__init__.py

#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# 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
# 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 *

import rpy2.robjects as robjects
import tempfile
import shutil
import numpy as np

title = "Animal dominance archive (2022)"
description = """Animal dominance interaction data published over a century of research. The archive contains 434 agonistic interaction datasets, totaling over 241,000 interactions. A directed edge (i,j) corresponds to an antagonist interaction between i (winner) and j (loser). If a 'weight' edge property map exists, it counts the number of such interactions."""
tags = ['Social', 'Animal', 'Weighted']
url = 'https://github.com/DomArchive/DomArchive'
citation = [('Strauss Eli D., DeCasien Alex R., Galindo Gabriela, Hobson Elizabeth A., Shizuka Daizaburo and Curley James P., "DomArchive: a century of published dominance data", Phil. Trans. R. Soc. B377: 20200436 (2022)',
             'https://doi.org/10.1098/rstb.2020.0436')]
icon_hash = None
upstream_prefix = 'https://github.com/DomArchive/DomArchive/raw/master/data'

names = [
    'Adcock_2015a',
    'Adcock_2015b',
    'Alados_1992a',
    'Alados_1992b',
    'Alados_1992c',
    'Alados_1992d',
    'Alados_1992e',
    'Allee_1954',
    'Anderson_2016a',
    'Anderson_2016d',
    'Appleby_1983',
    'Archie_2006a',
    'Archie_2006b',
    'Archie_2006c',
    'Archie_2006d',
    'Archie_2006e',
    'Archie_2006f',
    'Archie_2006g',
    'Archie_2006h',
    'Archie_2006i',
    'Arlet_2015f',
    'Barette_1986',
    'Bennett_1939',
    'BergstromFedigan_2010b',
    'BergstromFedigan_2010c',
    'Berman_2004a',
    'Berman_2004b',
    'Berman_2004c',
    'Blatrix_2004b',
    'Blatrix_2004c',
    'Blatrix_2004d',
    'Blatrix_2004e',
    'Bonanni_2007a',
    'Bonanni_2007b',
    'Bonanni_2007c',
    'Bonanni_2017a',
    'Bonanni_2017b',
    'Bonanni_2017c',
    'Bonanni_2017d',
    'Bromley_1991',
    'Cafazzo_2010a',
    'Cafazzo_2010b',
    'Cheney_1977',
    'Cheney_1977b',
    'CluttonBrock_1976',
    'Collias_1950a',
    'Collias_1950b',
    'Collias_1950c',
    'Collias_1951a',
    'Collias_1951b',
    'Collias_1951c',
    'Correa_2013a',
    'Correa_2013d',
    'Cote_2000',
    'Cote_2000b',
    'Cote_2000c',
    'Cote_2000d',
    'Cui_2014',
    'David_2003a',
    'David_2003b',
    'DeLaFuente_2019',
    'DeLaO_2019a',
    'DeLaO_2019b',
    'DeLaO_2019c',
    'DeLaO_2019d',
    'deVries_2006',
    'deWaal_1977a',
    'deWaal_1977b',
    'deWaal_1985',
    'Diniz_2019',
    'Douglis_1948a',
    'Douglis_1948b',
    'Dubosq2013a',
    'Dubosq2013b',
    'Dubosq2013c',
    'Dubosq2013d',
    'Dubosq2013e',
    'Dubosq2013f',
    'Ellard_1989',
    'Essler_2016a',
    'Essler_2016c',
    'Essler_2016d',
    'Fairbanks_1994a',
    'Fairbanks_1994b',
    'Fairbanks_1994c',
    'Fairbanks_1994d',
    'Fairbanks_1994e',
    'Farentinos_1972a',
    'Farentinos_1972b',
    'Farentinos_1972c',
    'Farentinos_1972d',
    'Farentinos_1972e',
    'Farentinos_1972f',
    'Foerster_2016a',
    'Foerster_2016b',
    'Fournier_1995',
    'Fournier_1995b',
    'Frank_1986a',
    'Frank_1986b',
    'Franz_2015a',
    'Franz_2015b',
    'Franz_2015c',
    'Franz_2015d',
    'Franz_2015e',
    'Funkhouser_2018a',
    'Funkhouser_2018b',
    'Harcourt_1979',
    'Harcourt_1989',
    'Hartzler_1970',
    'Hass_1991',
    'Hass_1991b',
