History of sp_hospital
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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index 224ebf5..5b3069d 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__init__.py
@@ -29,7 +29,7 @@ The network has the following properties:
tags = ['Social', 'Offline', 'Unweighted', 'Temporal', 'Metadata']
url = 'https://sociopatterns.org/datasets/hospital-ward-dynamic-contact-network/'
citation = [('P. Vanhems et al., "Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors." PLoS ONE 8(9), e73970 (2013).', 'https://doi.org/10.1371/journal.pone.0073970')]
-icon_hash = '56a85c8e26855e083a2f78d8'
+date_added = '2020-08-11'
upstream_license = ("Creative Commons Attribution-NonCommercial-ShareAlike",
"http://creativecommons.org/licenses/by-nc-sa/3.0/")
upstream_prefix = 'https://sociopatterns.org/assets/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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index 5eab556..224ebf5 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__init__.py
@@ -23,9 +23,9 @@ description = r"""Temporal network of face-to-face proximity contacts among pati
The network has the following properties:
-- `id`: the anonymous identifier of the person.
-- `status`: the role of the person: `NUR` (paramedical staff, i.e. nurses and nurses' aides), `PAT` (patient), `MED` (medical doctor) or `ADM` (administrative staff).
-- `time`: the end of the 20-second interval $[t - 20\,\text{s}, t]$ during which the contact was active, in seconds since the beginning of the data collection."""
+- (Node) `id`: the anonymous identifier of the person.
+- (Node) `status`: the role of the person: `NUR` (paramedical staff, i.e. nurses and nurses' aides), `PAT` (patient), `MED` (medical doctor) or `ADM` (administrative staff).
+- (Edge) `time`: the end of the 20-second interval $[t - 20\,\text{s}, t]$ during which the contact was active, in seconds since the beginning of the data collection."""
tags = ['Social', 'Offline', 'Unweighted', 'Temporal', 'Metadata']
url = 'https://sociopatterns.org/datasets/hospital-ward-dynamic-contact-network/'
citation = [('P. Vanhems et al., "Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors." PLoS ONE 8(9), e73970 (2013).', 'https://doi.org/10.1371/journal.pone.0073970')]
[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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index 3440810..5eab556 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__init__.py
@@ -43,7 +43,6 @@ 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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index ff86510..3440810 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__init__.py
@@ -19,20 +19,21 @@
from .. import *
title = "Hospital ward dynamic contacts (2010)"
-description = """This dataset contains the temporal network of contacts between patients, patients and health-care workers (HCWs) and among HCWs in a hospital ward in Lyon, France, from Monday, December 6, 2010 at 1:00 pm to Friday, December 10, 2010 at 2:00 pm. The study included 46 HCWs and 29 patients.[^icon]
+description = r"""Temporal network of face-to-face proximity contacts among patients and health-care workers in a geriatric unit of a hospital in Lyon, France, measured by the SocioPatterns collaboration with wearable sensors from Monday, 6 December 2010 at 1:00 pm to Friday, 10 December 2010 at 2:00 pm. The study included 46 health-care workers and 29 patients. Nodes are persons, and each edge is a contact between two persons active during a 20-second interval of the data collection, so that a pair of persons is connected by one edge per interval in which they were in contact.
-The file contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j Si Sj“, where i and j are the anonymous IDs of the persons in contact, Si and Sj are their statuses (NUR=paramedical staff, i.e. nurses and nurses’ aides; PAT=Patient; MED=Medical doctor; ADM=administrative staff), and the interval during which this contact was active is [ t – 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds.
+The network has the following properties:
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project.
-"""
+- `id`: the anonymous identifier of the person.
+- `status`: the role of the person: `NUR` (paramedical staff, i.e. nurses and nurses' aides), `PAT` (patient), `MED` (medical doctor) or `ADM` (administrative staff).
+- `time`: the end of the 20-second interval $[t - 20\,\text{s}, t]$ during which the contact was active, in seconds since the beginning of the data collection."""
