package scipy

Get an attribute of this module as a Py.Object.t. This is useful to pass a Python function to another function.

Compute the Bray-Curtis distance between two 1-D arrays.

Bray-Curtis distance is defined as

.. math::

\sum |u_i-v_i| / \sum |u_i+v_i|

The Bray-Curtis distance is in the range 0, 1 if all coordinates are positive, and is undefined if the inputs are of length zero.

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. w : (N,) array_like, optional The weights for each value in `u` and `v`. Default is None, which gives each value a weight of 1.0

Returns ------- braycurtis : double The Bray-Curtis distance between 1-D arrays `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.braycurtis(1, 0, 0, 0, 1, 0) 1.0 >>> distance.braycurtis(1, 1, 0, 0, 1, 0) 0.33333333333333331

Compute the Canberra distance between two 1-D arrays.

The Canberra distance is defined as

.. math::

d(u,v) = \sum_i \frac |u_i-v_i| |u_i|+|v_i| .

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. w : (N,) array_like, optional The weights for each value in `u` and `v`. Default is None, which gives each value a weight of 1.0

Returns ------- canberra : double The Canberra distance between vectors `u` and `v`.

Notes ----- When `ui` and `vi` are 0 for given i, then the fraction 0/0 = 0 is used in the calculation.

Examples -------- >>> from scipy.spatial import distance >>> distance.canberra(1, 0, 0, 0, 1, 0) 2.0 >>> distance.canberra(1, 1, 0, 0, 1, 0) 1.0

Compute distance between each pair of the two collections of inputs.

See Notes for common calling conventions.

Parameters ---------- XA : ndarray An :math:`m_A` by :math:`n` array of :math:`m_A` original observations in an :math:`n`-dimensional space. Inputs are converted to float type. XB : ndarray An :math:`m_B` by :math:`n` array of :math:`m_B` original observations in an :math:`n`-dimensional space. Inputs are converted to float type. metric : str or callable, optional The distance metric to use. If a string, the distance function can be 'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'kulsinski', 'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'wminkowski', 'yule'. *args : tuple. Deprecated. Additional arguments should be passed as keyword arguments **kwargs : dict, optional Extra arguments to `metric`: refer to each metric documentation for a list of all possible arguments.

Some possible arguments:

p : scalar The p-norm to apply for Minkowski, weighted and unweighted. Default: 2.

w : ndarray The weight vector for metrics that support weights (e.g., Minkowski).

V : ndarray The variance vector for standardized Euclidean. Default: var(vstack(XA, XB), axis=0, ddof=1)

VI : ndarray The inverse of the covariance matrix for Mahalanobis. Default: inv(cov(vstack(XA, XB.T))).T

out : ndarray The output array If not None, the distance matrix Y is stored in this array. Note: metric independent, it will become a regular keyword arg in a future scipy version

Returns ------- Y : ndarray A :math:`m_A` by :math:`m_B` distance matrix is returned. For each :math:`i` and :math:`j`, the metric ``dist(u=XAi, v=XBj)`` is computed and stored in the :math:`ij` th entry.

Raises ------ ValueError An exception is thrown if `XA` and `XB` do not have the same number of columns.

Notes ----- The following are common calling conventions:

1. ``Y = cdist(XA, XB, 'euclidean')``

Computes the distance between :math:`m` points using Euclidean distance (2-norm) as the distance metric between the points. The points are arranged as :math:`m` :math:`n`-dimensional row vectors in the matrix X.

2. ``Y = cdist(XA, XB, 'minkowski', p=2.)``

Computes the distances using the Minkowski distance :math:`||u-v||_p` (:math:`p`-norm) where :math:`p \geq 1`.

3. ``Y = cdist(XA, XB, 'cityblock')``

Computes the city block or Manhattan distance between the points.

4. ``Y = cdist(XA, XB, 'seuclidean', V=None)``

Computes the standardized Euclidean distance. The standardized Euclidean distance between two n-vectors ``u`` and ``v`` is

.. math::

\sqrt\sum {(u_i-v_i)^2 / V[x_i]

}

.

V is the variance vector; Vi is the variance computed over all the i'th components of the points. If not passed, it is automatically computed.

5. ``Y = cdist(XA, XB, 'sqeuclidean')``

Computes the squared Euclidean distance :math:`||u-v||_2^2` between the vectors.

6. ``Y = cdist(XA, XB, 'cosine')``

Computes the cosine distance between vectors u and v,

.. math::

1 - \fracu \cdot v { ||u|| _2 ||v|| _2

}

where :math:`||*||_2` is the 2-norm of its argument ``*``, and :math:`u \cdot v` is the dot product of :math:`u` and :math:`v`.

7. ``Y = cdist(XA, XB, 'correlation')``

Computes the correlation distance between vectors u and v. This is

.. math::

1 - \frac(u - \bar{u) \cdot (v - \bar

})}
               {{ ||(u - \bar{u})|| }_2 { ||(v - \bar{v})|| }_2}

   where :math:`\bar{v}` is the mean of the elements of vector v,
   and :math:`x \cdot y` is the dot product of :math:`x` and :math:`y`.


8. ``Y = cdist(XA, XB, 'hamming')``

   Computes the normalized Hamming distance, or the proportion of
   those vector elements between two n-vectors ``u`` and ``v``
   which disagree. To save memory, the matrix ``X`` can be of type
   boolean.

9. ``Y = cdist(XA, XB, 'jaccard')``

   Computes the Jaccard distance between the points. Given two
   vectors, ``u`` and ``v``, the Jaccard distance is the
   proportion of those elements ``u[i]`` and ``v[i]`` that
   disagree where at least one of them is non-zero.

