abydos.distance._gilbert.Gilbert.__init__() - Code Metrics - chrislit/abydos - Measure and Improve Code Quality continuously with Scrutinizer

abydos.distance._gilbert.Gilbert.init() A
last analyzed 2020-12-31 20:10 UTC

↳ Parent: abydos.distance._gilbert

Complexity

Conditions

Size

Total Lines	48
Code Lines	13

Duplication

Lines	48
Ratio	100 %

Code Coverage

Tests	2
CRAP Score	1

Importance

Changes

Metric	Value
eloc	13
dl	48
loc	48
ccs	2
cts	2
cp	1
rs	9.75
c	0
b	0
f	0
cc	1
nop	5
crap	1

# 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._gilbert.

Gilbert correlation
"""

from typing import Any, Counter as TCounter, Optional, Sequence, Set, Union

from ._token_distance import _TokenDistance
from ..tokenizer import _Tokenizer

__all__ = ['Gilbert']


class Gilbert(_TokenDistance):

    r"""Gilbert correlation.

    For two sets X and Y and a population N, the Gilbert correlation
    :cite:`Gilbert:1884` is

        .. math::

            corr_{Gilbert}(X, Y) =
            \frac{2(|X \cap Y| \cdot |(N \setminus X) \setminus Y| -
            |X \setminus Y| \cdot |Y \setminus X|)}
            {|N|^2 - |X \cap Y|^2 + |X \setminus Y|^2 + |Y \setminus X|^2 -
            |(N \setminus X) \setminus Y|^2}

    For lack of access to the original, this formula is based on the concurring
    formulae presented in :cite:`Peirce:1884` and :cite:`Doolittle:1884`.

    In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n,
    this is

        .. math::

            corr_{Gilbert} =
            \frac{2(ad-cd)}{n^2-a^2+b^2+c^2-d^2}

    .. versionadded:: 0.4.0
    """

    def __init__(
        self,
        alphabet: Optional[
            Union[TCounter[str], Sequence[str], Set[str], int]
        ] = None,
        tokenizer: Optional[_Tokenizer] = None,
        intersection_type: str = 'crisp',
        **kwargs: Any
    ) -> None:
        """Initialize Gilbert 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(Gilbert, self).__init__(
            alphabet=alphabet,
            tokenizer=tokenizer,
            intersection_type=intersection_type,
            **kwargs
        )

    def corr(self, src: str, tar: str) -> float:
        """Return the Gilbert 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
            Gilbert correlation

        Examples
        --------
        >>> cmp = Gilbert()
        >>> cmp.corr('cat', 'hat')
        0.3310580204778157
        >>> cmp.corr('Niall', 'Neil')
        0.21890122402504983
        >>> cmp.corr('aluminum', 'Catalan')
        0.057094811018577836
        >>> cmp.corr('ATCG', 'TAGC')
        -0.003198976327575176


        .. versionadded:: 0.4.0

        """
        if src == tar:
            return 1.0

        self._tokenize(src, tar)

        a = self._intersection_card()
        b = self._src_only_card()
        c = self._tar_only_card()
        n = self._population_unique_card()

        num = a * n - (a + b) * (a + c)
        if num:
            return num / (n * (a + b + c) - (a + b) * (a + c))
        return 0.0

    def sim(self, src: str, tar: str) -> float:
        """Return the Gilbert 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
            Gilbert similarity

        Examples
        --------
        >>> cmp = Gilbert()
        >>> cmp.sim('cat', 'hat')
        0.6655290102389079
        >>> cmp.sim('Niall', 'Neil')
        0.6094506120125249
        >>> cmp.sim('aluminum', 'Catalan')
        0.5285474055092889
        >>> cmp.sim('ATCG', 'TAGC')
        0.4984005118362124


        .. versionadded:: 0.4.0

        """
        return (1.0 + self.corr(src, tar)) / 2.0


if __name__ == '__main__':
    import doctest

    doctest.testmod()


