History of physics_collab
The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.
[entries] Add the date when each entry was added, and remove icon_hash beff7c9
The dates are those of the commits that first added the entries' files (2020-08-11 for the entries of the initial commit); renamed entries keep the date of their first name. Changed: none
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 6307dfc..1cc52e4 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -34,7 +34,7 @@ The networks have the following properties:
tags = ['Social', 'Collaboration', 'Weighted', 'Multilayer', 'Projection']
url = 'https://manliodedomenico.com/data.php'
citation = [('M. De Domenico et al., "Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems." Physical Review X 5(1), 011027 (2015).', 'https://arxiv.org/abs/1408.2925')]
-icon_hash = '58a4c4caa411221d0e7c67e5'
+date_added = '2020-08-11'
upstream_license = ("Open Data Commons Open Database License (ODbL)",
"https://opendatacommons.org/licenses/odbl/")
upstream_prefix = 'https://manliodedomenico.com/data'
[entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) bc3dbbd
The lists of properties at the end of the descriptions marked edge properties with "Edge" but left node properties unmarked, or grouped them in "Nodes: `a`, ...; `b`, ..." items, so the kind of a property was often unclear. Every item now starts with (Node), (Edge) or (Graph), followed by the property names, a colon and the explanation, one item per property or group of properties; qualifications (kinds of nodes, networks) follow the names in parentheses. Properties that were only named got a short explanation, and a few items that named the wrong kind of property were corrected.
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 302aa1b..6307dfc 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -28,9 +28,9 @@ The edges are weighted as follows: for each report or preprint with $N > 1$ auth
The networks have the following properties:
-- `name`: empty, since the identities of the authors are not provided.
-- `layer`: the layer of the edge, numbered as listed above (see the graph property `layer_key`).
-- `weight`: the edge weight, as defined above."""
+- (Node) `name`: empty, since the identities of the authors are not provided.
+- (Edge) `layer`: the layer of the edge, numbered as listed above (see the graph property `layer_key`).
+- (Edge) `weight`: the edge weight, as defined above."""
tags = ['Social', 'Collaboration', 'Weighted', 'Multilayer', 'Projection']
url = 'https://manliodedomenico.com/data.php'
citation = [('M. De Domenico et al., "Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems." Physical Review X 5(1), 011027 (2015).', 'https://arxiv.org/abs/1408.2925')]
[entries] Remove unneeded code from the entries 2c69f19
Unneeded "global files" statements, unused imports and variables, f-strings without placeholders, duplicate keys in foodweb_little_rock (keeping the order and the values used), and the second definition of get_lines() in twitter_higgs. Nothing changes in the networks or descriptions. Changed: none
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 6210343..302aa1b 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -49,7 +49,6 @@ def fetch_upstream(force=False):
@coerce_props()
@annotate()
def parse(alts=None):
- global files
name = __name__.split(".")[-1]
for fnames, alt, fmt in files:
if alts is not None and alt not in alts:
[entries] Fix parse bugs and improve the metadata of existing entries c996a0e
From a review of the dataset descriptions against the upstream sources and papers, and from user reports: - parse fixes (wrong edge direction or directedness, shifted or misnamed properties, merged node identities, duplicated or missing edges and nodes, wrong types), e.g. arxiv_citation (the HepTh dates were a copy of the HepPh ones; now from the KDD Cup 2003 data), eu_procurements, foursquare_global, hiv_transmission, genetic_multiplex, gnutella (adds the 05 snapshot), roadnet, macaque_neural, python_dependency - descriptions rewritten from the upstream sources, documenting every property - corrected titles, citations and DOIs, licences (ustream_license typo, the data's own terms), tags and ICON ids - url lists for entries with several sources or dataset pages - SocioPatterns entries moved to the site's new data location, with the daily networks of sp_infectious and sp_primary_school - the Michael Fire entries marked as orphans (served from the mirror) - redundant type forcings removed after the graph-tool coercion fixes
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index e215118..6210343 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -19,8 +19,18 @@
from .. import *
title = "Multilayer physicist collaborations (2015)"