10. ``Y = cdist(XA, XB, 'chebyshev')``

   Computes the Chebyshev distance between the points. The
   Chebyshev distance between two n-vectors ``u`` and ``v`` is the
   maximum norm-1 distance between their respective elements. More
   precisely, the distance is given by

   .. math::

      d(u,v) = \max_i { |u_i-v_i| }.

11. ``Y = cdist(XA, XB, 'canberra')``

   Computes the Canberra distance between the points. The
   Canberra distance between two points ``u`` and ``v`` is

   .. math::

     d(u,v) = \sum_i \frac{ |u_i-v_i| }
                          { |u_i|+|v_i| }.

12. ``Y = cdist(XA, XB, 'braycurtis')``

   Computes the Bray-Curtis distance between the points. The
   Bray-Curtis distance between two points ``u`` and ``v`` is


   .. math::

        d(u,v) = \frac{\sum_i (|u_i-v_i|)}
                      {\sum_i (|u_i+v_i|)}

13. ``Y = cdist(XA, XB, 'mahalanobis', VI=None)``

   Computes the Mahalanobis distance between the points. The
   Mahalanobis distance between two points ``u`` and ``v`` is
   :math:`\sqrt{(u-v)(1/V)(u-v)^T}` where :math:`(1/V)` (the ``VI``
   variable) is the inverse covariance. If ``VI`` is not None,
   ``VI`` will be used as the inverse covariance matrix.

14. ``Y = cdist(XA, XB, 'yule')``

   Computes the Yule distance between the boolean
   vectors. (see `yule` function documentation)

15. ``Y = cdist(XA, XB, 'matching')``

   Synonym for 'hamming'.

16. ``Y = cdist(XA, XB, 'dice')``

   Computes the Dice distance between the boolean vectors. (see
   `dice` function documentation)

17. ``Y = cdist(XA, XB, 'kulsinski')``

   Computes the Kulsinski distance between the boolean
   vectors. (see `kulsinski` function documentation)

18. ``Y = cdist(XA, XB, 'rogerstanimoto')``

   Computes the Rogers-Tanimoto distance between the boolean
   vectors. (see `rogerstanimoto` function documentation)

19. ``Y = cdist(XA, XB, 'russellrao')``

   Computes the Russell-Rao distance between the boolean
   vectors. (see `russellrao` function documentation)

20. ``Y = cdist(XA, XB, 'sokalmichener')``

   Computes the Sokal-Michener distance between the boolean
   vectors. (see `sokalmichener` function documentation)

21. ``Y = cdist(XA, XB, 'sokalsneath')``

   Computes the Sokal-Sneath distance between the vectors. (see
   `sokalsneath` function documentation)


22. ``Y = cdist(XA, XB, 'wminkowski', p=2., w=w)``

   Computes the weighted Minkowski distance between the
   vectors. (see `wminkowski` function documentation)

23. ``Y = cdist(XA, XB, f)``

   Computes the distance between all pairs of vectors in X
   using the user supplied 2-arity function f. For example,
   Euclidean distance between the vectors could be computed
   as follows::

     dm = cdist(XA, XB, lambda u, v: np.sqrt(((u-v)**2).sum()))

   Note that you should avoid passing a reference to one of
   the distance functions defined in this library. For example,::

     dm = cdist(XA, XB, sokalsneath)

   would calculate the pair-wise distances between the vectors in
   X using the Python function `sokalsneath`. This would result in
   sokalsneath being called :math:`{n \choose 2}` times, which
   is inefficient. Instead, the optimized C version is more
   efficient, and we call it using the following syntax::

     dm = cdist(XA, XB, 'sokalsneath')

Examples
--------
Find the Euclidean distances between four 2-D coordinates:

>>> from scipy.spatial import distance
>>> coords = [(35.0456, -85.2672),
...           (35.1174, -89.9711),
...           (35.9728, -83.9422),
...           (36.1667, -86.7833)]
>>> distance.cdist(coords, coords, 'euclidean')
array([[ 0.    ,  4.7044,  1.6172,  1.8856],
       [ 4.7044,  0.    ,  6.0893,  3.3561],
       [ 1.6172,  6.0893,  0.    ,  2.8477],
       [ 1.8856,  3.3561,  2.8477,  0.    ]])


Find the Manhattan distance from a 3-D point to the corners of the unit
cube:

>>> a = np.array([[0, 0, 0],
...               [0, 0, 1],
...               [0, 1, 0],
...               [0, 1, 1],
...               [1, 0, 0],
...               [1, 0, 1],
...               [1, 1, 0],
...               [1, 1, 1]])
>>> b = np.array([[ 0.1,  0.2,  0.4]])
>>> distance.cdist(a, b, 'cityblock')
array([[ 0.7],
       [ 0.9],
       [ 1.3],
       [ 1.5],
       [ 1.5],
       [ 1.7],
       [ 2.1],
       [ 2.3]])

Compute the Chebyshev distance.

Computes the Chebyshev distance between two 1-D arrays `u` and `v`, which is defined as

.. math::

\max_i |u_i-v_i| .

Parameters ---------- u : (N,) array_like Input vector. v : (N,) array_like Input vector. w : (N,) array_like, optional Unused, as 'max' is a weightless operation. Here for API consistency.

Returns ------- chebyshev : double The Chebyshev distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.chebyshev(1, 0, 0, 0, 1, 0) 1 >>> distance.chebyshev(1, 1, 0, 0, 1, 0) 1

Compute the City Block (Manhattan) distance.

Computes the Manhattan distance between two 1-D arrays `u` and `v`, which is defined as

.. math::

\sum_i \left| u_i - v_i \right| .

