History of macaques
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] Move more KONECT-derived entries to their original sources bf9dc0e
The entries now download the data from where KONECT obtained them (live, or via the Wayback Machine), using the same release as KONECT where it is still available, and gain the metadata KONECT dropped; descriptions and citations are rewritten from the original sources: - Linton Freeman's UCINET data page: bible_nouns, bison, cattle, hens, highschool, kangaroo, macaques, moreno_sheep, physician_trust (the three relations and the physicians' attributes), rhesus_monkey, train_terrorists, windsurfers (now the networks `interaction` and `closeness`), college_freshmen, crime, interactome_yeast (from the primary source), moreno_taro (undirected), residence_hall, zebras - other pages, archived: contiguous_usa, advogato, google, github, digg_reply, twitter, bookcrossing, dbtropes_feature (without KONECT's spurious "ItemName" tropes) - movielens_100k (in fact the MovieLens 10M tag assignments) - dblp release 2017-05-02: dblp_author_paper, dblp_cite, dblp_coauthor - DBpedia 3.9: dbpedia_country, dbpedia_genre, dbpedia_location, dbpedia_occupation, dbpedia_producer, dbpedia_recordlabel, dbpedia_starring, dbpedia_team, dbpedia_writer, dbpedia_all, dbpedia_link - Discogs releases dump of October 2015: discogs_affiliation, discogs_genre and discogs_label (now with genre and style networks)
diff --git a/entries/macaques/__init__.py b/entries/macaques/__init__.py
index 9983e24..b78cbac 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__init__.py
@@ -19,21 +19,35 @@
from .. import *
title = "Japanese macaques (1976)"
-description = """Dominance interactions among a group of adult female Japanese macaques (Macaca fuscata fuscata), observed during a non-mating season in 1976. Edge weights represent the frequency of interaction.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
-tags = ['Social', 'Animal', 'Weighted']
-url = 'http://konect.cc/networks/moreno_mac'
-citation = [('Y. Takahata. "Diachronic changes in the dominance relations of adult female Japanese monkeys of the Arashiyama B group. The Monkeys of Arashiyama." State University of New York Press, Albany, 123-139 (1991)', 'http://www.sunypress.edu/p-1128-the-monkeys-of-arashiyama.aspx')]
-icon_hash = '5734a096461efe0c7a67832f'
-upstream_prefix = 'http://konect.cc/files'
-files = [('download.tsv.moreno_mac.tar.bz2', None, 'konect')]
+description = """Dominance interactions among the 62 adult females of a colony of Japanese macaques (Macaca fuscata fuscata) known as the "Arashiyama B group", observed by Y. Takahata during the non-mating season, from April to early October 1976. Approach-retreat episodes involving food were recorded. The source also reports the lineages of the animals: five lineages of 4, 14, 31, 6 and 6 animals (in the order of the file), plus one animal unrelated to the others. The data were distributed by L. C. Freeman on his network data page at the University of California, Irvine (no longer online), from which this version was obtained via the Internet Archive.
+
+A directed edge (i, j) indicates that female i dominated female j in at least one episode.
+
+The network has the following properties:
+
+- Nodes: `name`, the name of the animal (the name "Gl60" appears twice in the source file, for two different animals); `lineage`, the lineage of the animal (1 to 5, or 0 for the unrelated animal), as given in the source by the order of the animals.
+- Edges: `weight`, the number of episodes in which i dominated j."""
+tags = ['Social', 'Animal', 'Weighted', 'Metadata']
+url = 'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#mac'
+citation = [('Y. Takahata. "Diachronic changes in the dominance relations of adult female Japanese monkeys of the Arashiyama B group." In L. M. Fedigan and P. J. Asquith (eds.), The Monkeys of Arashiyama, State University of New York Press, Albany, 123-139 (1991)', 'http://www.sunypress.edu/p-1128-the-monkeys-of-arashiyama.aspx')]
+icon_hash = ['5734a096461efe0c7a67832f',
+ '586eaa2fa411221d0e7c5bd8']
+upstream_license = None
+upstream_prefix = 'https://web.archive.org/web/20210115130726id_/http://moreno.ss.uci.edu'
+files = [('mac.dat', None, None)]
+
+# sizes of the lineages, in the order of the animals in the file (the last
+# animal is unrelated to the others)
+lineages = [4, 14, 31, 6, 6, 1]
def fetch_upstream(force=False):
- return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
- force)
+ # The Wayback Machine refuses connections or fails when rate-limited, so
+ # retry with increasing pauses (files already fetched are skipped)
+ return retry_download(fetch_upstream_files, __name__.split(".")[-1],
+ upstream_prefix, files, force)
@cache_network()
-@coerce_props()
+@coerce_props(vforce={"name": "string"})
@annotate()
def parse(alts=None):
global files
@@ -44,6 +58,14 @@ def parse(alts=None):
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=True)
+ fs = [stack.enter_context(open_upstream_file(name, fn, "rb"))
+ for fn in fnames]
+ ds = [read_dl(f, pad=False) for f in fs]
+ d = ds[0]
+ g = matrix_graph(d["data"], True)
+ g.vp.name = g.new_vp("string", vals=d["rows"])
+ lin = [k + 1 if k < len(lineages) - 1 else 0
+ for k, n in enumerate(lineages) for i in range(n)]
+ assert len(lin) == g.num_vertices()
+ g.vp.lineage = g.new_vp("int", vals=lin)
yield alt, g
Update copyright information 73a4f0d
diff --git a/entries/macaques/__init__.py b/entries/macaques/__init__.py
index a441250..9983e24 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__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/macaques/__init__.py b/entries/macaques/__init__.py
index 57b6c07..a441250 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__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/macaques/__init__.py b/entries/macaques/__init__.py
index e370713..57b6c07 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__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/macaques/__init__.py b/entries/macaques/__init__.py
index f903851..e370713 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__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
Un-orphan KONECT datasets 894eba5
KONECT has been brought back from the dead for the time being.
