History of rhesus_monkey

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.

2026-11-03 [entries] Add the date when each entry was added, and remove icon_hash by Tiago de Paula Peixoto 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/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 4c8f5e5..f1a1122 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -31,7 +31,7 @@ The network has the following properties:
 tags = ['Social', 'Animal', 'Weighted', 'Metadata']
 url = 'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#rhesus'
 citation = [('D. S. Sade. "Sociometrics of Macaca mulatta I. Linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://doi.org/10.1159/000155480')]
-icon_hash = '57349432461efe0c7a678324'
+date_added = '2020-08-11'
 upstream_license = None
 upstream_prefix = 'https://web.archive.org/web/20210115130726id_/http://moreno.ss.uci.edu'
 files = [('rhesus.dat', None, None)]

2026-11-03 [entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) by Tiago de Paula Peixoto 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/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 1c87174..4c8f5e5 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -25,8 +25,9 @@ A directed edge (i, j) indicates that monkey i was observed grooming monkey j. (
 
 The network has the following properties:
 
-- Nodes: `name`, the identifier of the monkey; `male`, whether the monkey is male.
-- Edges: `weight`, the number of grooming episodes."""
+- (Node) `name`: the identifier of the monkey.
+- (Node) `male`: whether the monkey is male.
+- (Edge) `weight`: the number of grooming episodes."""
 tags = ['Social', 'Animal', 'Weighted', 'Metadata']
 url = 'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#rhesus'
 citation = [('D. S. Sade. "Sociometrics of Macaca mulatta I. Linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://doi.org/10.1159/000155480')]

2026-11-02 [entries] Remove unneeded code from the entries by Tiago de Paula Peixoto 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/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 0d7f8f5..1c87174 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -48,7 +48,6 @@ def fetch_upstream(force=False):
 @coerce_props(vforce={"name": "string"})
 @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:

2026-10-25 [entries] Move more KONECT-derived entries to their original sources by Tiago de Paula Peixoto 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/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 776ce7f..0d7f8f5 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -19,21 +19,33 @@
 from .. import *
 
 title = "Rhesus monkey grooming (1963)"
-description = """Grooming interactions among a group of wild adult rhesus monkeys (Macaca mulatta) in Cayo Santiago, during a two month period in 1963. Edge weights represent the frequency of interaction. The two versions below are equivalent.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
-tags = ['Social', 'Animal', 'Weighted']
-url = 'http://konect.cc/networks/moreno_rhesus'
-citation = [('D.S. Sade. "Sociometrics of macaca mulatta I. linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://doi.org/10.1159/000155480')]
+description = """Grooming episodes among 16 adult rhesus monkeys (Macaca mulatta) of a free-ranging community in Cayo Santiago (Puerto Rico), observed by D. S. Sade in June and July 1963. Seven of the monkeys are males, and the other nine are females. 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 monkey i was observed grooming monkey j. (The direction is not stated explicitly in the source, which describes the data as a non-symmetric table of grooming episodes; the row animal is taken as the groomer.)
+
+The network has the following properties:
+
+- Nodes: `name`, the identifier of the monkey; `male`, whether the monkey is male.
+- Edges: `weight`, the number of grooming episodes."""
+tags = ['Social', 'Animal', 'Weighted', 'Metadata']
+url = 'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#rhesus'
+citation = [('D. S. Sade. "Sociometrics of Macaca mulatta I. Linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://doi.org/10.1159/000155480')]
 icon_hash = '57349432461efe0c7a678324'
-upstream_prefix = 'http://konect.cc/files'
-files = [('download.tsv.moreno_rhesus.tar.bz2', None, 'konect')]
+upstream_license = None
+upstream_prefix = 'https://web.archive.org/web/20210115130726id_/http://moreno.ss.uci.edu'
+files = [('rhesus.dat', None, None)]
+
+# the males, as listed in the source
+males = ["066", "ER", "R006", "EZ", "EC", "CY", "CN"]
 
 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 +56,12 @@ 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]
+        assert all(m in d["rows"] for m in males)
+        g = matrix_graph(d["data"], True)
+        g.vp.name = g.new_vp("string", vals=d["rows"])
+        g.vp.male = g.new_vp("bool", vals=[l in males for l in d["rows"]])
         yield alt, g

2026-10-24 Update copyright information by Tiago de Paula Peixoto 73a4f0d

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index f5c1737..776ce7f 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__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

2024-05-27 Update copyright information by Tiago de Paula Peixoto 3d288ea

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 016b941..f5c1737 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__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

2023-02-19 Update copyright information by Tiago de Paula Peixoto 8d005ae

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 5ee4a46..016b941 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__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

2021-06-22 Update copyright info by Tiago de Paula Peixoto db2efcc

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 1f4d65e..5ee4a46 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__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

2021-02-01 Un-orphan KONECT datasets by Tiago de Paula Peixoto 894eba5

KONECT has been brought back from the dead for the time being.

