History of nematode_mammal

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/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index 6501f35..a3235a9 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__init__.py
@@ -33,7 +33,7 @@ The network has the following properties:
 tags = ['Biological', 'Food web', 'Unweighted', 'Metadata']
 url = 'https://github.com/cjcarlson/brevity/tree/master/Figure%201%20Demo%20Networks'
 citation = [('T. Dallas et al. "Gauging support for macroecological patterns in helminth parasites." Glob. Ecol. Biogeogr. 27, 1437–1447 (2018)', 'https://doi.org/10.1111/geb.12819')]
-icon_hash = '5d0d28f751da6551647736a8'
+date_added = '2020-09-26'
 upstream_license = None
 upstream_prefix = 'https://raw.githubusercontent.com/cjcarlson/brevity/master/Figure%201%20Demo%20Networks'
 files = [('helminths.csv', None, 'csv')]

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/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index 1b40b97..6501f35 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__init__.py
@@ -25,11 +25,11 @@ Nodes are host and parasite species (the network is bipartite), and an edge conn
 
 The network has the following properties:
 
-- `name`: the species name of the host or parasite.
-- `is_host`: whether the node is a host (otherwise it is a parasite).
-- `group`: for parasites, the parasite group (Trematoda, Nematoda, Cestoda or Acanthocephala); for hosts, the host group (e.g. Teleostei, Aves, Mammalia, or NA if not available).
-- `full_name` (edges): the full name of the parasite with taxonomic authority, as given in the record (it can vary between records of the same parasite, e.g. for synonyms or subspecies).
-- `locality` (edges): the locality of the record."""
+- (Node) `name`: the species name of the host or parasite.
+- (Node) `is_host`: whether the node is a host (otherwise it is a parasite).
+- (Node) `group`: for parasites, the parasite group (Trematoda, Nematoda, Cestoda or Acanthocephala); for hosts, the host group (e.g. Teleostei, Aves, Mammalia, or NA if not available).
+- (Edge) `full_name`: the full name of the parasite with taxonomic authority, as given in the record (it can vary between records of the same parasite, e.g. for synonyms or subspecies).
+- (Edge) `locality`: the locality of the record."""
 tags = ['Biological', 'Food web', 'Unweighted', 'Metadata']
 url = 'https://github.com/cjcarlson/brevity/tree/master/Figure%201%20Demo%20Networks'
 citation = [('T. Dallas et al. "Gauging support for macroecological patterns in helminth parasites." Glob. Ecol. Biogeogr. 27, 1437–1447 (2018)', 'https://doi.org/10.1111/geb.12819')]

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/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index 667da33..1b40b97 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__init__.py
@@ -46,7 +46,6 @@ 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:

2026-10-25 [entries] Fix parse bugs and improve the metadata of existing entries by Tiago de Paula Peixoto 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/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index bed17a9..667da33 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__init__.py
@@ -18,14 +18,23 @@
 
 from .. import *
 
-title = "Global nematode–mammal interactions (2018)"
-description = """A global interaction web of interactions between nematodes and their host mammal species, extracted from the helminthR package and dataset. Nodes are annotated with species-level information.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+title = "Global helminth–host associations (NHM, 2018)"
+description = """Global network of host–parasite associations between helminth parasites and their host species, obtained with the R package helminthR (T. Dallas), which queries the Host-Parasite Database of the Natural History Museum, London, a compilation of host–parasite records from the published literature. The data were used by T. Dallas and collaborators to examine macroecological patterns in helminth parasites, and were distributed as a demonstration network by C. J. Carlson. The data are not restricted to nematodes and mammals (as the name of the dataset suggests): the parasites are trematodes, nematodes, cestodes and acanthocephalans, and the hosts include fish, birds, mammals, reptiles, amphibians and invertebrates.
+
+Nodes are host and parasite species (the network is bipartite), and an edge connects a host to a parasite recorded on it. Each edge corresponds to one record of the database, which lists the locality of the record, so a host–parasite pair recorded at several localities is connected by several parallel edges (the 146,683 edges connect 61,597 distinct pairs).
+
+The network has the following properties:
+
+- `name`: the species name of the host or parasite.
+- `is_host`: whether the node is a host (otherwise it is a parasite).
+- `group`: for parasites, the parasite group (Trematoda, Nematoda, Cestoda or Acanthocephala); for hosts, the host group (e.g. Teleostei, Aves, Mammalia, or NA if not available).
+- `full_name` (edges): the full name of the parasite with taxonomic authority, as given in the record (it can vary between records of the same parasite, e.g. for synonyms or subspecies).
+- `locality` (edges): the locality of the record."""
 tags = ['Biological', 'Food web', 'Unweighted', 'Metadata']
 url = 'https://github.com/cjcarlson/brevity/tree/master/Figure%201%20Demo%20Networks'
 citation = [('T. Dallas et al. "Gauging support for macroecological patterns in helminth parasites." Glob. Ecol. Biogeogr. 27, 1437–1447 (2018)', 'https://doi.org/10.1111/geb.12819')]
 icon_hash = '5d0d28f751da6551647736a8'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'https://raw.githubusercontent.com/cjcarlson/brevity/master/Figure%201%20Demo%20Networks'
 files = [('helminths.csv', None, 'csv')]
 