    'Hass_1991c',
    'Hausfater_1975a',
    'Hausfater_1975b',
    'Hausfater_1975c',
    'Hausfater_1982a',
    'Hausfater_1982b',
    'Hayaki_1989a',
    'Hayaki_1989b',
    'Heitor_2006',
    'HeitorVicente_2010',
    'Hewitt_2009a',
    'Hewitt_2009b',
    'Hewitt_2009c',
    'Hewitt_2009d',
    'Hirotani_1994',
    'Hirsch_2007a',
    'Hirsch_2007b',
    'Hirsch_2007c',
    'Hirsch_2007d',
    'Hobson_2015a',
    'Hobson_2015b',
    'Holekamp_1991',
    'Holekamp_1993a',
    'Holekamp_1993b',
    'Isbell_1998a',
    'Isbell_1998b',
    'Ito_1993a',
    'Ito_1993b',
    'Ito_1993c',
    'Izar_2006',
    'IzawaWatanabe_2011',
    'Jenks_1995a',
    'Jenks_1995b',
    'Johnson_2017',
    'Jones_1980a',
    'Jones_1980b',
    'Kaufmann_1974',
    'Kikkawa_1980',
    'Koenig_2004',
    'Kohda_1991',
    'Kolodziejczyk_2005',
    'Korstjens_2002',
    'Koutnik_1981',
    'Koutnik_1981b',
    'Kurvers_2009',
    'Lahti_1994a',
    'Lahti_1994b',
    'Langbein_2004a',
    'Langbein_2004b',
    'Langbein_2004c',
    'Langbein_2004d',
    'Langley_2018',
    'Lee_1979a',
    'Lee_1979b',
    'Lee_2017a',
    'Lee_2017b',
    'Lee_2017c',
    'Lee_2017d',
    'Lee_2017e',
    'Lee_2017f',
    'Lee_2018a',
    'Lee_2018b',
    'Lee_2018c',
    'Lee_2018d',
    'Lee_2018e',
    'Lee_2019a',
    'Lee_2019b',
    'Lee_2019c',
    'Lee_2019d',
    'Lee_2019e',
    'Lott_1979',
    'Lott_1987',
    'Lu_2008a',
    'Lu_2008b',
    'Malherbe_2007',
    'Marler_1955',
    'Masure_1934',
    'Masure_1934a',
    'Masure_1934b',
    'Mather_1985',
    'Matsuda_2012',
    'McCune_2019a',
    'McCune_2019c',
    'McCune_2019d',
    'McCune_2019e',
    'McCune_2019f',
    'McDougall_2010',
    'McMahan_1984',
    'Miller_2010a',
    'Miller_2010b',
    'Miller_2010c',
    'Moller_1987a',
    'Moller_1987b',
    'Moller_1987c',
    'Monnin_1999',
    'Moore_1978a',
    'Moore_1978b',
    'Murray_2007',
    'Mwamende_2009a',
    'Mwamende_2009b',
    'Myrberg_1972',
    'Myrberg_1974',
    'Nakano_1994',
    'Nakano_1995',
    'Natoli_1991',
    'Nelissen_1985a',
    'Nelissen_1985b',
    'NewtonFisher_2004a',
    'NewtonFisher_2004b',
    'Norscia_2015a',
    'Norscia_2015b',
    'Norscia_2015c',
    'Norscia_2015d',
    'Norscia_2015e',
    'Norscia_2015f',
    'Norscia_2015g',
    'Norscia_2015h',
    'Norscia_2015i',
    'Norscia_2015j',
    'Ortius_1995',
    'Oshea_1976',
    'Owens_1996',
    'Painter_2018',
    'Paoli_2006',
    'Pardi_1948a',
    'Pardi_1948b',
    'Parsons_1980a',
    'Parsons_1980b',
    'Patterson_1977',
    'Payne_2003',
    'Poisbleau_2005a',
    'Poisbleau_2005b',
    'Poisbleau_2005c',
    'Poisbleau_2006a',
    'Poisbleau_2006b',
    'Post_1992',
    'Prieto_1978',
    'Reason_1988',
    'Richter_2009',
    'RizaldiWatanabe_2010a',
    'RizaldiWatanabe_2010b',
    'Robbins_2008',
    'Roell_1978',
    'Rossler_2017',
    'Rovero_1999a',
    'Rovero_1999b',
    'Russell_1970a',
    'Russell_1970b',
    'Rutberg_1986a',
    'Rutberg_1986b',
    'Samuels_1987',
    'Samuels_1987b',
    'Sandel_2017a',
    'Sandel_2017b',
    'SatohOhkawara_2008a',
    'SatohOhkawara_2008b',
    'SatohOhkawara_2008c',
    'ScheinFohrman_1955',
    'SchjelderupEbbe_1922a',
    'SchjelderupEbbe_1922b',
    'ScottLockhard_1999a',
    'ScottLockhard_1999b',
    'Seibert_2001',
    'Setchell_2005a',
    'Setchell_2005b',
    'SetiaVanSchaik_2007',
    'Seyfarth_1976a',
