# Copyright 2019-2020 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._raup_crick.
Raup-Crick similarity
"""
from math import factorial
from ._token_distance import _TokenDistance
__all__ = ['RaupCrick']
[docs]class RaupCrick(_TokenDistance):
r"""Raup-Crick similarity.
For two sets X and Y and a population N, Raup-Crick similarity
:cite:`Raup:1979` is:
.. math:
sim_{Raup-Crick}(X, Y) = \sum_{i=0}^{|X \cap Y|}
\frac{|X|! |Y|! (|N| - |X|)!
(|N|- |Y|)!}{|N|! |X \cap Y|! (|X| - i)!
(|Y| - i)! (|N| - |X| - |Y| + i)!}
Notes
-----
Observe that Raup-Crick similarity is related to Henderson-Heron similarity
in that the former is the sum of all Henderson-Heron similarities for an
intersection size ranging from 0 to the true intersection size.
.. versionadded:: 0.4.1
"""
def __init__(self, **kwargs):
"""Initialize RaupCrick instance.
Parameters
----------
**kwargs
Arbitrary keyword arguments
.. versionadded:: 0.4.1
"""
super(RaupCrick, self).__init__(**kwargs)
[docs] def sim(self, src, tar):
"""Return the Raup-Crick similarity of two strings.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Raup-Crick similarity
Examples
--------
>>> cmp = RaupCrick()
>>> cmp.sim('cat', 'hat')
0.9999998002120004
>>> cmp.sim('Niall', 'Neil')
0.9999975146378747
>>> cmp.sim('aluminum', 'Catalan')
0.9968397599851411
>>> cmp.sim('ATCG', 'TAGC')
0.9684367974410505
.. versionadded:: 0.4.1
"""
if src == tar:
return 1.0
self._tokenize(src, tar)
a = self._intersection_card()
ab = self._src_card()
ac = self._tar_card()
n = self._population_unique_card()
def _henderson_heron(ab, ac, a, n):
return (
factorial(ab)
* factorial(ac)
* factorial(n - ab)
* factorial(n - ac)
/ (
factorial(n)
* factorial(a)
* factorial(ab - a)
* factorial(ac - a)
* factorial((n - ac - ab + a))
)
)
return sum(_henderson_heron(ab, ac, i, n) for i in range(0, a + 1))
if __name__ == '__main__':
import doctest
doctest.testmod()