Source code for abydos.distance._stiles

# Copyright 2018-2020 by Christopher C. Little.
# This file is part of Abydos.
#
# Abydos is free software: you can redistribute it and/or modify
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# the Free Software Foundation, either version 3 of the License, or
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"""abydos.distance._stiles.

Stiles similarity
"""

from math import copysign, log10

from ._token_distance import _TokenDistance

__all__ = ['Stiles']


[docs]class Stiles(_TokenDistance): r"""Stiles similarity. For two sets X and Y and a population N, Stiles similarity :cite:`Stiles:1961` is .. math:: sim_{Stiles}(X, Y) = log_{10} \frac{|N| \Big(||X \cap Y| \cdot |N| - |X \setminus Y| \cdot |Y \setminus X|| - \frac{|N|}{2}\Big)^2} {|X \setminus Y| \cdot |Y \setminus X| \cdot (|N| - |X \setminus Y|) \cdot (|N| - |Y \setminus X|)} In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n, this is .. math:: sim_{Stiles} = log_{10} \frac{n(|an-bc|-\frac{1}{2}n)^2}{bc(n-b)(n-c)} .. versionadded:: 0.4.0 """ def __init__( self, alphabet=None, tokenizer=None, intersection_type='crisp', **kwargs ): """Initialize Stiles 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(Stiles, self).__init__( alphabet=alphabet, tokenizer=tokenizer, intersection_type=intersection_type, **kwargs )
[docs] def sim_score(self, src, tar): """Return the Stiles 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 Stiles similarity Examples -------- >>> cmp = Stiles() >>> cmp.sim_score('cat', 'hat') 2.6436977886009236 >>> cmp.sim_score('Niall', 'Neil') 2.1622951406967723 >>> cmp.sim_score('aluminum', 'Catalan') 0.41925115106844024 >>> cmp.sim_score('ATCG', 'TAGC') -0.8426334527850912 .. versionadded:: 0.4.0 """ self._tokenize(src, tar) eps = 0.0000001 a = max(self._intersection_card(), eps) b = max(self._src_only_card(), eps) c = max(self._tar_only_card(), eps) n = max(self._total_complement_card(), eps) + a + b + c anmbc = a * n - b * c return copysign( log10( n * max((abs(anmbc) - n / 2) ** 2, eps) / (b * (n - b) * c * (n - c)) ), anmbc, )
[docs] def corr(self, src, tar): """Return the Stiles correlation 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 Stiles correlation Examples -------- >>> cmp = Stiles() >>> cmp.corr('cat', 'hat') 0.14701542182970487 >>> cmp.corr('Niall', 'Neil') 0.11767566062554877 >>> cmp.corr('aluminum', 'Catalan') 0.022355640924908403 >>> cmp.corr('ATCG', 'TAGC') -0.046296656196428934 .. versionadded:: 0.4.0 """ return self.sim_score(src, tar) / max( self.sim_score(src, src), self.sim_score(tar, tar) )
[docs] def sim(self, src, tar): """Return the normalized Stiles 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 Normalized Stiles similarity Examples -------- >>> cmp = Stiles() >>> cmp.sim('cat', 'hat') 0.5735077109148524 >>> cmp.sim('Niall', 'Neil') 0.5588378303127743 >>> cmp.sim('aluminum', 'Catalan') 0.5111778204624542 >>> cmp.sim('ATCG', 'TAGC') 0.4768516719017855 .. versionadded:: 0.4.0 """ return (1.0 + self.corr(src, tar)) / 2.0
if __name__ == '__main__': import doctest doctest.testmod()