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. w : (N,) array_like, optional The weights for each value in `u` and `v`. Default is None, which gives each value a weight of 1.0

Returns ------- cityblock : double The City Block (Manhattan) distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.cityblock(1, 0, 0, 0, 1, 0) 2 >>> distance.cityblock(1, 0, 0, 0, 2, 0) 3 >>> distance.cityblock(1, 0, 0, 1, 1, 0) 1

Compute the correlation distance between two 1-D arrays.

The correlation distance between `u` and `v`, is defined as

.. math::

1 - \frac(u - \bar{u) \cdot (v - \bar

})}
              {{ ||(u - \bar{u})|| }_2 { ||(v - \bar{v})|| }_2}

where :math:`\bar{u}` is the mean of the elements of `u`
and :math:`x \cdot y` is the dot product of :math:`x` and :math:`y`.

Parameters
----------
u : (N,) array_like
    Input array.
v : (N,) array_like
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
correlation : double
    The correlation distance between 1-D array `u` and `v`.

Compute the Cosine distance between 1-D arrays.

The Cosine distance between `u` and `v`, is defined as

.. math::

1 - \fracu \cdot v ||u||_2 ||v||_2.

where :math:`u \cdot v` is the dot product of :math:`u` and :math:`v`.

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. w : (N,) array_like, optional The weights for each value in `u` and `v`. Default is None, which gives each value a weight of 1.0

Returns ------- cosine : double The Cosine distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.cosine(1, 0, 0, 0, 1, 0) 1.0 >>> distance.cosine(100, 0, 0, 0, 1, 0) 1.0 >>> distance.cosine(1, 1, 0, 0, 1, 0) 0.29289321881345254

Compute the Dice dissimilarity between two boolean 1-D arrays.

The Dice dissimilarity between `u` and `v`, is

.. math::

\fracc_{TF + c_FT

}

c_TT + c_FT + c_TF

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n`.

Parameters
----------
u : (N,) ndarray, bool
    Input 1-D array.
v : (N,) ndarray, bool
    Input 1-D array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
dice : double
    The Dice dissimilarity between 1-D arrays `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.dice([1, 0, 0], [0, 1, 0])
1.0
>>> distance.dice([1, 0, 0], [1, 1, 0])
0.3333333333333333
>>> distance.dice([1, 0, 0], [2, 0, 0])
-0.3333333333333333

Compute the directed Hausdorff distance between two N-D arrays.

Distances between pairs are calculated using a Euclidean metric.

Parameters ---------- u : (M,N) ndarray Input array. v : (O,N) ndarray Input array. seed : int or None Local `numpy.random.RandomState` seed. Default is 0, a random shuffling of u and v that guarantees reproducibility.

Returns ------- d : double The directed Hausdorff distance between arrays `u` and `v`,

index_1 : int index of point contributing to Hausdorff pair in `u`

index_2 : int index of point contributing to Hausdorff pair in `v`

Raises ------ ValueError An exception is thrown if `u` and `v` do not have the same number of columns.

Notes ----- Uses the early break technique and the random sampling approach described by 1_. Although worst-case performance is ``O(m * o)`` (as with the brute force algorithm), this is unlikely in practice as the input data would have to require the algorithm to explore every single point interaction, and after the algorithm shuffles the input points at that. The best case performance is O(m), which is satisfied by selecting an inner loop distance that is less than cmax and leads to an early break as often as possible. The authors have formally shown that the average runtime is closer to O(m).

.. versionadded:: 0.19.0

References ---------- .. 1 A. A. Taha and A. Hanbury, 'An efficient algorithm for calculating the exact Hausdorff distance.' IEEE Transactions On Pattern Analysis And Machine Intelligence, vol. 37 pp. 2153-63, 2015.

See Also -------- scipy.spatial.procrustes : Another similarity test for two data sets

Examples -------- Find the directed Hausdorff distance between two 2-D arrays of coordinates:

>>> from scipy.spatial.distance import directed_hausdorff >>> u = np.array((1.0, 0.0), ... (0.0, 1.0), ... (-1.0, 0.0), ... (0.0, -1.0)) >>> v = np.array((2.0, 0.0), ... (0.0, 2.0), ... (-2.0, 0.0), ... (0.0, -4.0))

>>> directed_hausdorff(u, v)0 2.23606797749979 >>> directed_hausdorff(v, u)0 3.0

Find the general (symmetric) Hausdorff distance between two 2-D arrays of coordinates:

>>> max(directed_hausdorff(u, v)0, directed_hausdorff(v, u)0) 3.0

Find the indices of the points that generate the Hausdorff distance (the Hausdorff pair):

>>> directed_hausdorff(v, u)1: (3, 3)

Computes the Euclidean distance between two 1-D arrays.

The Euclidean distance between 1-D arrays `u` and `v`, is defined as

.. math::

||u-v|| _2

\left(\sum(w_i |(u_i - v_i)|^2)\right)^

/2

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. w : (N,) array_like, optional The weights for each value in `u` and `v`. Default is None, which gives each value a weight of 1.0

Returns ------- euclidean : double The Euclidean distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.euclidean(1, 0, 0, 0, 1, 0) 1.4142135623730951 >>> distance.euclidean(1, 1, 0, 0, 1, 0) 1.0

Compute the Hamming distance between two 1-D arrays.

The Hamming distance between 1-D arrays `u` and `v`, is simply the proportion of disagreeing components in `u` and `v`. If `u` and `v` are boolean vectors, the Hamming distance is

.. math::

\fracc_{01 + c_

}

n

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n`.

Parameters
----------
u : (N,) array_like
    Input array.
v : (N,) array_like
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
hamming : double
    The Hamming distance between vectors `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.hamming([1, 0, 0], [0, 1, 0])
0.66666666666666663
>>> distance.hamming([1, 0, 0], [1, 1, 0])
0.33333333333333331
>>> distance.hamming([1, 0, 0], [2, 0, 0])
0.33333333333333331
>>> distance.hamming([1, 0, 0], [3, 0, 0])
0.33333333333333331

Return True if input array is a valid distance matrix.

