Source code for abydos.distance._millar

# Copyright 2019-2020 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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"""abydos.distance._millar.

Millar's binomial deviance dissimilarity
"""

from math import log

from ._token_distance import _TokenDistance

__all__ = ['Millar']


[docs]class Millar(_TokenDistance): r"""Millar's binomial deviance dissimilarity. For two sets X and Y drawn from a population S, Millar's binomial deviance dissimilarity :cite:`Anderson:2004` is: .. math:: dist_{Millar}(X, Y) = \sum_{i=0}^{|S|} \frac{1}{x_i+y_i} \bigg\{x_i log(\frac{x_i}{x_i+y_i}) + y_i log(\frac{y_i}{x_i+y_i}) - (x_i+y_i) log(\frac{1}{2})\bigg\} .. versionadded:: 0.4.1 """ def __init__(self, **kwargs): """Initialize Millar instance. Parameters ---------- **kwargs Arbitrary keyword arguments .. versionadded:: 0.4.1 """ super(Millar, self).__init__(**kwargs)
[docs] def dist_abs(self, src, tar): """Return Millar's binomial deviance dissimilarity of two strings. Parameters ---------- src : str Source string for comparison tar : str Target string for comparison Returns ------- float Millar's binomial deviance dissimilarity Examples -------- >>> cmp = Millar() >>> cmp.dist_abs('cat', 'hat') 2.772588722239781 >>> cmp.dist_abs('Niall', 'Neil') 4.852030263919617 >>> cmp.dist_abs('aluminum', 'Catalan') 9.704060527839234 >>> cmp.dist_abs('ATCG', 'TAGC') 6.931471805599453 .. versionadded:: 0.4.1 """ self._tokenize(src, tar) src_tok = self._src_tokens tar_tok = self._tar_tokens alphabet = set(src_tok.keys() | tar_tok.keys()) log2 = log(2) score = 0 for tok in alphabet: n_k = src_tok[tok] + tar_tok[tok] src_val = 0 if src_tok[tok]: src_val = src_tok[tok] * log(src_tok[tok] / n_k) tar_val = 0 if tar_tok[tok]: tar_val = tar_tok[tok] * log(tar_tok[tok] / n_k) score += (src_val + tar_val + n_k * log2) / n_k if score > 0: return score return 0.0
[docs] def sim(self, *args, **kwargs): """Raise exception when called. Parameters ---------- *args Variable length argument list **kwargs Arbitrary keyword arguments Raises ------ NotImplementedError Method disabled for Millar dissimilarity. .. versionadded:: 0.3.6 """ raise NotImplementedError('Method disabled for Millar dissimilarity.')
[docs] def dist(self, *args, **kwargs): """Raise exception when called. Parameters ---------- *args Variable length argument list **kwargs Arbitrary keyword arguments Raises ------ NotImplementedError Method disabled for Millar dissimilarity. .. versionadded:: 0.3.6 """ raise NotImplementedError('Method disabled for Millar dissimilarity.')
if __name__ == '__main__': import doctest doctest.testmod()