index 4fe8ca6..db56759 100644 --- a/22-network-stats.py +++ b/22-network-stats.py @@ -49,7 +49,7 @@ G = pk.load(open(rGfile, 'rb')) B = pk.load(open(rBfile, 'rb')) - df = pd.DataFrame(columns=['n-nodes', 'n-edges', 'density', '%-edges-metric','%-edges-ultrametric'], + df = pd.DataFrame(columns=['n-nodes', 'n-edges', 'density', 'tau-edges-metric','tau-edges-ultrametric'], index=['min', 'max', 'avg', 'harm']) for type in ['min', 'max', 'avg', 'harm']: @@ -59,11 +59,11 @@ df['density'][type] = nx.density(G[type]) if df['n-edges'][type] > 0: - df['%-edges-metric'][type] = B[type].number_of_edges()/df['n-edges'][type] - df['%-edges-ultrametric'][type] = sum([int(d) for _, _, d in B[type].edges(data='ultrametric')])/df['n-edges'][type] + df['tau-edges-metric'][type] = B[type].number_of_edges()/df['n-edges'][type] + df['tau-edges-ultrametric'][type] = sum([int(d) for _, _, d in B[type].edges(data='ultrametric')])/df['n-edges'][type] else: - df['%-edges-metric'][type] = 0.0 - df['%-edges-ultrametric'][type] = 0.0 + df['tau-edges-metric'][type] = 0.0 + df['tau-edges-ultrametric'][type] = 0.0 # Print print(df) diff --git a/networks/academic_hiring/business/undirected_networks-stats.csv b/networks/academic_hiring/business/undirected_networks-stats.csv index ed2f066..471862c 100644 --- a/networks/academic_hiring/business/undirected_networks-stats.csv +++ b/networks/academic_hiring/business/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,113,2944,0.46523388116308473,0.17459239130434784,0.043138586956521736 max,113,488,0.07711757269279393,0.6290983606557377,0.1762295081967213 avg,113,488,0.07711757269279393,0.6618852459016393,0.1721311475409836 diff --git a/networks/academic_hiring/computer_science/undirected_networks-stats.csv b/networks/academic_hiring/computer_science/undirected_networks-stats.csv index 0a90a11..2755dda 100644 --- a/networks/academic_hiring/computer_science/undirected_networks-stats.csv +++ b/networks/academic_hiring/computer_science/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,206,2741,0.12981292919725312,0.3349142648668369,0.11309740970448741 max,206,188,0.008903623016812693,0.824468085106383,0.4787234042553192 avg,206,188,0.008903623016812693,0.8776595744680851,0.4574468085106383 diff --git a/networks/academic_hiring/history/undirected_networks-stats.csv b/networks/academic_hiring/history/undirected_networks-stats.csv index 643823d..6299071 100644 --- a/networks/academic_hiring/history/undirected_networks-stats.csv +++ b/networks/academic_hiring/history/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,145,2266,0.21704980842911878,0.2436010591350397,0.10326566637246248 max,145,162,0.015517241379310345,0.7716049382716049,0.42592592592592593 avg,145,162,0.015517241379310345,0.8148148148148148,0.36419753086419754 diff --git a/networks/bike-sharing/undirected_networks-stats.csv b/networks/bike-sharing/undirected_networks-stats.csv index 540ab8c..cf5125a 100644 --- a/networks/bike-sharing/undirected_networks-stats.csv +++ b/networks/bike-sharing/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,725,35063,0.13359878072013717,0.5589367709551379,0.020762627270912357 max,725,18055,0.0687940560106687,0.6353918582110218,0.04004430905566325 avg,725,18055,0.0687940560106687,0.6767654389365827,0.03998892273608419 diff --git a/networks/caviar_proj/undirected_networks-stats.csv b/networks/caviar_proj/undirected_networks-stats.csv index b1373aa..74a271f 100644 --- a/networks/caviar_proj/undirected_networks-stats.csv +++ b/networks/caviar_proj/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,110,205,0.03419516263552961,0.5902439024390244,0.5560975609756098 max,110,90,0.015012510425354461,0.7555555555555555,0.6888888888888889 avg,110,90,0.015012510425354461,0.7444444444444445,0.6888888888888889 diff --git a/networks/celegans/hermaphrodite/undirected_networks-stats.csv b/networks/celegans/hermaphrodite/undirected_networks-stats.csv index a77856c..d6d81e1 100644 --- a/networks/celegans/hermaphrodite/undirected_networks-stats.csv +++ b/networks/celegans/hermaphrodite/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,313,2932,0.06004751372163513,0.32162346521145974,0.11425648021828104 max,313,568,0.011632669779634636,0.823943661971831,0.43485915492957744 avg,313,568,0.011632669779634636,0.8433098591549296,0.39436619718309857 diff --git a/networks/celegans/male/undirected_networks-stats.csv b/networks/celegans/male/undirected_networks-stats.csv index fac2bf2..77c4e84 100644 --- a/networks/celegans/male/undirected_networks-stats.csv +++ b/networks/celegans/male/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,328,2832,0.052808234504363394,0.330861581920904,0.1228813559322034 max,328,642,0.01197135824569255,0.6947040498442367,0.397196261682243 avg,328,642,0.01197135824569255,0.7305295950155763,0.38161993769470404 diff --git a/networks/colombia_social/calls/undirected_networks-stats.csv b/networks/colombia_social/calls/undirected_networks-stats.csv index f0b922f..b2d504d 100644 --- a/networks/colombia_social/calls/undirected_networks-stats.csv +++ b/networks/colombia_social/calls/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,863,238586,0.6414412573631615,0.009799401473682445,0.0036381011459180337 max,863,199898,0.5374281159178713,0.01570300853435252,0.004317201772904181 avg,863,199898,0.5374281159178713,0.01511771003211638,0.004312199221603017 diff --git a/networks/colombia_social/mobility/undirected_networks-stats.csv b/networks/colombia_social/mobility/undirected_networks-stats.csv index 4a39cb5..c7e2f06 100644 --- a/networks/colombia_social/mobility/undirected_networks-stats.csv +++ b/networks/colombia_social/mobility/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,863,106707,0.2868830201665264,0.013054438790332405,0.008087566888770183 max,863,67150,0.1805335620360637,0.018183172002978407,0.012836932241250931 avg,863,67150,0.1805335620360637,0.018093819806403573,0.012836932241250931 diff --git a/networks/comorbidity/undirected_networks-stats.csv b/networks/comorbidity/undirected_networks-stats.csv index 3fe254b..49ded75 100644 --- a/networks/comorbidity/undirected_networks-stats.csv +++ b/networks/comorbidity/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,95,4465,1.0,0.3659574468085106,0.021052631578947368 max,95,4465,1.0,0.5117581187010078,0.021052631578947368 avg,95,4465,1.0,0.5068309070548712,0.021052631578947368 diff --git a/networks/giraffe/undirected_networks-stats.csv b/networks/giraffe/undirected_networks-stats.csv index bac8580..cc9e332 100644 --- a/networks/giraffe/undirected_networks-stats.csv +++ b/networks/giraffe/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,6,15,1.0,0.7333333333333333,0.3333333333333333 max,6,15,1.0,0.8,0.3333333333333333 avg,6,15,1.0,0.8666666666666667,0.3333333333333333 diff --git a/networks/host-pathogen/undirected_networks-stats.csv b/networks/host-pathogen/undirected_networks-stats.csv