Distance matrices must be 2-dimensional numpy arrays. They must have a zero-diagonal, and they must be symmetric.

Parameters ---------- D : ndarray The candidate object to test for validity. tol : float, optional The distance matrix should be symmetric. `tol` is the maximum difference between entries ``ij`` and ``ji`` for the distance metric to be considered symmetric. throw : bool, optional An exception is thrown if the distance matrix passed is not valid. name : str, optional The name of the variable to checked. This is useful if throw is set to True so the offending variable can be identified in the exception message when an exception is thrown. warning : bool, optional Instead of throwing an exception, a warning message is raised.

Returns ------- valid : bool True if the variable `D` passed is a valid distance matrix.

Notes ----- Small numerical differences in `D` and `D.T` and non-zeroness of the diagonal are ignored if they are within the tolerance specified by `tol`.

Return True if the input array is a valid condensed distance matrix.

Condensed distance matrices must be 1-dimensional numpy arrays. Their length must be a binomial coefficient :math:`n \choose 2` for some positive integer n.

Parameters ---------- y : ndarray The condensed distance matrix. warning : bool, optional Invokes a warning if the variable passed is not a valid condensed distance matrix. The warning message explains why the distance matrix is not valid. `name` is used when referencing the offending variable. throw : bool, optional Throws an exception if the variable passed is not a valid condensed distance matrix. name : bool, optional Used when referencing the offending variable in the warning or exception message.

Compute the Jaccard-Needham dissimilarity between two boolean 1-D arrays.

The Jaccard-Needham dissimilarity between 1-D boolean arrays `u` and `v`, is defined as

.. math::

\fracc_{TF + c_FT

}

c_{TT + c_FT + c_TF

}

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n`.

Parameters
----------
u : (N,) array_like, bool
    Input array.
v : (N,) array_like, bool
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
jaccard : double
    The Jaccard distance between vectors `u` and `v`.

Notes
-----
When both `u` and `v` lead to a `0/0` division i.e. there is no overlap
between the items in the vectors the returned distance is 0. See the
Wikipedia page on the Jaccard index [1]_, and this paper [2]_.

.. versionchanged:: 1.2.0
    Previously, when `u` and `v` lead to a `0/0` division, the function
    would return NaN. This was changed to return 0 instead.

References
----------
.. [1] https://en.wikipedia.org/wiki/Jaccard_index
.. [2] S. Kosub, 'A note on the triangle inequality for the Jaccard
   distance', 2016, Available online: https://arxiv.org/pdf/1612.02696.pdf

Examples
--------
>>> from scipy.spatial import distance
>>> distance.jaccard([1, 0, 0], [0, 1, 0])
1.0
>>> distance.jaccard([1, 0, 0], [1, 1, 0])
0.5
>>> distance.jaccard([1, 0, 0], [1, 2, 0])
0.5
>>> distance.jaccard([1, 0, 0], [1, 1, 1])
0.66666666666666663

Compute the Jensen-Shannon distance (metric) between two 1-D probability arrays. This is the square root of the Jensen-Shannon divergence.

The Jensen-Shannon distance between two probability vectors `p` and `q` is defined as,

.. math::

\sqrt\frac{D(p \parallel m) + D(q \parallel m)

}

where :math:`m` is the pointwise mean of :math:`p` and :math:`q` and :math:`D` is the Kullback-Leibler divergence.

This routine will normalize `p` and `q` if they don't sum to 1.0.

Parameters ---------- p : (N,) array_like left probability vector q : (N,) array_like right probability vector base : double, optional the base of the logarithm used to compute the output if not given, then the routine uses the default base of scipy.stats.entropy.

Returns ------- js : double The Jensen-Shannon distance between `p` and `q`

.. versionadded:: 1.2.0

Examples -------- >>> from scipy.spatial import distance >>> distance.jensenshannon(1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0) 1.0 >>> distance.jensenshannon(1.0, 0.0, 0.5, 0.5) 0.46450140402245893 >>> distance.jensenshannon(1.0, 0.0, 0.0, 1.0, 0.0, 0.0) 0.0

Compute the Kulsinski dissimilarity between two boolean 1-D arrays.

The Kulsinski dissimilarity between two boolean 1-D arrays `u` and `v`, is defined as

.. math::

\fracc_{TF + c_FT - c_TT + n

}

c_{FT + c_TF + n

}

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n`.

Parameters
----------
u : (N,) array_like, bool
    Input array.
v : (N,) array_like, bool
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
kulsinski : double
    The Kulsinski distance between vectors `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.kulsinski([1, 0, 0], [0, 1, 0])
1.0
>>> distance.kulsinski([1, 0, 0], [1, 1, 0])
0.75
>>> distance.kulsinski([1, 0, 0], [2, 1, 0])
0.33333333333333331
>>> distance.kulsinski([1, 0, 0], [3, 1, 0])
-0.5

Compute the Mahalanobis distance between two 1-D arrays.

The Mahalanobis distance between 1-D arrays `u` and `v`, is defined as

.. math::

\sqrt (u-v) V^{-1 (u-v)^T

}

where ``V`` is the covariance matrix. Note that the argument `VI` is the inverse of ``V``.

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. VI : ndarray The inverse of the covariance matrix.

Returns ------- mahalanobis : double The Mahalanobis distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> iv = [1, 0.5, 0.5], [0.5, 1, 0.5], [0.5, 0.5, 1] >>> distance.mahalanobis(1, 0, 0, 0, 1, 0, iv) 1.0 >>> distance.mahalanobis(0, 2, 0, 0, 1, 0, iv) 1.0 >>> distance.mahalanobis(2, 0, 0, 0, 1, 0, iv) 1.7320508075688772

`matching` is deprecated! spatial.distance.matching is deprecated in scipy 1.0.0; use spatial.distance.hamming instead.

