# 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_iii.
Sokal & Sneath III similarity
"""
from ._token_distance import _TokenDistance
__all__ = ['SokalSneathIII']
[docs]class SokalSneathIII(_TokenDistance):
r"""Sokal & Sneath III similarity.
For two sets X and Y and a population N, Sokal & Sneath III similarity
:cite:`Sokal:1963` is
.. math::
sim_{SokalSneathIII}(X, Y) =
\frac{|X \cap Y| + |(N \setminus X) \setminus Y|}
{|X \triangle Y|}
This is the third of five "Unnamed coefficients" presented in
:cite:`Sokal:1963`. It corresponds to the "Unmatched pairs only in the
Denominator" with "Negative Matches in Numerator Excluded".
"Negative Matches in Numerator Included" corresponds to the Kulczynski I
coefficient, :class:`.KulczynskiI`.
In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n,
this is
.. math::
sim_{SokalSneathIII} =
\frac{a+d}{b+c}
.. versionadded:: 0.4.0
"""
def __init__(self, tokenizer=None, intersection_type='crisp', **kwargs):
"""Initialize SokalSneathIII instance.
Parameters
----------
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(SokalSneathIII, self).__init__(
tokenizer=tokenizer, intersection_type=intersection_type, **kwargs
)
[docs] def sim_score(self, src, tar):
"""Return the Sokal & Sneath III 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 III similarity
Examples
--------
>>> cmp = SokalSneathIII()
>>> cmp.sim_score('cat', 'hat')
195.0
>>> cmp.sim_score('Niall', 'Neil')
111.0
>>> cmp.sim_score('aluminum', 'Catalan')
51.333333333333336
>>> cmp.sim_score('ATCG', 'TAGC')
77.4
.. versionadded:: 0.4.0
"""
if src == tar:
return float('inf')
self._tokenize(src, tar)
a = self._intersection_card()
b = self._src_only_card()
c = self._tar_only_card()
d = self._total_complement_card()
if a + d > 0 and b + c == 0:
return float('inf')
return (a + d) / (b + c)
[docs] def sim(self, *args, **kwargs):
"""Raise exception when called.
Parameters
----------
*args
Variable length argument list
**kwargs
Arbitrary keyword arguments
Raises
------
NotImplementedError
Method disabled for Sokal & Sneath III similarity.
.. versionadded:: 0.3.6
"""
raise NotImplementedError(
'Method disabled for Sokal & Sneath III similarity.'
)
[docs] def dist(self, *args, **kwargs):
"""Raise exception when called.
Parameters
----------
*args
Variable length argument list
**kwargs
Arbitrary keyword arguments
Raises
------
NotImplementedError
Method disabled for Sokal & Sneath III similarity.
.. versionadded:: 0.3.6
"""
raise NotImplementedError(
'Method disabled for Sokal & Sneath III similarity.'
)
if __name__ == '__main__':
import doctest
doctest.testmod()