# 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
# (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._dice.
Sørensen–Dice coefficient & distance
"""
from deprecation import deprecated
from ._tversky import Tversky
from .. import __version__
__all__ = ['Dice', 'dist_dice', 'sim_dice']
[docs]class Dice(Tversky):
r"""Sørensen–Dice coefficient.
For two sets X and Y, the Sørensen–Dice coefficient
:cite:`Dice:1945,Sorensen:1948,Czekanowski:1909,Motyka:1950` is
.. math::
sim_{Dice}(X, Y) = \frac{2 \cdot |X \cap Y|}{|X| + |Y|}
This is the complement of Bray & Curtis dissimilarity :cite:`Bray:1957`,
also known as the Lance & Williams dissimilarity :cite:`Lance:1967`.
This is identical to the Tanimoto similarity coefficient
:cite:`Tanimoto:1958` and the Tversky index :cite:`Tversky:1977` for
:math:`\alpha = \beta = 0.5`.
In the Ruby text library this is identified as White similarity, after
:cite:`White:Nd`.
In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n,
this is
.. math::
sim_{Dice} =
\frac{2a}{2a+b+c}
Notes
-----
In terms of a confusion matrix, this is equivalent to :math:`F_1` score
:py:meth:`ConfusionTable.f1_score`.
The multiset variant is termed Gleason similarity :cite:`Gleason:1920`.
.. versionadded:: 0.3.6
"""
def __init__(self, tokenizer=None, intersection_type='crisp', **kwargs):
"""Initialize Dice 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(Dice, self).__init__(
alpha=0.5,
beta=0.5,
bias=None,
tokenizer=tokenizer,
intersection_type=intersection_type,
**kwargs
)
[docs] def sim(self, src, tar):
"""Return the Sørensen–Dice 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
Sørensen–Dice similarity
Examples
--------
>>> cmp = Dice()
>>> cmp.sim('cat', 'hat')
0.5
>>> cmp.sim('Niall', 'Neil')
0.36363636363636365
>>> cmp.sim('aluminum', 'Catalan')
0.11764705882352941
>>> cmp.sim('ATCG', 'TAGC')
0.0
.. versionadded:: 0.1.0
.. versionchanged:: 0.3.6
Encapsulated in class
"""
return super(Dice, self).sim(src, tar)
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the Dice.sim method instead.',
)
def sim_dice(src, tar, qval=2):
"""Return the Sørensen–Dice coefficient of two strings.
This is a wrapper for :py:meth:`Dice.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
Sørensen–Dice similarity
Examples
--------
>>> sim_dice('cat', 'hat')
0.5
>>> sim_dice('Niall', 'Neil')
0.36363636363636365
>>> sim_dice('aluminum', 'Catalan')
0.11764705882352941
>>> sim_dice('ATCG', 'TAGC')
0.0
.. versionadded:: 0.1.0
"""
return Dice(qval=qval).sim(src, tar)
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the Dice.dist method instead.',
)
def dist_dice(src, tar, qval=2):
"""Return the Sørensen–Dice distance between two strings.
This is a wrapper for :py:meth:`Dice.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
Sørensen–Dice distance
Examples
--------
>>> dist_dice('cat', 'hat')
0.5
>>> dist_dice('Niall', 'Neil')
0.6363636363636364
>>> dist_dice('aluminum', 'Catalan')
0.8823529411764706
>>> dist_dice('ATCG', 'TAGC')
1.0
.. versionadded:: 0.1.0
"""
return Dice(qval=qval).dist(src, tar)
if __name__ == '__main__':
import doctest
doctest.testmod()