index c7d9634..b83c734 100644 --- a/networks/host-pathogen/undirected_networks-stats.csv +++ b/networks/host-pathogen/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,10578,18529,0.00033121950969251893,0.6638242754600896,0.591451238598953 max,10578,0,0,0.0,0.0 avg,10578,0,0,0.0,0.0 diff --git a/networks/mobility/manizales/undirected_networks-stats.csv b/networks/mobility/manizales/undirected_networks-stats.csv index 9dd00af..f2eef06 100644 --- a/networks/mobility/manizales/undirected_networks-stats.csv +++ b/networks/mobility/manizales/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,57,1281,0.8026315789473685,0.11943793911007025,0.04371584699453552 max,57,1237,0.775062656641604,0.2651576394502829,0.04527081649151172 avg,57,1237,0.775062656641604,0.2497978981406629,0.04527081649151172 diff --git a/networks/mobility/medellin/undirected_networks-stats.csv b/networks/mobility/medellin/undirected_networks-stats.csv index 8e36707..42241ab 100644 --- a/networks/mobility/medellin/undirected_networks-stats.csv +++ b/networks/mobility/medellin/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,413,18381,0.2160488022755589,0.15146074751101682,0.02459060986888635 max,413,15503,0.1822210207104069,0.1897697219892924,0.02715603431593885 avg,413,15503,0.1822210207104069,0.20537960394762303,0.026640005160291556 diff --git a/networks/phone-calls/undirected_networks-stats.csv b/networks/phone-calls/undirected_networks-stats.csv index bf76cb0..308f900 100644 --- a/networks/phone-calls/undirected_networks-stats.csv +++ b/networks/phone-calls/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,322,430,0.00832027244054875,0.8651162790697674,0.7465116279069768 max,322,179,0.0034635552717633173,0.9497206703910615,0.9273743016759777 avg,322,179,0.0034635552717633173,0.9553072625698324,0.9273743016759777 diff --git a/networks/tennis_losses/undirected_networks-stats.csv b/networks/tennis_losses/undirected_networks-stats.csv index 1632cfe..1dab4e1 100644 --- a/networks/tennis_losses/undirected_networks-stats.csv +++ b/networks/tennis_losses/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,4245,85084,0.009445497225210344,0.15920737153871467,0.09086314700766301 max,4245,16352,0.0018152974780997547,0.5377323874755382,0.0912426614481409 avg,4245,16352,0.0018152974780997547,0.6114848336594912,0.07772749510763209 diff --git a/networks/us-airports-2006/undirected_networks-stats.csv b/networks/us-airports-2006/undirected_networks-stats.csv index eff8fd9..fa61ad9 100644 --- a/networks/us-airports-2006/undirected_networks-stats.csv +++ b/networks/us-airports-2006/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,1075,11973,0.02074054826555801,0.13822767894429133,0.09003591414014867 max,1075,6933,0.012009873976874107,0.22717438338381654,0.1339968267705178 avg,1075,6933,0.012009873976874107,0.243473243905957,0.13385258906678205 diff --git a/networks/weblinks_us/undirected_networks-stats.csv b/networks/weblinks_us/undirected_networks-stats.csv index e74ab27..bf8b270 100644 --- a/networks/weblinks_us/undirected_networks-stats.csv +++ b/networks/weblinks_us/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,42800,450539,0.0004919092572037996,0.16068975160862878,0.11274939572378861 max,42800,54937,5.9981530706565113e-05,0.5996141034275625,0.44960591222673246 avg,42800,54937,5.9981530706565113e-05,0.579208912026503,0.3865336658354115 diff --git a/networks/yeast_grn/undirected_networks-stats.csv