diff --git a/entries/macaques/__init__.py b/entries/macaques/__init__.py
index 44a7223..f903851 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__init__.py
@@ -26,7 +26,6 @@ url = 'http://konect.cc/networks/moreno_mac'
citation = [('Y. Takahata. "Diachronic changes in the dominance relations of adult female Japanese monkeys of the Arashiyama B group. The Monkeys of Arashiyama." State University of New York Press, Albany, 123-139 (1991)', 'http://www.sunypress.edu/p-1128-the-monkeys-of-arashiyama.aspx')]
icon_hash = '5734a096461efe0c7a67832f'
upstream_prefix = 'http://konect.cc/files'
-orphan = True
files = [('download.tsv.moreno_mac.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Add support for 'orphan' datasets and tag konect entries e330b80
diff --git a/entries/macaques/__init__.py b/entries/macaques/__init__.py
index f903851..44a7223 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__init__.py
@@ -26,6 +26,7 @@ url = 'http://konect.cc/networks/moreno_mac'
citation = [('Y. Takahata. "Diachronic changes in the dominance relations of adult female Japanese monkeys of the Arashiyama B group. The Monkeys of Arashiyama." State University of New York Press, Albany, 123-139 (1991)', 'http://www.sunypress.edu/p-1128-the-monkeys-of-arashiyama.aspx')]
icon_hash = '5734a096461efe0c7a67832f'
upstream_prefix = 'http://konect.cc/files'
+orphan = True
files = [('download.tsv.moreno_mac.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/macaques/__init__.py b/entries/macaques/__init__.py
index 166100f..f903851 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__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/macaques/__init__.py b/entries/macaques/__init__.py
index 950f86d..166100f 100644
--- a/entries/macaques/__init__.py
+++ b/entries/macaques/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "Japanese macaques (1976)"
-description = "Dominance interactions among a group of adult female Japanese macaques (Macaca fuscata fuscata), observed during a non-mating season in 1976. Edge weights represent the frequency of interaction."
+description = """Dominance interactions among a group of adult female Japanese macaques (Macaca fuscata fuscata), observed during a non-mating season in 1976. Edge weights represent the frequency of interaction.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Social', 'Animal', 'Weighted']
url = 'http://konect.cc/networks/moreno_mac'
citation = [('Y. Takahata. "Diachronic changes in the dominance relations of adult female Japanese monkeys of the Arashiyama B group. The Monkeys of Arashiyama." State University of New York Press, Albany, 123-139 (1991)', 'http://www.sunypress.edu/p-1128-the-monkeys-of-arashiyama.aspx')]
Initial commit cc85872
diff --git a/entries/macaques/__init__.py b/entries/macaques/__init__.py
new file mode 100644
index 0000000..950f86d
--- /dev/null
+++ b/entries/macaques/__init__.py
@@ -0,0 +1,48 @@
+#! /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 = "Japanese macaques (1976)"
+description = "Dominance interactions among a group of adult female Japanese macaques (Macaca fuscata fuscata), observed during a non-mating season in 1976. Edge weights represent the frequency of interaction."
+tags = ['Social', 'Animal', 'Weighted']
+url = 'http://konect.cc/networks/moreno_mac'
+citation = [('Y. Takahata. "Diachronic changes in the dominance relations of adult female Japanese monkeys of the Arashiyama B group. The Monkeys of Arashiyama." State University of New York Press, Albany, 123-139 (1991)', 'http://www.sunypress.edu/p-1128-the-monkeys-of-arashiyama.aspx')]
+icon_hash = '5734a096461efe0c7a67832f'
+upstream_prefix = 'http://konect.cc/files'
+files = [('download.tsv.moreno_mac.tar.bz2', None, 'konect')]
+
+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=True)
+ yield alt, g