1			# Copyright 2018-2020 by Christopher C. Little.
2			# This file is part of Abydos.
3			#
4			# Abydos is free software: you can redistribute it and/or modify
5			# it under the terms of the GNU General Public License as published by
6			# the Free Software Foundation, either version 3 of the License, or
7			# (at your option) any later version.
8			#
9			# Abydos is distributed in the hope that it will be useful,
10			# but WITHOUT ANY WARRANTY; without even the implied warranty of
11			# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12			# GNU General Public License for more details.
13			#
14			# You should have received a copy of the GNU General Public License
15			# along with Abydos. If not, see <http://www.gnu.org/licenses/>.
16
17			"""abydos.distance._gilbert.
18
19	1		Gilbert correlation
20			"""
21
22			from typing import Any, Counter as TCounter, Optional, Sequence, Set, Union
23
24	1		from ._token_distance import _TokenDistance
25			from ..tokenizer import _Tokenizer
26
27			__all__ = ['Gilbert']
28
29
30		View Code Duplication	class Gilbert(_TokenDistance):
			0 ignored issues – show Duplication introduced 2019-02-15 07:24 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
31	1		r"""Gilbert correlation.
32
33	1		For two sets X and Y and a population N, the Gilbert correlation
34			:cite:`Gilbert:1884` is
35
36	1		.. math::
37
38			corr_{Gilbert}(X, Y) =
39			\frac{2(\|X \cap Y\| \cdot \|(N \setminus X) \setminus Y\| -
40			\|X \setminus Y\| \cdot \|Y \setminus X\|)}
41			{\|N\|^2 - \|X \cap Y\|^2 + \|X \setminus Y\|^2 + \|Y \setminus X\|^2 -
42			\|(N \setminus X) \setminus Y\|^2}
43
44			For lack of access to the original, this formula is based on the concurring
45			formulae presented in :cite:`Peirce:1884` and :cite:`Doolittle:1884`.
46
47			In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n,
48			this is
49
50			.. math::
51
52			corr_{Gilbert} =
53			\frac{2(ad-cd)}{n^2-a^2+b^2+c^2-d^2}
54
55			.. versionadded:: 0.4.0
56			"""
57
58			def __init__(
59			self,
60			alphabet: Optional[
61			Union[TCounter[str], Sequence[str], Set[str], int]
62			] = None,
63			tokenizer: Optional[_Tokenizer] = None,
64	1		intersection_type: str = 'crisp',
65			**kwargs: Any
66			) -> None:
67			"""Initialize Gilbert instance.
68
69			Parameters
70			----------
71			alphabet : Counter, collection, int, or None
72			This represents the alphabet of possible tokens.
73			See :ref:`alphabet <alphabet>` description in
74			:py:class:`_TokenDistance` for details.
75			tokenizer : _Tokenizer
76			A tokenizer instance from the :py:mod:`abydos.tokenizer` package
77			intersection_type : str
78			Specifies the intersection type, and set type as a result:
79			See :ref:`intersection_type <intersection_type>` description in
80			:py:class:`_TokenDistance` for details.
81			**kwargs
82			Arbitrary keyword arguments
83
84			Other Parameters
85			----------------
86			qval : int
87			The length of each q-gram. Using this parameter and tokenizer=None
88			will cause the instance to use the QGram tokenizer with this
89			q value.
90			metric : _Distance
91			A string distance measure class for use in the ``soft`` and
92			``fuzzy`` variants.
93			threshold : float
94			A threshold value, similarities above which are counted as
95			members of the intersection for the ``fuzzy`` variant.
96
97
98			.. versionadded:: 0.4.0
99
100			"""
101			super(Gilbert, self).__init__(
102			alphabet=alphabet,
103			tokenizer=tokenizer,
104			intersection_type=intersection_type,
105	1		**kwargs
106			)
107
108			def corr(self, src: str, tar: str) -> float:
109			"""Return the Gilbert correlation of two strings.
110
111			Parameters
112	1		----------
113			src : str
114			Source string (or QGrams/Counter objects) for comparison
115			tar : str
116			Target string (or QGrams/Counter objects) for comparison
117
118			Returns
119			-------
120			float
121			Gilbert correlation
122
123			Examples
124			--------
125			>>> cmp = Gilbert()
126			>>> cmp.corr('cat', 'hat')
127			0.3310580204778157
128			>>> cmp.corr('Niall', 'Neil')
129			0.21890122402504983
130			>>> cmp.corr('aluminum', 'Catalan')
131			0.057094811018577836
132			>>> cmp.corr('ATCG', 'TAGC')
133			-0.003198976327575176
134
135
136			.. versionadded:: 0.4.0
137
138			"""
139			if src == tar:
140			return 1.0
141
142			self._tokenize(src, tar)
143	1
144	1		a = self._intersection_card()
145			b = self._src_only_card()
146	1		c = self._tar_only_card()
147			n = self._population_unique_card()
148	1
149	1		num = a * n - (a + b) * (a + c)
150	1		if num:
151	1		return num / (n * (a + b + c) - (a + b) * (a + c))
152			return 0.0
153	1
154	1		def sim(self, src: str, tar: str) -> float:
155	1		"""Return the Gilbert similarity of two strings.
156	1
157			Parameters
158	1		----------
159			src : str
160			Source string (or QGrams/Counter objects) for comparison
161			tar : str
162			Target string (or QGrams/Counter objects) for comparison
163
164			Returns
165			-------
166			float
167			Gilbert similarity
168
169			Examples
170			--------
171			>>> cmp = Gilbert()
172			>>> cmp.sim('cat', 'hat')
173			0.6655290102389079
174			>>> cmp.sim('Niall', 'Neil')
175			0.6094506120125249
176			>>> cmp.sim('aluminum', 'Catalan')
177			0.5285474055092889
178			>>> cmp.sim('ATCG', 'TAGC')
179			0.4984005118362124
180
181
182			.. versionadded:: 0.4.0
183
184			"""
185			return (1.0 + self.corr(src, tar)) / 2.0
186
187
188			if __name__ == '__main__':
189	1		import doctest
190
191			doctest.testmod()
192

chrislit / abydos

abydos.distance._gilbert.Gilbert.__init__() A last analyzed 2020-12-31 20:10 UTC

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abydos.distance._gilbert.Gilbert.init() A
last analyzed 2020-12-31 20:10 UTC