    'Seyfarth_1976b',
    'Seyfarth_1976c',
    'Seyfarth_1976d',
    'Seyfarth_1976e',
    'Seyfarth_1976f',
    'Sharpe_2013a',
    'Sharpe_2013b',
    'Sharpe_2013c',
    'Sharpe_2013d',
    'Shimoji_2014a',
    'Shimoji_2014b',
    'Shimoji_2014c',
    'Shoemaker_1939',
    'Silk_2019a',
    'Slotow_1993',
    'Smith_1976',
    'Smith_2011a',
    'Solberg_1997a',
    'Solberg_1997b',
    'Solberg_1997c',
    'SomersNel_1998a',
    'SomersNel_1998b',
    'SomersNel_1998c',
    'Stamps_1978',
    'Sterck_1997',
    'Strauss_2019a',
    'Strauss_2019b',
    'Strauss_2019c',
    'Strauss_2019d',
    'StrayerCummins_1980',
    'StrayerCummins_1980b',
    'StrayerCummins_1980c',
    'StrayerCummins_1980d',
    'Struhsaker_1967a',
    'Struhsaker_1967b',
    'Sullivan_1982',
    'Surbeck_2011',
    'SurbeckHohmann_2013b',
    'Tamm_1977',
    'Tamura_1988',
    'Tarvin_1997',
    'Thompson_1960a',
    'Thompson_1960b',
    'Thompson_1960c',
    'Thompson_1960d',
    'Thompson_1960e',
    'Thompson_1993a',
    'Thompson_1993b',
    'Tilson_1984',
    'Tong_2020a',
    'Tong_2020b',
    'Tong_2020c',
    'Tong_2020d',
    'Tong_2020e',
    'Tong_2020f',
    'Tong_2020g',
    'Tong_2020h',
    'Tong_2020i',
    'Tong_2020j',
    'Torr_1996a',
    'Torr_1996b',
    'Torr_1996c',
    'Trebouet_2019a',
    'Trebouet_2019b',
    'Trebouet_2019c',
    'Trebouet_2019d',
    'Trunzer_1999',
    'Utt_2008a',
    'ValLaillet_2008a',
    'ValLaillet_2008b',
    'ValLaillet_2008c',
    'ValLaillet_2008d',
    'ValLaillet_2008e',
    'ValLaillet_2008f',
    'VanDessel_2018a',
    'VanDessel_2018b',
    'VanDierendonck_1995',
    'VanHooffWensing_1987',
    'Varley_1966',
    'Varley_1966b',
    'Vervaecke_2000',
    'Vervaecke_2010a',
    'Vervaecke_2010b',
    'Vervaecke_2010c',
    'Vervaecke_2010d',
    'Vilette_2020',
    'Waterhouse_1976a',
    'Waterhouse_1976b',
    'Waterhouse_1976c',
    'Watson_1970a',
    'Watson_1970b',
    'Watt_1986a',
    'Watt_1986b',
    'Watt_1986c',
    'Watt_1986d',
    'Watt_1986e',
    'Watt_1986f',
    'Watts_1985',
    'Watts_1994a',
    'Watts_1994b',
    'Watts_1994c',
    'Wells_1979',
    'WestEberhard_1986',
    'White_2007a',
    'White_2007b',
    'White_2007c',
    'Wikberg_2013a',
    'Wikberg_2013b',
    'Wikberg_2013c',
    'Wikberg_2013d',
    'Wikberg_2013e',
    'Wikberg_2013f',
    'Williams_1972',
    'Williamson_2016a',
    'Williamson_2016b',
    'Williamson_2016c',
    'Williamson_2016d',
    'Williamson_2016e',
    'Williamson_2016f',
    'Williamson_2016g',
    'Williamson_2016h',
    'Williamson_2016i',
    'Williamson_2016j',
    'Williamson_2016k',
    'Williamson_2017a',
    'Williamson_2017b',
    'Williamson_2017c',
    'Williamson_2017d',
    'Williamson_2017e',
    'Williamson_2017f',
    'Williamson_2017g',
    'Williamson_2017h',
    'Williamson_2017i',
    'Williamson_2017j',
    'Williamson_2017k',
    'Williamson_2017l',
    'Williamson_2017m',
    'Williamson_2017n',
    'Williamson_2017o',
    'Williamson_2019a',
    'Williamson_2019b',
    'Williamson_2019c',
    'Williamson_2019d',
    'Williamson_2019e',
    'Williamson_2019f',
    'Williamson_2019g',
    'Williamson_2019h',
    'Wittemeyer_2007',
    'Wittig_2003',
    'Yasukawa_1983a',
    'Yasukawa_1983b',
    'Yasukawa_1983c',
    'Yasukawa_1983d',
    'Yasukawa_1983e',
    'Yasukawa_1983f',
    'Yasukawa_1983g',
    'Yasukawa_1983h',
    'Zine_2000'
]