Compute the Hamming distance between two boolean 1-D arrays.

This is a deprecated synonym for :func:`hamming`.

Compute the Minkowski distance between two 1-D arrays.

The Minkowski distance between 1-D arrays `u` and `v`, is defined as

.. math::

||u-v|| _p = (\sum |u_i - v_i|^p)^

/p

.

\left(\sumw_i(|(u_i - v_i)|^p)\right)^

/p

.

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. p : int The order of the norm of the difference :math:` ||u-v|| _p`. w : (N,) array_like, optional The weights for each value in `u` and `v`. Default is None, which gives each value a weight of 1.0

Returns ------- minkowski : double The Minkowski distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.minkowski(1, 0, 0, 0, 1, 0, 1) 2.0 >>> distance.minkowski(1, 0, 0, 0, 1, 0, 2) 1.4142135623730951 >>> distance.minkowski(1, 0, 0, 0, 1, 0, 3) 1.2599210498948732 >>> distance.minkowski(1, 1, 0, 0, 1, 0, 1) 1.0 >>> distance.minkowski(1, 1, 0, 0, 1, 0, 2) 1.0 >>> distance.minkowski(1, 1, 0, 0, 1, 0, 3) 1.0

Returns a new subclass of tuple with named fields.

>>> Point = namedtuple('Point', 'x', 'y') >>> Point.__doc__ # docstring for the new class 'Point(x, y)' >>> p = Point(11, y=22) # instantiate with positional args or keywords >>> p0 + p1 # indexable like a plain tuple 33 >>> x, y = p # unpack like a regular tuple >>> x, y (11, 22) >>> p.x + p.y # fields also accessible by name 33 >>> d = p._asdict() # convert to a dictionary >>> d'x' 11 >>> Point( **d) # convert from a dictionary Point(x=11, y=22) >>> p._replace(x=100) # _replace() is like str.replace() but targets named fields Point(x=100, y=22)

Matrix or vector norm.

This function is able to return one of seven different matrix norms, or one of an infinite number of vector norms (described below), depending on the value of the ``ord`` parameter.

Parameters ---------- a : (M,) or (M, N) array_like Input array. If `axis` is None, `a` must be 1D or 2D. ord : non-zero int, inf, -inf, 'fro', optional Order of the norm (see table under ``Notes``). inf means NumPy's `inf` object axis : nt, 2-tuple of ints, None, optional If `axis` is an integer, it specifies the axis of `a` along which to compute the vector norms. If `axis` is a 2-tuple, it specifies the axes that hold 2-D matrices, and the matrix norms of these matrices are computed. If `axis` is None then either a vector norm (when `a` is 1-D) or a matrix norm (when `a` is 2-D) is returned. keepdims : bool, optional If this is set to True, the axes which are normed over are left in the result as dimensions with size one. With this option the result will broadcast correctly against the original `a`. check_finite : bool, optional Whether to check that the input matrix contains only finite numbers. Disabling may give a performance gain, but may result in problems (crashes, non-termination) if the inputs do contain infinities or NaNs.

Returns ------- n : float or ndarray Norm of the matrix or vector(s).

Notes ----- For values of ``ord <= 0``, the result is, strictly speaking, not a mathematical 'norm', but it may still be useful for various numerical purposes.

The following norms can be calculated:

===== ============================ ========================== ord norm for matrices norm for vectors ===== ============================ ========================== None Frobenius norm 2-norm 'fro' Frobenius norm -- inf max(sum(abs(x), axis=1)) max(abs(x)) -inf min(sum(abs(x), axis=1)) min(abs(x)) 0 -- sum(x != 0) 1 max(sum(abs(x), axis=0)) as below -1 min(sum(abs(x), axis=0)) as below 2 2-norm (largest sing. value) as below -2 smallest singular value as below other -- sum(abs(x)**ord)**(1./ord) ===== ============================ ==========================

The Frobenius norm is given by 1_:

:math:`||A||_F = \sum_{i,j} abs(a_{i,j})^2^

/2

`

The ``axis`` and ``keepdims`` arguments are passed directly to ``numpy.linalg.norm`` and are only usable if they are supported by the version of numpy in use.

References ---------- .. 1 G. H. Golub and C. F. Van Loan, *Matrix Computations*, Baltimore, MD, Johns Hopkins University Press, 1985, pg. 15

Examples -------- >>> from scipy.linalg import norm >>> a = np.arange(9) - 4.0 >>> a array(-4., -3., -2., -1., 0., 1., 2., 3., 4.) >>> b = a.reshape((3, 3)) >>> b array([-4., -3., -2.], [-1., 0., 1.], [ 2., 3., 4.])

>>> norm(a) 7.745966692414834 >>> norm(b) 7.745966692414834 >>> norm(b, 'fro') 7.745966692414834 >>> norm(a, np.inf) 4 >>> norm(b, np.inf) 9 >>> norm(a, -np.inf) 0 >>> norm(b, -np.inf) 2

>>> norm(a, 1) 20 >>> norm(b, 1) 7 >>> norm(a, -1) -4.6566128774142013e-010 >>> norm(b, -1) 6 >>> norm(a, 2) 7.745966692414834 >>> norm(b, 2) 7.3484692283495345

>>> norm(a, -2) 0 >>> norm(b, -2) 1.8570331885190563e-016 >>> norm(a, 3) 5.8480354764257312 >>> norm(a, -3) 0

Return the number of original observations that correspond to a square, redundant distance matrix.

Parameters ---------- d : ndarray The target distance matrix.

