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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._morisita. |
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Morisita index of overlap |
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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__ = ['Morisita'] |
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class Morisita(_TokenDistance): |
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r"""Morisita index of overlap. |
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Morisita index of overlap :cite:`Morisita:1959`, following the description |
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of :cite:`Horn:1966`, given two populations X and Y drawn from S species, |
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is: |
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.. math:: |
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sim_{Morisita}(X, Y) = |
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C_{\lambda} = \frac{2\sum_{i=1}^S x_i y_i}{(\lambda_x + \lambda_y)XY} |
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where |
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.. math:: |
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X = \sum_{i=1}^S x_i ~~;~~ Y = \sum_{i=1}^S y_i |
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.. math:: |
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\lambda_x = \frac{\sum_{i=1}^S x_i(x_i-1)}{X(X-1)} ~~;~~ |
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\lambda_y = \frac{\sum_{i=1}^S y_i(y_i-1)}{Y(Y-1)} |
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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 Morisita 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(Morisita, self).__init__(**kwargs) |
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def sim_score(self, src, tar): |
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"""Return the Morisita similarity 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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Morisita similarity |
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Examples |
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-------- |
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>>> cmp = Morisita() |
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>>> cmp.sim_score('cat', 'hat') |
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0.25 |
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>>> cmp.sim_score('Niall', 'Neil') |
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0.13333333333333333 |
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>>> cmp.sim_score('aluminum', 'Catalan') |
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1.0 |
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>>> cmp.sim_score('ATCG', 'TAGC') |
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0.0 |
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.. versionadded:: 0.4.1 |
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""" |
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self._tokenize(src, tar) |
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intersection = self._intersection() |
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src_card = self._src_card() |
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tar_card = self._tar_card() |
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src_lambda = 0 |
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tar_lambda = 0 |
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for val in self._src_tokens.values(): |
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src_lambda += val * (val - 1) |
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if src_lambda: |
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src_lambda /= src_card * (src_card - 1) |
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for val in self._tar_tokens.values(): |
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tar_lambda += val * (val - 1) |
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if tar_lambda: |
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tar_lambda /= tar_card * (tar_card - 1) |
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sim = 0 |
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for symbol in intersection.keys(): |
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sim += self._src_tokens[symbol] * self._tar_tokens[symbol] |
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sim *= 2 |
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if src_card: |
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sim /= src_card |
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if tar_card: |
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sim /= tar_card |
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if src_lambda + tar_lambda: |
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sim /= src_lambda + tar_lambda |
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return sim |
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def sim(self, *args, **kwargs): |
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"""Raise exception when called. |
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Parameters |
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---------- |
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*args |
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Variable length argument list |
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**kwargs |
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Arbitrary keyword arguments |
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Raises |
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------ |
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NotImplementedError |
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Method disabled for Morisita similarity. |
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.. versionadded:: 0.3.6 |
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""" |
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raise NotImplementedError('Method disabled for Morisita similarity.') |
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def dist(self, *args, **kwargs): |
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"""Raise exception when called. |
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Parameters |
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---------- |
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*args |
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Variable length argument list |
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**kwargs |
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Arbitrary keyword arguments |
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Raises |
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------ |
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NotImplementedError |
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Method disabled for Morisita similarity. |
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.. versionadded:: 0.3.6 |
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""" |
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raise NotImplementedError('Method disabled for Morisita similarity.') |
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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