@@ -50,8 +59,8 @@ def parse(alts=None):
             g = Graph(directed=False)
 
             g.vp.name = g.new_vp("string")
-            g.vp.full_name = g.new_vp("string")
-            g.vp.locality = g.new_vp("string")
+            g.ep.full_name = g.new_ep("string")
+            g.ep.locality = g.new_ep("string")
             g.vp.group = g.new_vp("string")
             g.vp.is_host = g.new_vp("bool")
 
@@ -69,11 +78,13 @@ def parse(alts=None):
                 if t is None:
                     t = ps[row[2]] = g.add_vertex()
                     g.vp.name[t] = row[2]
-                g.add_edge(s, t)
+                e = g.add_edge(s, t)
                 g.vp.is_host[s] = True
-                g.vp.full_name[s] = row[3]
-                g.vp.group[s] = row[4]
-                g.vp.locality[s] = row[5]
-                g.vp.group[t] = row[6]
+                g.ep.full_name[e] = row[3]
+                g.ep.locality[e] = row[5]
+                g.vp.group[t] = row[4]
+                # host group; one host is listed with both a group and NA
+                if g.vp.group[s] in ("", "NA"):
+                    g.vp.group[s] = row[6]
 
         yield alt, g

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

diff --git a/entries/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index 37cf90c..bed17a9 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__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/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index b5c0fdb..37cf90c 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__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/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index a19592d..b5c0fdb 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__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/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index e92956b..a19592d 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__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

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

diff --git a/entries/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
index 09a5c5c..e92956b 100644
--- a/entries/nematode_mammal/__init__.py
+++ b/entries/nematode_mammal/__init__.py
@@ -23,7 +23,7 @@ description = """A global interaction web of interactions between nematodes and
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Food web', 'Unweighted', 'Metadata']
 url = 'https://github.com/cjcarlson/brevity/tree/master/Figure%201%20Demo%20Networks'
-citation = [('T. Dallas et al. "Gauging support for macroecological patterns in helminth parasites." Glob. Ecol. Biogeogr. 27, 1437–1447 (2018)', 'https://onlinelibrary.wiley.com/doi/full/10.1111/geb.12819')]
+citation = [('T. Dallas et al. "Gauging support for macroecological patterns in helminth parasites." Glob. Ecol. Biogeogr. 27, 1437–1447 (2018)', 'https://doi.org/10.1111/geb.12819')]
 icon_hash = '5d0d28f751da6551647736a8'
 ustream_license = None
 upstream_prefix = 'https://raw.githubusercontent.com/cjcarlson/brevity/master/Figure%201%20Demo%20Networks'

2020-09-26 Add nematode_mammal by Tiago de Paula Peixoto e04a83d

diff --git a/entries/nematode_mammal/__init__.py b/entries/nematode_mammal/__init__.py
new file mode 100644
index 0000000..09a5c5c
--- /dev/null
+++ b/entries/nematode_mammal/__init__.py
@@ -0,0 +1,79 @@
+#! /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 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 Affero General Public License for more
+# details.
+#
+# 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 *
+
+title = "Global nematode–mammal interactions (2018)"
+description = """A global interaction web of interactions between nematodes and their host mammal species, extracted from the helminthR package and dataset. Nodes are annotated with species-level information.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+tags = ['Biological', 'Food web', 'Unweighted', 'Metadata']
+url = 'https://github.com/cjcarlson/brevity/tree/master/Figure%201%20Demo%20Networks'
+citation = [('T. Dallas et al. "Gauging support for macroecological patterns in helminth parasites." Glob. Ecol. Biogeogr. 27, 1437–1447 (2018)', 'https://onlinelibrary.wiley.com/doi/full/10.1111/geb.12819')]
+icon_hash = '5d0d28f751da6551647736a8'
+ustream_license = None
+upstream_prefix = 'https://raw.githubusercontent.com/cjcarlson/brevity/master/Figure%201%20Demo%20Networks'
+files = [('helminths.csv', None, 'csv')]
+
+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", encoding="ISO-8859-1")) for fn in fnames]
+
+            g = Graph(directed=False)
+
+            g.vp.name = g.new_vp("string")
+            g.vp.full_name = g.new_vp("string")
+            g.vp.locality = g.new_vp("string")
+            g.vp.group = g.new_vp("string")
+            g.vp.is_host = g.new_vp("bool")
+
+            hs = {}
+            ps = {}
+            reader = csv.reader(fs[0])
+
+            next(reader)
+            for row in reader:
+                s = hs.get(row[1], None)
+                if s is None:
+                    s = hs[row[1]] = g.add_vertex()
+                    g.vp.name[s] = row[1]
+                t = ps.get(row[2], None)
+                if t is None:
+                    t = ps[row[2]] = g.add_vertex()
+                    g.vp.name[t] = row[2]
+                g.add_edge(s, t)
+                g.vp.is_host[s] = True
+                g.vp.full_name[s] = row[3]
+                g.vp.group[s] = row[4]
+                g.vp.locality[s] = row[5]
+                g.vp.group[t] = row[6]
+
+        yield alt, g