Returns ------- num_obs_dm : int The number of observations in the redundant distance matrix.

Return the number of original observations that correspond to a condensed distance matrix.

Parameters ---------- Y : ndarray Condensed distance matrix.

Returns ------- n : int The number of observations in the condensed distance matrix `Y`.

Pairwise distances between observations in n-dimensional space.

See Notes for common calling conventions.

Parameters ---------- X : ndarray An m by n array of m original observations in an n-dimensional space. metric : str or function, optional The distance metric to use. The distance function can be 'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'kulsinski', 'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'. *args : tuple. Deprecated. Additional arguments should be passed as keyword arguments **kwargs : dict, optional Extra arguments to `metric`: refer to each metric documentation for a list of all possible arguments.

Some possible arguments:

p : scalar The p-norm to apply for Minkowski, weighted and unweighted. Default: 2.

w : ndarray The weight vector for metrics that support weights (e.g., Minkowski).

V : ndarray The variance vector for standardized Euclidean. Default: var(X, axis=0, ddof=1)

VI : ndarray The inverse of the covariance matrix for Mahalanobis. Default: inv(cov(X.T)).T

out : ndarray. The output array If not None, condensed distance matrix Y is stored in this array. Note: metric independent, it will become a regular keyword arg in a future scipy version

Returns ------- Y : ndarray Returns a condensed distance matrix Y. For each :math:`i` and :math:`j` (where :math:`i<j<m`),where m is the number of original observations. The metric ``dist(u=Xi, v=Xj)`` is computed and stored in entry ``ij``.

See Also -------- squareform : converts between condensed distance matrices and square distance matrices.

Notes ----- See ``squareform`` for information on how to calculate the index of this entry or to convert the condensed distance matrix to a redundant square matrix.

The following are common calling conventions.

1. ``Y = pdist(X, 'euclidean')``

Computes the distance between m points using Euclidean distance (2-norm) as the distance metric between the points. The points are arranged as m n-dimensional row vectors in the matrix X.

2. ``Y = pdist(X, 'minkowski', p=2.)``

Computes the distances using the Minkowski distance :math:`||u-v||_p` (p-norm) where :math:`p \geq 1`.

3. ``Y = pdist(X, 'cityblock')``

Computes the city block or Manhattan distance between the points.

4. ``Y = pdist(X, 'seuclidean', V=None)``

Computes the standardized Euclidean distance. The standardized Euclidean distance between two n-vectors ``u`` and ``v`` is

.. math::

\sqrt\sum {(u_i-v_i)^2 / V[x_i]

}

V is the variance vector; Vi is the variance computed over all the i'th components of the points. If not passed, it is automatically computed.

5. ``Y = pdist(X, 'sqeuclidean')``

Computes the squared Euclidean distance :math:`||u-v||_2^2` between the vectors.

6. ``Y = pdist(X, 'cosine')``

Computes the cosine distance between vectors u and v,

.. math::

1 - \fracu \cdot v { ||u|| _2 ||v|| _2

}

where :math:`||*||_2` is the 2-norm of its argument ``*``, and :math:`u \cdot v` is the dot product of ``u`` and ``v``.

7. ``Y = pdist(X, 'correlation')``

Computes the correlation distance between vectors u and v. This is

.. math::

1 - \frac(u - \bar{u) \cdot (v - \bar

})}
               {{ ||(u - \bar{u})|| }_2 { ||(v - \bar{v})|| }_2}

   where :math:`\bar{v}` is the mean of the elements of vector v,
   and :math:`x \cdot y` is the dot product of :math:`x` and :math:`y`.

8. ``Y = pdist(X, 'hamming')``

   Computes the normalized Hamming distance, or the proportion of
   those vector elements between two n-vectors ``u`` and ``v``
   which disagree. To save memory, the matrix ``X`` can be of type
   boolean.

9. ``Y = pdist(X, 'jaccard')``

   Computes the Jaccard distance between the points. Given two
   vectors, ``u`` and ``v``, the Jaccard distance is the
   proportion of those elements ``u[i]`` and ``v[i]`` that
   disagree.

10. ``Y = pdist(X, 'chebyshev')``

   Computes the Chebyshev distance between the points. The
   Chebyshev distance between two n-vectors ``u`` and ``v`` is the
   maximum norm-1 distance between their respective elements. More
   precisely, the distance is given by

   .. math::

      d(u,v) = \max_i { |u_i-v_i| }

11. ``Y = pdist(X, 'canberra')``

   Computes the Canberra distance between the points. The
   Canberra distance between two points ``u`` and ``v`` is

   .. math::

     d(u,v) = \sum_i \frac{ |u_i-v_i| }
                          { |u_i|+|v_i| }


12. ``Y = pdist(X, 'braycurtis')``

   Computes the Bray-Curtis distance between the points. The
   Bray-Curtis distance between two points ``u`` and ``v`` is


   .. math::

        d(u,v) = \frac{\sum_i { |u_i-v_i| }}
                       {\sum_i { |u_i+v_i| }}

13. ``Y = pdist(X, 'mahalanobis', VI=None)``

   Computes the Mahalanobis distance between the points. The
   Mahalanobis distance between two points ``u`` and ``v`` is
   :math:`\sqrt{(u-v)(1/V)(u-v)^T}` where :math:`(1/V)` (the ``VI``
   variable) is the inverse covariance. If ``VI`` is not None,
   ``VI`` will be used as the inverse covariance matrix.

14. ``Y = pdist(X, 'yule')``

   Computes the Yule distance between each pair of boolean
   vectors. (see yule function documentation)

15. ``Y = pdist(X, 'matching')``

   Synonym for 'hamming'.