-description = """Two multiplex networks of coauthorships among the Pierre Auger Collaboration of physicists (2010-2012) and among researchers who have posted preprints on arXiv.org (all papers up to May 2014). Layers represent different categories of publication, and an edge's weight indicates the number of reports written by the authors. These layers are one-mode projections from the underlying author-paper bipartite network[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """Two multilayer coauthorship networks of scientists, assembled by M. De Domenico, A. Lancichinetti, A. Arenas and M. Rosvall. Nodes are scientists (anonymized) and edges are coauthorships, with layers corresponding to research topics:
+
+- `pierreAuger`: coauthorships of internal technical reports of the Pierre Auger Collaboration, which operates an observatory of ultra-high-energy cosmic rays, submitted between 2010 and 2012. Each report was assigned to one or more of 16 layers corresponding to working tasks (neutrinos, detector, enhancements, anisotropy, point source, mass composition, horizontal showers, hybrid reconstruction, spectrum, photons, atmospheric, SD reconstruction, hadronic interactions, exotics, magnetic fields, astrophysical scenarios), according to its keywords and content, with manual disambiguation.
+- `arXiv`: coauthorships of preprints posted on arXiv up to May 2014 with "networks" in the title or abstract, with 13 layers corresponding to the arXiv categories of the preprints (physics.soc-ph, physics.data-an, physics.bio-ph, math-ph, math.OC, cond-mat.dis-nn, cond-mat.stat-mech, q-bio.MN, q-bio, q-bio.BM, nlin.AO, cs.SI, cs.CV).
+
+The edges are weighted as follows: for each report or preprint with $N > 1$ authors, classified into $L$ layers, a weight $1/[L(N-1)]$ is added to the edge between each pair of its coauthors in each of these layers. Hence, the sum of the weights of the edges of an author over all layers is the number of (multi-author) papers they wrote. Each pair of authors has at most one edge per layer.
+
+The networks have the following properties:
+
+- `name`: empty, since the identities of the authors are not provided.
+- `layer`: the layer of the edge, numbered as listed above (see the graph property `layer_key`).
+- `weight`: the edge weight, as defined above."""
tags = ['Social', 'Collaboration', 'Weighted', 'Multilayer', 'Projection']
url = 'https://manliodedomenico.com/data.php'
citation = [('M. De Domenico et al., "Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems." Physical Review X 5(1), 011027 (2015).', 'https://arxiv.org/abs/1408.2925')]
Update copyright information 73a4f0d
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 0701614..e215118 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2026 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright information 3d288ea
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 2a7c8d9..0701614 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright information 8d005ae
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 1bf4cc1..2a7c8d9 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright info db2efcc
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index d868d2e..1bf4cc1 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update comunelab's datasets ddccc3b
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 8ceb053..d868d2e 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -22,12 +22,12 @@ title = "Multilayer physicist collaborations (2015)"
description = """Two multiplex networks of coauthorships among the Pierre Auger Collaboration of physicists (2010-2012) and among researchers who have posted preprints on arXiv.org (all papers up to May 2014). Layers represent different categories of publication, and an edge's weight indicates the number of reports written by the authors. These layers are one-mode projections from the underlying author-paper bipartite network[^icon]
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Social', 'Collaboration', 'Weighted', 'Multilayer', 'Projection']
-url = 'https://comunelab.fbk.eu/data.php'
+url = 'https://manliodedomenico.com/data.php'
citation = [('M. De Domenico et al., "Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems." Physical Review X 5(1), 011027 (2015).', 'https://arxiv.org/abs/1408.2925')]
icon_hash = '58a4c4caa411221d0e7c67e5'
upstream_license = ("Open Data Commons Open Database License (ODbL)",
"https://opendatacommons.org/licenses/odbl/")
-upstream_prefix = 'https://comunelab.fbk.eu/data'
+upstream_prefix = 'https://manliodedomenico.com/data'
files = [('PierreAuger_Multiplex_Coauthorship.zip', 'pierreAuger', 'comunelab'),
('arXiv-Netscience_Multiplex_Coauthorship.zip', 'arXiv', 'comunelab')]
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index e8f4bf9..8ceb053 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -3,18 +3,18 @@
#
# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+# details.