b/networks/yeast_grn/undirected_networks-stats.csv index 1b9694d..50825b5 100644 --- a/networks/yeast_grn/undirected_networks-stats.csv +++ b/networks/yeast_grn/undirected_networks-stats.csv @@ -1,4 +1,4 @@ -,n-nodes,n-edges,density,%-edges-metric,%-edges-ultrametric +,n-nodes,n-edges,density,tau-edges-metric,tau-edges-ultrametric min,6216,1613628,0.08353746229852424,0.00934911887994011,0.003910442803421854 max,6216,52478,0.0027167841327133363,0.09838408475932772,0.02519150882274477 avg,6216,52478,0.0027167841327133363,0.09392507336407638,0.023324059605930102 From f692d58444a91c4710e05f67229e825e548f9bff Mon Sep 17 00:00:00 2001 From: fcphysics Date: Thu, 18 May 2023 14:57:51 -0400 Subject: [PATCH 05/12] Summary of entire undirected vs LSCC and WCC --- .gitignore | 2 +- Summary/BackboneCompareStats.csv | 21 + Summary/BackboneCompareStats_LSCC.csv | 20 + Summary/BackboneCompareStats_WCC.csv | 21 + Summary/BackboneStats.csv | 21 + combining_data.html | 15493 ++++++++++++++++++++++++ 6 files changed, 15577 insertions(+), 1 deletion(-) create mode 100644 Summary/BackboneCompareStats.csv create mode 100644 Summary/BackboneCompareStats_LSCC.csv create mode 100644 Summary/BackboneCompareStats_WCC.csv create mode 100644 Summary/BackboneStats.csv create mode 100644 combining_data.html diff --git a/.gitignore b/.gitignore index 653d0f7..4a80fb5 100644 --- a/.gitignore +++ b/.gitignore @@ -14,7 +14,7 @@ networks/example.py *old/ *.ipynb nohup.out -Summary/ +Summary/BackboneStats.tex # New stuff for now new_networks/ diff --git a/Summary/BackboneCompareStats.csv b/Summary/BackboneCompareStats.csv new file mode 100644 index 0000000..f2a317b --- /dev/null +++ b/Summary/BackboneCompareStats.csv @@ -0,0 +1,21 @@ +,n-edges,n-min-edges,n-max-edges,%-metric,%-min-metric,%-max-metric,%-avg-metric,%-harm-metric,%-ultrametric,%-min-ultrametric,%-max-ultrametric,%-avg-ultrametric,%-harm-ultrametric +business-faculty,3432.0,2944,488,0.3508158508158508,0.1745923913043478,0.6290983606557377,0.6618852459016393,0.1864809782608695,0.0976107226107226,0.0431385869565217,0.1762295081967213,0.1721311475409836,0.0407608695652173 +cs-faculty,2929.0,2741,188,0.5148514851485149,0.3349142648668369,0.824468085106383,0.8776595744680851,0.3283473184968989,0.2266985319221577,0.1130974097044874,0.4787234042553192,0.4574468085106383,0.0981393651951842 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b/Summary/BackboneCompareStats_WCC.csv @@ -0,0 +1,21 @@ +,n-nodes,n-edges,n-min-edges,tau-metric,tau-min-metric,tau-harm-metric,tau-ultrametric,tau-min-ultrametric,tau-harm-ultrametric +business-faculty,113.0,3432.0,2944,0.3508158508158508,0.1745923913043478,0.1864809782608695,0.0976107226107226,0.0431385869565217,0.0407608695652173 +cs-faculty,206.0,2929.0,2741,0.5148514851485149,0.3349142648668369,0.3283473184968989,0.2266985319221577,0.1130974097044874,0.0981393651951842 +history-faculty,145.0,2428.0,2266,0.414332784184514,0.2436010591350397,0.2471315092674316,0.2199341021416803,0.1032656663724624,0.0966460723742277 +caviar-proj,110.0,295.0,205,0.7050847457627119,0.5902439024390244,0.5951219512195122,0.6474576271186441,0.5560975609756098,0.5317073170731708 +celegans-her,313.0,3500.0,2932,0.5568571428571428,0.3216234652114597,0.3219645293315143,0.2677142857142857,0.114256480218281,0.1105047748976807 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+history-faculty,145.0,2428.0,0.1162835249042145,0.414332784184514,0.2199341021416803,0.5308151093439363,116.0,1897.0,0.430152872957301,0.2087506589351608,0.4852941176470589 +caviar-proj,110.0,295.0,0.024603836530442,0.7050847457627119,0.6474576271186441,0.9182692307692308,66.0,242.0,0.6611570247933884,0.5991735537190083,0.90625 +celegans-her,313.0,3500.0,0.0358400917506348,0.5568571428571428,0.2677142857142857,0.4807593637762956,249.0,3046.0,0.5531845042678923,0.2567301378857518,0.4640949554896142 +celegans-male,328.0,3474.0,0.0323897963750279,0.5400115141047783,0.2769142199194012,0.5127931769722814,289.0,3206.0,0.5343106674984405,0.2682470368059887,0.5020431990659661 +colombia-calls,863.0,438484.0,0.5894346866405165,0.026014632232875,0.0089011229600167,0.3421583238362409,863.0,438484.0,0.026014632232875,0.0089011229600167,0.3421583238362409 +colombia-mobility,863.0,173857.0,0.233708291101295,0.0170887568518955,0.0121651702261053,0.7118815213732751,863.0,173857.0,0.0170887568518955,0.0121651702261053,0.7118815213732751 +mobility-manizales,57.0,2518.0,0.7888471177944862,0.2664813343923749,0.0766481334392374,0.2876304023845007,57.0,2518.0,0.2664813343923749,0.0766481334392374,0.2876304023845007 +mobility-medellin,413.0,33884.0,0.1991349114929829,0.2467241175776177,0.0544209656475032,0.2205741626794258,413.0,33884.0,0.2467241175776177,0.0544209656475032,0.2205741626794258 +tennis-loss,4245.0,101436.0,0.005630397351655,0.5961985882724082,0.2377656847667494,0.3988028308750578,2428.0,98102.0,0.5824753827648774,0.2118611241361032,0.3637254558818382 +yeast-grn,6216.0,1666106.0,0.0431271232156187,0.0637174345449809,0.0137824364116088,0.2163055764883195,1229.0,367432.0,0.0662244986827494,0.0154913017918961,0.2339210126166112 +bike-sharing,725.0,53118.0,0.1011964183654029,0.5953160887081592,0.0275236266425693,0.0462336348112073,723.0,53115.0,0.5952932316671373,0.0274875270639179,0.0461747683354944 +giraffe,6.0,30.0,1.0,0.7666666666666667,0.3333333333333333,0.4347826086956521,6.0,30.0,0.7666666666666667,0.3333333333333333,0.4347826086956521 +comorbidity,95.0,8930.0,1.0,0.4743561030235162,0.0217245240761478,0.0457979225684608,95.0,8930.0,0.4743561030235162,0.0217245240761478,0.0457979225684608 +phone-calls,322.0,609.0,0.005891913856156,0.916256157635468,0.8489326765188834,0.9265232974910392,114.0,274.0,0.8832116788321168,0.7737226277372263,0.8760330578512397 +us-airports,1075.0,18906.0,0.016375211121216,0.2743044536126097,0.1898339151592087,0.692055534130351,995.0,18820.0,0.2710945802337938,0.1862911795961742,0.6871814974519795 +DDI,412.0,2966.0,0.0175158859518578,0.5900202292650034,0.4049224544841537,0.6862857142857143,412.0,2966.0,0.5900202292650034,0.4049224544841537,0.6862857142857143 +us-weblinks,42800.0,505476.0,0.0002759453939551,0.367809747643805,0.2536678299266434,0.6896713084730447,27725.0,372626.0,0.3800352095666969,0.2562837805198778,0.6743685165700404 +host-pathogen,10578.0,18529.0,0.0001656097548462,0.9985967942144746,0.9984348858546064,0.9998378641301412,1.0,0.0,0.0,0.0,0.0 diff --git a/combining_data.html b/combining_data.html new file mode 100644 index 0000000..ab66881 --- /dev/null +++ b/combining_data.html @@ -0,0 +1,15493 @@ + + + + + +combining_data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From bf6bb8a35b575ec9084b487ba2f2e7d407ed5186 Mon Sep 17 00:00:00 2001 From: fcphysics Date: Thu, 18 May 2023 15:02:49 -0400 Subject: [PATCH 06/12] Results undirected within LSCC --- 22-network-stats.py | 24 ++++++++++++++++++- Summary/BackboneCompareStats_LSCC.csv | 6 ++--- combining_data.html | 18 +++----------- .../business/undirected_networks-stats.csv | 4 ++-- .../undirected_networks-stats.csv | 4 ++-- .../history/undirected_networks-stats.csv | 4 ++-- .../undirected_networks-stats.csv | 4 ++-- .../caviar_proj/undirected_networks-stats.csv | 4 ++-- .../undirected_networks-stats.csv | 4 ++-- .../male/undirected_networks-stats.csv | 4 ++-- .../undirected_networks-stats.csv | 4 ++-- .../phone-calls/undirected_networks-stats.csv | 4 ++-- .../undirected_networks-stats.csv | 4 ++-- .../undirected_networks-stats.csv | 4 ++-- .../weblinks_us/undirected_networks-stats.csv | 4 ++-- .../yeast_grn/undirected_networks-stats.csv | 4 ++-- 16 files changed, 55 insertions(+), 45 deletions(-) diff --git a/22-network-stats.py b/22-network-stats.py index db56759..e7b79c7 100644 --- a/22-network-stats.py +++ b/22-network-stats.py @@ -52,7 +52,8 @@ df = pd.DataFrame(columns=['n-nodes', 'n-edges', 'density', 'tau-edges-metric','tau-edges-ultrametric'], index=['min', 'max', 'avg', 'harm']) - for type in ['min', 'max', 'avg', 'harm']: + # Min and Harm can be done in entrie network + for type in ['min', 'harm']: print(type) df['n-nodes'][type] = G[type].number_of_nodes() df['n-edges'][type] = G[type].number_of_edges() @@ -64,6 +65,27 @@ else: df['tau-edges-metric'][type] = 0.0 df['tau-edges-ultrametric'][type] = 0.0 + + # Max and Avg Should be in a subset of the LSCC + rDfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) + D = nx.read_graphml(rDfile) + lscc_nodes = max(nx.strongly_connected_components(D), key=len) + for type in ['max', 'avg']: + print(type) + g = G[type].subgraph(lscc_nodes) + + df['n-nodes'][type] = g.number_of_nodes() + df['n-edges'][type] = g.number_of_edges() + df['density'][type] = nx.density(g) + + if df['n-edges'][type] > 0: + b = B[type].subgraph(lscc_nodes) + df['tau-edges-metric'][type] = b.number_of_edges()/df['n-edges'][type] + df['tau-edges-ultrametric'][type] = sum([int(d) for _, _, d in b.edges(data='ultrametric')])/df['n-edges'][type] + else: + df['tau-edges-metric'][type] = 0.0 + df['tau-edges-ultrametric'][type] = 0.0 + # Print print(df) diff --git a/Summary/BackboneCompareStats_LSCC.csv b/Summary/BackboneCompareStats_LSCC.csv index 391ba8a..9a12889 100644 --- a/Summary/BackboneCompareStats_LSCC.csv +++ b/Summary/BackboneCompareStats_LSCC.csv @@ -14,7 +14,7 @@ yeast-grn,1229.0,367432.0,52478,0.0662244986827494,0.0983840847593277,0.09392507 bike-sharing,723.0,53115.0,18055,0.5952932316671373,0.6353918582110218,0.6767654389365827,0.0274875270639179,0.0400443090556632,0.0399889227360841 giraffe,6.0,30.0,15,0.7666666666666667,0.8,0.8666666666666667,0.3333333333333333,0.3333333333333333,0.3333333333333333 comorbidity,95.0,8930.0,4465,0.4743561030235162,0.5117581187010078,0.5068309070548712,0.0217245240761478,0.0210526315789473,0.0210526315789473 -phone-calls,114.0,274.0,179,0.8832116788321168,0.9497206703910616,0.9553072625698324,0.7737226277372263,0.9273743016759776,0.9273743016759776 -us-airports,995.0,18820.0,6933,0.2710945802337938,0.2271743833838165,0.243473243905957,0.1862911795961742,0.1339968267705178,0.133852589066782 +phone-calls,114.0,274.0,97,0.8832116788321168,0.9484536082474226,0.9587628865979382,0.7737226277372263,0.9072164948453608,0.9072164948453608 +us-airports,995.0,18820.0,6932,0.2710945802337938,0.2270628967109059,0.2433641084824004,0.1862911795961742,0.133871898442008,0.1337276399307559 