16. ``Y = pdist(X, 'dice')``

   Computes the Dice distance between each pair of boolean
   vectors. (see dice function documentation)

17. ``Y = pdist(X, 'kulsinski')``

   Computes the Kulsinski distance between each pair of
   boolean vectors. (see kulsinski function documentation)

18. ``Y = pdist(X, 'rogerstanimoto')``

   Computes the Rogers-Tanimoto distance between each pair of
   boolean vectors. (see rogerstanimoto function documentation)

19. ``Y = pdist(X, 'russellrao')``

   Computes the Russell-Rao distance between each pair of
   boolean vectors. (see russellrao function documentation)

20. ``Y = pdist(X, 'sokalmichener')``

   Computes the Sokal-Michener distance between each pair of
   boolean vectors. (see sokalmichener function documentation)

21. ``Y = pdist(X, 'sokalsneath')``

   Computes the Sokal-Sneath distance between each pair of
   boolean vectors. (see sokalsneath function documentation)

22. ``Y = pdist(X, 'wminkowski', p=2, w=w)``

   Computes the weighted Minkowski distance between each pair of
   vectors. (see wminkowski function documentation)

23. ``Y = pdist(X, f)``

   Computes the distance between all pairs of vectors in X
   using the user supplied 2-arity function f. For example,
   Euclidean distance between the vectors could be computed
   as follows::

     dm = pdist(X, lambda u, v: np.sqrt(((u-v)**2).sum()))

   Note that you should avoid passing a reference to one of
   the distance functions defined in this library. For example,::

     dm = pdist(X, sokalsneath)

   would calculate the pair-wise distances between the vectors in
   X using the Python function sokalsneath. This would result in
   sokalsneath being called :math:`{n \choose 2}` times, which
   is inefficient. Instead, the optimized C version is more
   efficient, and we call it using the following syntax.::

     dm = pdist(X, 'sokalsneath')

rel_entr(x1, x2, /, out=None, *, where=True, casting='same_kind', order='K', dtype=None, subok=True, signature, extobj)

rel_entr(x, y, out=None)

Elementwise function for computing relative entropy.

.. math::

\mathrmrel\_entr(x, y) = \begincases x \log(x / y) & x > 0, y > 0 \\ 0 & x = 0, y \ge 0 \\ \infty & \textotherwise \endcases

Parameters ---------- x, y : array_like Input arrays out : ndarray, optional Optional output array for the function results

Returns ------- scalar or ndarray Relative entropy of the inputs

See Also -------- entr, kl_div

Notes ----- .. versionadded:: 0.15.0

This function is jointly convex in x and y.

The origin of this function is in convex programming; see 1_. Given two discrete probability distributions :math:`p_1, \ldots, p_n` and :math:`q_1, \ldots, q_n`, to get the relative entropy of statistics compute the sum

.. math::

\sum_= 1^n \mathrmrel\_entr(p_i, q_i).

See 2_ for details.

References ---------- .. 1 Grant, Boyd, and Ye, 'CVX: Matlab Software for Disciplined Convex Programming', http://cvxr.com/cvx/ .. 2 Kullback-Leibler divergence, https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence

Compute the Rogers-Tanimoto dissimilarity between two boolean 1-D arrays.

The Rogers-Tanimoto dissimilarity between two boolean 1-D arrays `u` and `v`, is defined as

.. math:: \frac

c_{TT + c_FF + R

}

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n` and :math:`R = 2(c_{TF} + c_{FT})`.

Parameters
----------
u : (N,) array_like, bool
    Input array.
v : (N,) array_like, bool
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
rogerstanimoto : double
    The Rogers-Tanimoto dissimilarity between vectors
    `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.rogerstanimoto([1, 0, 0], [0, 1, 0])
0.8
>>> distance.rogerstanimoto([1, 0, 0], [1, 1, 0])
0.5
>>> distance.rogerstanimoto([1, 0, 0], [2, 0, 0])
-1.0

Compute the Russell-Rao dissimilarity between two boolean 1-D arrays.

The Russell-Rao dissimilarity between two boolean 1-D arrays, `u` and `v`, is defined as

.. math::

\fracn - c_{TT

}

n

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n`.

Parameters
----------
u : (N,) array_like, bool
    Input array.
v : (N,) array_like, bool
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
russellrao : double
    The Russell-Rao dissimilarity between vectors `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.russellrao([1, 0, 0], [0, 1, 0])
1.0
>>> distance.russellrao([1, 0, 0], [1, 1, 0])
0.6666666666666666
>>> distance.russellrao([1, 0, 0], [2, 0, 0])
0.3333333333333333

Return the standardized Euclidean distance between two 1-D arrays.

The standardized Euclidean distance between `u` and `v`.

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. V : (N,) array_like `V` is an 1-D array of component variances. It is usually computed among a larger collection vectors.

Returns ------- seuclidean : double The standardized Euclidean distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.seuclidean(1, 0, 0, 0, 1, 0, 0.1, 0.1, 0.1) 4.4721359549995796 >>> distance.seuclidean(1, 0, 0, 0, 1, 0, 1, 0.1, 0.1) 3.3166247903553998 >>> distance.seuclidean(1, 0, 0, 0, 1, 0, 10, 0.1, 0.1) 3.1780497164141406

Compute the Sokal-Michener dissimilarity between two boolean 1-D arrays.

The Sokal-Michener dissimilarity between boolean 1-D arrays `u` and `v`, is defined as

.. math::

\frac

S + R

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n`, :math:`R = 2 * (c_{TF} + c_{FT})` and
:math:`S = c_{FF} + c_{TT}`.