#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU Affero General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
from .. import *
Add explicit attribution to descriptions obtained from ICON 1645314
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
index 947f2bf..e8f4bf9 100644
--- a/entries/physics_collab/__init__.py
+++ b/entries/physics_collab/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "Multilayer physicist collaborations (2015)"
-description = "Two multiplex networks of coauthorships among the Pierre Auger Collaboration of physicists (2010-2012) and among researchers who have posted preprints on arXiv.org (all papers up to May 2014). Layers represent different categories of publication, and an edge's weight indicates the number of reports written by the authors. These layers are one-mode projections from the underlying author-paper bipartite network"
+description = """Two multiplex networks of coauthorships among the Pierre Auger Collaboration of physicists (2010-2012) and among researchers who have posted preprints on arXiv.org (all papers up to May 2014). Layers represent different categories of publication, and an edge's weight indicates the number of reports written by the authors. These layers are one-mode projections from the underlying author-paper bipartite network[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Social', 'Collaboration', 'Weighted', 'Multilayer', 'Projection']
url = 'https://comunelab.fbk.eu/data.php'
citation = [('M. De Domenico et al., "Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems." Physical Review X 5(1), 011027 (2015).', 'https://arxiv.org/abs/1408.2925')]
Initial commit cc85872
diff --git a/entries/physics_collab/__init__.py b/entries/physics_collab/__init__.py
new file mode 100644
index 0000000..947f2bf
--- /dev/null
+++ b/entries/physics_collab/__init__.py
@@ -0,0 +1,51 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from .. import *
+
+title = "Multilayer physicist collaborations (2015)"
+description = "Two multiplex networks of coauthorships among the Pierre Auger Collaboration of physicists (2010-2012) and among researchers who have posted preprints on arXiv.org (all papers up to May 2014). Layers represent different categories of publication, and an edge's weight indicates the number of reports written by the authors. These layers are one-mode projections from the underlying author-paper bipartite network"
+tags = ['Social', 'Collaboration', 'Weighted', 'Multilayer', 'Projection']
+url = 'https://comunelab.fbk.eu/data.php'
+citation = [('M. De Domenico et al., "Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems." Physical Review X 5(1), 011027 (2015).', 'https://arxiv.org/abs/1408.2925')]
+icon_hash = '58a4c4caa411221d0e7c67e5'
+upstream_license = ("Open Data Commons Open Database License (ODbL)",
+ "https://opendatacommons.org/licenses/odbl/")
+upstream_prefix = 'https://comunelab.fbk.eu/data'
+files = [('PierreAuger_Multiplex_Coauthorship.zip', 'pierreAuger', 'comunelab'),
+ ('arXiv-Netscience_Multiplex_Coauthorship.zip', 'arXiv', 'comunelab')]
+
+def fetch_upstream(force=False):
+ return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+ force)
+
+@cache_network()
+@coerce_props()
+@annotate()
+def parse(alts=None):
+ global files
+ name = __name__.split(".")[-1]
+ for fnames, alt, fmt in files:
+ if alts is not None and alt not in alts:
+ continue
+ if isinstance(fnames, str):
+ fnames = [fnames]
+ with ExitStack() as stack:
+ fs = [stack.enter_context(open_upstream_file(name, fn, "rb")) for fn in fnames]
+ g = parse_graph(fs, fmt, directed=False)
+ yield alt, g