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# -*- coding: utf-8 -*- |
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# Copyright 2019 by Christopher C. Little. |
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# This file is part of Abydos. |
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# |
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# Abydos is free software: you can redistribute it and/or modify |
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# it under the terms of the GNU General Public License as published by |
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# the Free Software Foundation, either version 3 of the License, or |
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# (at your option) any later version. |
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# |
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# Abydos is distributed in the hope that it will be useful, |
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# but WITHOUT ANY WARRANTY; without even the implied warranty of |
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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# GNU General Public License for more details. |
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# |
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# You should have received a copy of the GNU General Public License |
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# along with Abydos. If not, see <http://www.gnu.org/licenses/>. |
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"""abydos.distance._clark. |
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Clark's coefficient of divergence |
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""" |
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from __future__ import ( |
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absolute_import, |
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division, |
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print_function, |
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unicode_literals, |
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) |
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from ._token_distance import _TokenDistance |
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__all__ = ['Clark'] |
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class Clark(_TokenDistance): |
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r"""Clark's coefficient of divergence. |
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For two sets X and Y and a population N, Clark's coefficient of divergence |
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:cite:`Clark:1952` is: |
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.. math:: |
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dist_{Clark}(X, Y) = \sqrt{\frac{\sum_{i=0}^{|N|} |
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\big(\frac{x_i-y_i}{x_i+y_i}\big)^2}{|N|}} |
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.. versionadded:: 0.4.1 |
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""" |
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def __init__(self, **kwargs): |
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"""Initialize Clark instance. |
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Parameters |
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---------- |
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**kwargs |
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Arbitrary keyword arguments |
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.. versionadded:: 0.4.1 |
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""" |
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super(Clark, self).__init__(**kwargs) |
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def dist(self, src, tar): |
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"""Return Clark's coefficient of divergence of two strings. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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Returns |
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------- |
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float |
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Clark's coefficient of divergence |
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Examples |
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-------- |
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>>> cmp = Clark() |
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>>> cmp.dist('cat', 'hat') |
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0.816496580927726 |
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>>> cmp.dist('Niall', 'Neil') |
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0.8819171036881969 |
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>>> cmp.dist('aluminum', 'Catalan') |
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0.9660917830792959 |
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>>> cmp.dist('ATCG', 'TAGC') |
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1.0 |
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.. versionadded:: 0.4.1 |
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""" |
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if src == tar: |
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return 0.0 |
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self._tokenize(src, tar) |
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src_tok = self._src_tokens |
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tar_tok = self._tar_tokens |
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alphabet = set(set(src_tok.keys()) | set(tar_tok.keys())) |
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return ( |
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sum( |
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((src_tok[ltr] - tar_tok[ltr]) / (src_tok[ltr] + tar_tok[ltr])) |
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** 2 |
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for ltr in alphabet |
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) |
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/ len(alphabet) |
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) ** 0.5 |
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if __name__ == '__main__': |
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import doctest |
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doctest.testmod() |
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chrislit /
abydos