Parameters
----------
u : (N,) array_like, bool
    Input array.
v : (N,) array_like, bool
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
sokalmichener : double
    The Sokal-Michener dissimilarity between vectors `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.sokalmichener([1, 0, 0], [0, 1, 0])
0.8
>>> distance.sokalmichener([1, 0, 0], [1, 1, 0])
0.5
>>> distance.sokalmichener([1, 0, 0], [2, 0, 0])
-1.0

Compute the Sokal-Sneath dissimilarity between two boolean 1-D arrays.

The Sokal-Sneath dissimilarity between `u` and `v`,

.. math::

\frac

c_{TT + R

}

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n` and :math:`R = 2(c_{TF} + c_{FT})`.

Parameters
----------
u : (N,) array_like, bool
    Input array.
v : (N,) array_like, bool
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
sokalsneath : double
    The Sokal-Sneath dissimilarity between vectors `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.sokalsneath([1, 0, 0], [0, 1, 0])
1.0
>>> distance.sokalsneath([1, 0, 0], [1, 1, 0])
0.66666666666666663
>>> distance.sokalsneath([1, 0, 0], [2, 1, 0])
0.0
>>> distance.sokalsneath([1, 0, 0], [3, 1, 0])
-2.0

Compute the squared Euclidean distance between two 1-D arrays.

The squared Euclidean distance between `u` and `v` is defined as

.. math::

||u-v|| _2^2

\left(\sum(w_i |(u_i - v_i)|^2)\right)

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. w : (N,) array_like, optional The weights for each value in `u` and `v`. Default is None, which gives each value a weight of 1.0

Returns ------- sqeuclidean : double The squared Euclidean distance between vectors `u` and `v`.

Examples -------- >>> from scipy.spatial import distance >>> distance.sqeuclidean(1, 0, 0, 0, 1, 0) 2.0 >>> distance.sqeuclidean(1, 1, 0, 0, 1, 0) 1.0

Convert a vector-form distance vector to a square-form distance matrix, and vice-versa.

Parameters ---------- X : ndarray Either a condensed or redundant distance matrix. force : str, optional As with MATLAB(TM), if force is equal to ``'tovector'`` or ``'tomatrix'``, the input will be treated as a distance matrix or distance vector respectively. checks : bool, optional If set to False, no checks will be made for matrix symmetry nor zero diagonals. This is useful if it is known that ``X - X.T1`` is small and ``diag(X)`` is close to zero. These values are ignored any way so they do not disrupt the squareform transformation.

Returns ------- Y : ndarray If a condensed distance matrix is passed, a redundant one is returned, or if a redundant one is passed, a condensed distance matrix is returned.

Notes ----- 1. ``v = squareform(X)``

Given a square n-by-n symmetric distance matrix ``X``, ``v = squareform(X)`` returns a ``n * (n-1) / 2`` (i.e. binomial coefficient n choose 2) sized vector `v` where :math:`v{n \choose 2} - {n-i \choose 2} + (j-i-1)` is the distance between distinct points ``i`` and ``j``. If ``X`` is non-square or asymmetric, an error is raised.

2. ``X = squareform(v)``

Given a ``n * (n-1) / 2`` sized vector ``v`` for some integer ``n >= 1`` encoding distances as described, ``X = squareform(v)`` returns a n-by-n distance matrix ``X``. The ``Xi, j`` and ``Xj, i`` values are set to :math:`v{n \choose 2} - {n-i \choose 2} + (j-i-1)` and all diagonal elements are zero.

In SciPy 0.19.0, ``squareform`` stopped casting all input types to float64, and started returning arrays of the same dtype as the input.

Compute the weighted Minkowski distance between two 1-D arrays.

The weighted Minkowski distance between `u` and `v`, defined as

.. math::

\left(\sum(|w_i (u_i - v_i)|^p)\right)^

/p

.

Parameters ---------- u : (N,) array_like Input array. v : (N,) array_like Input array. p : int The order of the norm of the difference :math:` ||u-v|| _p`. w : (N,) array_like The weight vector.

Returns ------- wminkowski : double The weighted Minkowski distance between vectors `u` and `v`.

Notes ----- `wminkowski` is DEPRECATED. It implements a definition where weights are powered. It is recommended to use the weighted version of `minkowski` instead. This function will be removed in a future version of scipy.

Examples -------- >>> from scipy.spatial import distance >>> distance.wminkowski(1, 0, 0, 0, 1, 0, 1, np.ones(3)) 2.0 >>> distance.wminkowski(1, 0, 0, 0, 1, 0, 2, np.ones(3)) 1.4142135623730951 >>> distance.wminkowski(1, 0, 0, 0, 1, 0, 3, np.ones(3)) 1.2599210498948732 >>> distance.wminkowski(1, 1, 0, 0, 1, 0, 1, np.ones(3)) 1.0 >>> distance.wminkowski(1, 1, 0, 0, 1, 0, 2, np.ones(3)) 1.0 >>> distance.wminkowski(1, 1, 0, 0, 1, 0, 3, np.ones(3)) 1.0

Compute the Yule dissimilarity between two boolean 1-D arrays.

The Yule dissimilarity is defined as

.. math::

\frac

c_{TT * c_FF + \frac

}

where :math:`c_j` is the number of occurrences of :math:`\mathttu[k] = i` and :math:`\mathtt

[k]} = j` for
:math:`k < n` and :math:`R = 2.0 * c_{TF} * c_{FT}`.

Parameters
----------
u : (N,) array_like, bool
    Input array.
v : (N,) array_like, bool
    Input array.
w : (N,) array_like, optional
    The weights for each value in `u` and `v`. Default is None,
    which gives each value a weight of 1.0

Returns
-------
yule : double
    The Yule dissimilarity between vectors `u` and `v`.

Examples
--------
>>> from scipy.spatial import distance
>>> distance.yule([1, 0, 0], [0, 1, 0])
2.0
>>> distance.yule([1, 1, 0], [0, 1, 0])
0.0