# Copyright 2018-2020 by Christopher C. Little.
# This file is part of Abydos.
#
# Abydos 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.
#
# Abydos 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 Abydos. If not, see <http://www.gnu.org/licenses/>.
"""abydos.distance._sokal_sneath_iv.
Sokal & Sneath IV similarity
"""
from ._token_distance import _TokenDistance
__all__ = ['SokalSneathIV']
[docs]class SokalSneathIV(_TokenDistance):
r"""Sokal & Sneath IV similarity.
For two sets X and Y and a population N, Sokal & Sneath IV similarity
:cite:`Sokal:1963` is
.. math::
sim_{SokalSneathIV}(X, Y) =
\frac{1}{4}\Bigg(
\frac{|X \cap Y|}{|X|}+
\frac{|X \cap Y|}{|Y|}+
\frac{|(N \setminus X) \setminus Y|}
{|N \setminus Y|}+
\frac{|(N \setminus X) \setminus Y|}
{|N \setminus X|}
\Bigg)
This is the fourth of five "Unnamed coefficients" presented in
:cite:`Sokal:1963`. It corresponds to the first "Marginal totals in the
Denominator" with "Negative Matches in Numerator Included".
"Negative Matches in Numerator Excluded" corresponds to the Kulczynski II
similarity, :class:`.KulczynskiII`. This is also Rogot & Goldberg's
"adjusted agreement" :math:`A_1` :cite:`Rogot:1966`.
In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n,
this is
.. math::
sim_{SokalSneathIV} =
\frac{1}{4}\Big(\frac{a}{a+b}+\frac{a}{a+c}+
\frac{d}{b+d}+\frac{d}{c+d}\Big)
.. versionadded:: 0.4.0
"""
def __init__(
self,
alphabet=None,
tokenizer=None,
intersection_type='crisp',
**kwargs
):
"""Initialize SokalSneathIV instance.
Parameters
----------
alphabet : Counter, collection, int, or None
This represents the alphabet of possible tokens.
See :ref:`alphabet <alphabet>` description in
:py:class:`_TokenDistance` for details.
tokenizer : _Tokenizer
A tokenizer instance from the :py:mod:`abydos.tokenizer` package
intersection_type : str
Specifies the intersection type, and set type as a result:
See :ref:`intersection_type <intersection_type>` description in
:py:class:`_TokenDistance` for details.
**kwargs
Arbitrary keyword arguments
Other Parameters
----------------
qval : int
The length of each q-gram. Using this parameter and tokenizer=None
will cause the instance to use the QGram tokenizer with this
q value.
metric : _Distance
A string distance measure class for use in the ``soft`` and
``fuzzy`` variants.
threshold : float
A threshold value, similarities above which are counted as
members of the intersection for the ``fuzzy`` variant.
.. versionadded:: 0.4.0
"""
super(SokalSneathIV, self).__init__(
alphabet=alphabet,
tokenizer=tokenizer,
intersection_type=intersection_type,
**kwargs
)
[docs] def sim(self, src, tar):
"""Return the Sokal & Sneath IV similarity of two strings.
Parameters
----------
src : str
Source string (or QGrams/Counter objects) for comparison
tar : str
Target string (or QGrams/Counter objects) for comparison
Returns
-------
float
Sokal & Sneath IV similarity
Examples
--------
>>> cmp = SokalSneathIV()
>>> cmp.sim('cat', 'hat')
0.7487179487179487
>>> cmp.sim('Niall', 'Neil')
0.6810856260030602
>>> cmp.sim('aluminum', 'Catalan')
0.5541986205645999
>>> cmp.sim('ATCG', 'TAGC')
0.496790757381258
.. versionadded:: 0.4.0
"""
self._tokenize(src, tar)
a = self._intersection_card()
b = self._src_only_card()
c = self._tar_only_card()
d = self._total_complement_card()
a_part = 0 if a == 0 else (a / (a + b) + a / (a + c))
d_part = 0 if d == 0 else (d / (b + d) + d / (c + d))
return 0.25 * (a_part + d_part)
if __name__ == '__main__':
import doctest
doctest.testmod()