DDI,412.0,2966.0,1483,0.5900202292650034,0.4389750505731625,0.4598786244099798,0.4049224544841537,0.2784895482130816,0.2771409305461901 -us-weblinks,27725.0,372626.0,54937,0.3800352095666969,0.5996141034275625,0.579208912026503,0.2562837805198778,0.4496059122267324,0.3865336658354115 +us-weblinks,27725.0,372626.0,54259,0.3800352095666969,0.5953850974031958,0.5753884148251903,0.2562837805198778,0.44735435595938,0.3844339187968816 diff --git a/combining_data.html b/combining_data.html index ab66881..5c87d48 100644 --- a/combining_data.html +++ b/combining_data.html @@ -15079,7 +15079,7 @@

Plot Comparison - LSCC - @@ -15202,7 +15202,7 @@

Comparability of LSCC and @@ -15453,18 +15453,6 @@

Which components are in the LSCC? - - @@ -15285,20 +15284,25 @@

Comparability of LSCC and - - -

ax[0].scatter(df['tau-metric'], df['tau-min-metric'], marker='v', c='r', label='Minimum') ax[0].scatter(df['tau-metric'], df['tau-harm-metric'], marker='o', c='k', label='Harmonic Average', alpha=0.5) -ax[0].plot([0, 1], [0, 1], 'k--') +ax[0].vlines(df['tau-metric'], ymin=df[['tau-min-metric', 'tau-harm-metric']].min(axis=1), ymax=df[['tau-min-metric', 'tau-harm-metric']].max(axis=1), linestyle='--', color='k') +ax[0].plot([0, 1], [0, 1], 'k-') + ax[0].legend() ax[0].set_xlabel('WCC Directed Network') ax[0].set_ylabel('Undirected Representation') @@ -14873,7 +14875,9 @@

Plot Comparison - WCCax[1].scatter(df['tau-ultrametric'], df['tau-min-ultrametric'], marker='v', c='r', label='Minimum') ax[1].scatter(df['tau-ultrametric'], df['tau-harm-ultrametric'], marker='o', c='k', label='Harmonic Average', alpha=0.5) -ax[1].plot([0, 1], [0, 1], 'k--') +ax[1].vlines(df['tau-ultrametric'], ymin=df[['tau-min-ultrametric', 'tau-harm-ultrametric']].min(axis=1), ymax=df[['tau-min-ultrametric', 'tau-harm-ultrametric']].max(axis=1), linestyle='--', color='k') +ax[1].plot([0, 1], [0, 1], 'k-') + ax[1].legend() ax[1].set_xlabel('WCC Directed Network') #ax[0].set_ylabel('Unirected Representation') @@ -14905,7 +14909,7 @@

Plot Comparison - WCC - @@ -15036,7 +15040,9 @@

Plot Comparison - LSCCax[0].scatter(df['tau-metric'], df['tau-max-metric'], marker='^', c='b', label='Maximum') ax[0].scatter(df['tau-metric'], df['tau-avg-metric'], marker='s', c='g', label='Average', alpha=0.5) -ax[0].plot([0, 1], [0, 1], 'k--') +ax[0].vlines(df['tau-metric'], ymin=df[['tau-max-metric', 'tau-avg-metric']].min(axis=1), ymax=df[['tau-max-metric', 'tau-avg-metric']].max(axis=1), linestyle='--', color='k') +ax[0].plot([0, 1], [0, 1], 'k-') + ax[0].legend() ax[0].set_xlabel('LSCC Directed Network') ax[0].set_ylabel('Undirected Representation') @@ -15047,7 +15053,9 @@

Plot Comparison - LSCCax[1].scatter(df['tau-ultrametric'], df['tau-max-ultrametric'], marker='^', c='b', label='Maximum') ax[1].scatter(df['tau-ultrametric'], df['tau-avg-ultrametric'], marker='s', c='g', label='Average', alpha=0.5) -ax[1].plot([0, 1], [0, 1], 'k--') +ax[1].vlines(df['tau-ultrametric'], ymin=df[['tau-max-ultrametric', 'tau-avg-ultrametric']].min(axis=1), ymax=df[['tau-max-ultrametric', 'tau-avg-ultrametric']].max(axis=1), linestyle='--', color='k') +ax[1].plot([0, 1], [0, 1], 'k-') + ax[1].legend() ax[1].set_xlabel('LSCC Directed Network') #ax[0].set_ylabel('Unirected Representation') @@ -15079,7 +15087,7 @@

Plot Comparison - LSCC - @@ -15424,6 +15432,386 @@

Components breaking points + + + + @@ -15292,25 +15344,27 @@

Which components are in the LSCC?