tags = ['Social', 'Offline', 'Unweighted', 'Temporal', 'Metadata']
-url = 'http://www.sociopatterns.org/datasets/hospital-ward-dynamic-contact-network/'
+url = 'https://sociopatterns.org/datasets/hospital-ward-dynamic-contact-network/'
citation = [('P. Vanhems et al., "Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors." PLoS ONE 8(9), e73970 (2013).', 'https://doi.org/10.1371/journal.pone.0073970')]
icon_hash = '56a85c8e26855e083a2f78d8'
-ustream_license = ("Creative Commons Attribution-NonCommercial-ShareAlike",
+upstream_license = ("Creative Commons Attribution-NonCommercial-ShareAlike",
"http://creativecommons.org/licenses/by-nc-sa/3.0/")
-upstream_prefix = 'http://www.sociopatterns.org/wp-content/uploads/2013/09'
-files = [('detailed_list_of_contacts_Hospital.dat_.gz', None, None)]
+upstream_prefix = 'https://sociopatterns.org/assets/data'
+files = [('hospital_lyon_contacts.dat.gz', None, None)]
def fetch_upstream(force=False):
return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
Update copyright information 73a4f0d
diff --git a/entries/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index f058297..ff86510 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index cfc4e1a..f058297 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index f158d63..cfc4e1a 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index 318fef1..f158d63 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__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 citations to use DOIs e878874
diff --git a/entries/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index 5c293aa..318fef1 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__init__.py
@@ -27,7 +27,7 @@ The file contains a tab-separated list representing the active contacts during 2
"""
tags = ['Social', 'Offline', 'Unweighted', 'Temporal', 'Metadata']
url = 'http://www.sociopatterns.org/datasets/hospital-ward-dynamic-contact-network/'
-citation = [('P. Vanhems et al., "Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors." PLoS ONE 8(9), e73970 (2013).', 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073970')]
+citation = [('P. Vanhems et al., "Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors." PLoS ONE 8(9), e73970 (2013).', 'https://doi.org/10.1371/journal.pone.0073970')]
icon_hash = '56a85c8e26855e083a2f78d8'
ustream_license = ("Creative Commons Attribution-NonCommercial-ShareAlike",
"http://creativecommons.org/licenses/by-nc-sa/3.0/")
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index a3f26f3..5c293aa 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__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/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
index 2a8ed0d..a3f26f3 100644
--- a/entries/sp_hospital/__init__.py
+++ b/entries/sp_hospital/__init__.py
@@ -19,9 +19,11 @@
from .. import *
title = "Hospital ward dynamic contacts (2010)"
-description = """This dataset contains the temporal network of contacts between patients, patients and health-care workers (HCWs) and among HCWs in a hospital ward in Lyon, France, from Monday, December 6, 2010 at 1:00 pm to Friday, December 10, 2010 at 2:00 pm. The study included 46 HCWs and 29 patients.
+description = """This dataset contains the temporal network of contacts between patients, patients and health-care workers (HCWs) and among HCWs in a hospital ward in Lyon, France, from Monday, December 6, 2010 at 1:00 pm to Friday, December 10, 2010 at 2:00 pm. The study included 46 HCWs and 29 patients.[^icon]
The file contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j Si Sj“, where i and j are the anonymous IDs of the persons in contact, Si and Sj are their statuses (NUR=paramedical staff, i.e. nurses and nurses’ aides; PAT=Patient; MED=Medical doctor; ADM=administrative staff), and the interval during which this contact was active is [ t – 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds.
+
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project.
"""
tags = ['Social', 'Offline', 'Unweighted', 'Temporal', 'Metadata']
url = 'http://www.sociopatterns.org/datasets/hospital-ward-dynamic-contact-network/'
Initial commit cc85872
diff --git a/entries/sp_hospital/__init__.py b/entries/sp_hospital/__init__.py
new file mode 100644
index 0000000..2a8ed0d
--- /dev/null
+++ b/entries/sp_hospital/__init__.py
@@ -0,0 +1,78 @@
+#! /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 = "Hospital ward dynamic contacts (2010)"
+description = """This dataset contains the temporal network of contacts between patients, patients and health-care workers (HCWs) and among HCWs in a hospital ward in Lyon, France, from Monday, December 6, 2010 at 1:00 pm to Friday, December 10, 2010 at 2:00 pm. The study included 46 HCWs and 29 patients.
+
+The file contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j Si Sj“, where i and j are the anonymous IDs of the persons in contact, Si and Sj are their statuses (NUR=paramedical staff, i.e. nurses and nurses’ aides; PAT=Patient; MED=Medical doctor; ADM=administrative staff), and the interval during which this contact was active is [ t – 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds.
+"""
+tags = ['Social', 'Offline', 'Unweighted', 'Temporal', 'Metadata']
+url = 'http://www.sociopatterns.org/datasets/hospital-ward-dynamic-contact-network/'
+citation = [('P. Vanhems et al., "Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors." PLoS ONE 8(9), e73970 (2013).', 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073970')]
+icon_hash = '56a85c8e26855e083a2f78d8'
+ustream_license = ("Creative Commons Attribution-NonCommercial-ShareAlike",
+ "http://creativecommons.org/licenses/by-nc-sa/3.0/")
+upstream_prefix = 'http://www.sociopatterns.org/wp-content/uploads/2013/09'
+files = [('detailed_list_of_contacts_Hospital.dat_.gz', None, None)]
+
+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, "r")) for fn in fnames]
+
+ g = Graph(directed=False)
+ g.ep.time = g.new_ep("string")
+ def get_edges():
+ reader = csv.reader(fs[0], delimiter="\t")
+ for row in reader:
+ t, i, j, Si, Sj = row
+ yield i, j, t
+ g.vp.id = g.add_edge_list(get_edges(), hashed=True,
+ hash_type="string",
+ eprops=[g.ep.time])
+ vs = {g.vp.id[v] : v for v in g.vertices()}
+
+ g.vp.status = g.new_vp("string")
+ fs[0].seek(0)
+ reader = csv.reader(fs[0], delimiter="\t")
+ for row in reader:
+ t, i, j, Si, Sj = row
+ s = vs[i]
+ g.vp.status[s] = Si
+
+ t = vs[j]
+ g.vp.status[t] = Sj
+
+ g = Graph(g, vorder=g.vp.id)
+
+ yield alt, g