files = [('dom.data.RData', name, None) for name in names]

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 = Graph()

            cols = ["order", "species",
                    "common_name", "study_site", "captivity", "sex", "age",
                    "measure", "data_location", "countbinary", "repeat_group",
                    "groupid", "matrix_edgelist", "edgelist_time_meaning",
                    "note", "full_citation"]

            for c in cols:
                g.gp[c] = g.new_gp("string")

            with tempfile.NamedTemporaryFile() as temp:
                shutil.copyfileobj(fs[0], temp)
                temp.flush()
                robjects.r["load"](temp.name)

                for x in robjects.r["dom.data"]:
                    if str(np.array(x[1][0])[0]) == alt:
                        edge_list = str(np.array(x[1][13])[0]) == "Edgelist"
                        a = np.array(x[0])
                        if edge_list:
                            g.ep.time = g.new_ep("double")
                            if len(a) > 3:
                                g.ep.date = g.new_ep("string")
                            def edges():
                                for vals in a.T:
                                    if len(a) > 3:
                                        yield vals[1], vals[2], vals[0], vals[3]
                                    else:
                                        yield vals[1], vals[2], vals[0]
                            try:
                                g.add_edge_list(edges(),
                                                eprops=[g.ep.time, g.ep.date] if len(a) > 3
                                                else [g.ep.time])
                            except ValueError:
                                g.vp.name = g.add_edge_list(edges(),
                                                            hashed=True,
                                                            eprops=[g.ep.time, g.ep.date] if len(a) > 3
                                                            else [g.ep.time])
                        else:
                            g.ep.weight = g.new_ep("int")

                            a[np.isnan(a)] = 0
                            a[a < 0] = 0
                            idx = a.nonzero()
                            ws = a[idx]
                            g.add_edge_list(np.array([idx[0], idx[1], ws]).T,
                                            eprops=[g.ep.weight])

                        for i, val in enumerate(x[1]):
                            if i == 0:
                                continue
                            if i > len(cols):
                                break
                            g.gp[cols[i-1]] = str(np.array(val)[0])

        yield alt, g