Source code for abydos.distance._overlap

# Copyright 2014-2020 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
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#
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"""abydos.distance._overlap.

Overlap similarity & distance
"""

from deprecation import deprecated

from ._token_distance import _TokenDistance
from .. import __version__

__all__ = ['Overlap', 'dist_overlap', 'sim_overlap']


[docs]class Overlap(_TokenDistance): r"""Overlap coefficient. For two sets X and Y, the overlap coefficient :cite:`Szymkiewicz:1934,Simpson:1949`, also called the Szymkiewicz-Simpson coefficient and Simpson's ecological coexistence coefficient, is .. math:: sim_{overlap}(X, Y) = \frac{|X \cap Y|}{min(|X|, |Y|)} In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n, this is .. math:: sim_{overlap} = \frac{a}{min(a+b, a+c)} .. versionadded:: 0.3.6 """ def __init__(self, tokenizer=None, intersection_type='crisp', **kwargs): """Initialize Overlap 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(Overlap, self).__init__( tokenizer=tokenizer, intersection_type=intersection_type, **kwargs )
[docs] def sim(self, src, tar): r"""Return the overlap coefficient 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 Overlap similarity Examples -------- >>> cmp = Overlap() >>> cmp.sim('cat', 'hat') 0.5 >>> cmp.sim('Niall', 'Neil') 0.4 >>> cmp.sim('aluminum', 'Catalan') 0.125 >>> cmp.sim('ATCG', 'TAGC') 0.0 .. versionadded:: 0.1.0 .. versionchanged:: 0.3.6 Encapsulated in class """ if src == tar: return 1.0 self._tokenize(src, tar) if not self._src_card() or not self._tar_card(): return 0.0 return self._intersection_card() / min( self._src_card(), self._tar_card() )
[docs]@deprecated( deprecated_in='0.4.0', removed_in='0.6.0', current_version=__version__, details='Use the Overlap.sim method instead.', ) def sim_overlap(src, tar, qval=2): r"""Return the overlap coefficient of two strings. This is a wrapper for :py:meth:`Overlap.sim`. Parameters ---------- src : str Source string (or QGrams/Counter objects) for comparison tar : str Target string (or QGrams/Counter objects) for comparison qval : int The length of each q-gram Returns ------- float Overlap similarity Examples -------- >>> sim_overlap('cat', 'hat') 0.5 >>> sim_overlap('Niall', 'Neil') 0.4 >>> sim_overlap('aluminum', 'Catalan') 0.125 >>> sim_overlap('ATCG', 'TAGC') 0.0 .. versionadded:: 0.1.0 """ return Overlap(qval=qval).sim(src, tar)
[docs]@deprecated( deprecated_in='0.4.0', removed_in='0.6.0', current_version=__version__, details='Use the Overlap.dist method instead.', ) def dist_overlap(src, tar, qval=2): """Return the overlap distance between two strings. This is a wrapper for :py:meth:`Overlap.dist`. Parameters ---------- src : str Source string (or QGrams/Counter objects) for comparison tar : str Target string (or QGrams/Counter objects) for comparison qval : int The length of each q-gram Returns ------- float Overlap distance Examples -------- >>> dist_overlap('cat', 'hat') 0.5 >>> dist_overlap('Niall', 'Neil') 0.6 >>> dist_overlap('aluminum', 'Catalan') 0.875 >>> dist_overlap('ATCG', 'TAGC') 1.0 .. versionadded:: 0.1.0 """ return Overlap(qval=qval).dist(src, tar)
if __name__ == '__main__': import doctest doctest.testmod()