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 3e20037..1f4d65e 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -26,7 +26,6 @@ url = 'http://konect.cc/networks/moreno_rhesus'
 citation = [('D.S. Sade. "Sociometrics of macaca mulatta I. linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://doi.org/10.1159/000155480')]
 icon_hash = '57349432461efe0c7a678324'
 upstream_prefix = 'http://konect.cc/files'
-orphan = True
 files = [('download.tsv.moreno_rhesus.tar.bz2', None, 'konect')]
 
 def fetch_upstream(force=False):

2020-11-28 Update citations to use DOIs by Tiago de Paula Peixoto e878874

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 39b670e..3e20037 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -23,7 +23,7 @@ description = """Grooming interactions among a group of wild adult rhesus monkey
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Animal', 'Weighted']
 url = 'http://konect.cc/networks/moreno_rhesus'
-citation = [('D.S. Sade. "Sociometrics of macaca mulatta I. linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://www.karger.com/Article/Abstract/155480')]
+citation = [('D.S. Sade. "Sociometrics of macaca mulatta I. linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://doi.org/10.1159/000155480')]
 icon_hash = '57349432461efe0c7a678324'
 upstream_prefix = 'http://konect.cc/files'
 orphan = True

2020-11-02 Add support for 'orphan' datasets and tag konect entries by Tiago de Paula Peixoto e330b80

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 57e5edb..39b670e 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -26,6 +26,7 @@ url = 'http://konect.cc/networks/moreno_rhesus'
 citation = [('D.S. Sade. "Sociometrics of macaca mulatta I. linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://www.karger.com/Article/Abstract/155480')]
 icon_hash = '57349432461efe0c7a678324'
 upstream_prefix = 'http://konect.cc/files'
+orphan = True
 files = [('download.tsv.moreno_rhesus.tar.bz2', None, 'konect')]
 
 def fetch_upstream(force=False):

2020-09-15 Change license from GPLv3 to AGPLv3 by Tiago de Paula Peixoto d754be5

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index dea1dda..57e5edb 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__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 *

2020-09-13 Add explicit attribution to descriptions obtained from ICON by Tiago de Paula Peixoto 1645314

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
index 1ab2e6e..dea1dda 100644
--- a/entries/rhesus_monkey/__init__.py
+++ b/entries/rhesus_monkey/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "Rhesus monkey grooming (1963)"
-description = "Grooming interactions among a group of wild adult rhesus monkeys (Macaca mulatta) in Cayo Santiago, during a two month period in 1963. Edge weights represent the frequency of interaction. The two versions below are equivalent."
+description = """Grooming interactions among a group of wild adult rhesus monkeys (Macaca mulatta) in Cayo Santiago, during a two month period in 1963. Edge weights represent the frequency of interaction. The two versions below are equivalent.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Animal', 'Weighted']
 url = 'http://konect.cc/networks/moreno_rhesus'
 citation = [('D.S. Sade. "Sociometrics of macaca mulatta I. linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://www.karger.com/Article/Abstract/155480')]

2020-08-11 Initial commit by Tiago de Paula Peixoto cc85872

diff --git a/entries/rhesus_monkey/__init__.py b/entries/rhesus_monkey/__init__.py
new file mode 100644
index 0000000..1ab2e6e
--- /dev/null
+++ b/entries/rhesus_monkey/__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 = "Rhesus monkey grooming (1963)"
+description = "Grooming interactions among a group of wild adult rhesus monkeys (Macaca mulatta) in Cayo Santiago, during a two month period in 1963. Edge weights represent the frequency of interaction. The two versions below are equivalent."
+tags = ['Social', 'Animal', 'Weighted']
+url = 'http://konect.cc/networks/moreno_rhesus'
+citation = [('D.S. Sade. "Sociometrics of macaca mulatta I. linkages and cliques in grooming matrices." Folia Primatologica 18(3-4), 196-223 (1972)', 'https://www.karger.com/Article/Abstract/155480')]
+icon_hash = '57349432461efe0c7a678324'
+upstream_prefix = 'http://konect.cc/files'
+files = [('download.tsv.moreno_rhesus.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