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@@ -160,3 +160,4 @@ llmeval-env/lib/python3.10/site-packages/torch/lib/libtorch_cuda.so filter=lfs d
 env-llmeval/lib/python3.10/site-packages/scipy/sparse/_sparsetools.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
 env-llmeval/lib/python3.10/site-packages/scipy/linalg/_flapack.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
 env-llmeval/lib/python3.10/site-packages/scipy/misc/face.dat filter=lfs diff=lfs merge=lfs -text
+env-llmeval/lib/python3.10/site-packages/nvidia/nccl/lib/libnccl.so.2 filter=lfs diff=lfs merge=lfs -text

env-llmeval/lib/python3.10/site-packages/nvidia/nccl/lib/libnccl.so.2

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ea129565baf96309bc48b440e9ff15afcd46c1a7f8ff1f1de5596a3f964d575c
+size 219454696

env-llmeval/lib/python3.10/site-packages/scipy/stats/_censored_data.py

@@ -0,0 +1,459 @@
+import numpy as np
+
+
+def _validate_1d(a, name, allow_inf=False):
+    if np.ndim(a) != 1:
+        raise ValueError(f'`{name}` must be a one-dimensional sequence.')
+    if np.isnan(a).any():
+        raise ValueError(f'`{name}` must not contain nan.')
+    if not allow_inf and np.isinf(a).any():
+        raise ValueError(f'`{name}` must contain only finite values.')
+
+
+def _validate_interval(interval):
+    interval = np.asarray(interval)
+    if interval.shape == (0,):
+        # The input was a sequence with length 0.
+        interval = interval.reshape((0, 2))
+    if interval.ndim != 2 or interval.shape[-1] != 2:
+        raise ValueError('`interval` must be a two-dimensional array with '
+                         'shape (m, 2), where m is the number of '
+                         'interval-censored values, but got shape '
+                         f'{interval.shape}')
+
+    if np.isnan(interval).any():
+        raise ValueError('`interval` must not contain nan.')
+    if np.isinf(interval).all(axis=1).any():
+        raise ValueError('In each row in `interval`, both values must not'
+                         ' be infinite.')
+    if (interval[:, 0] > interval[:, 1]).any():
+        raise ValueError('In each row of `interval`, the left value must not'
+                         ' exceed the right value.')
+
+    uncensored_mask = interval[:, 0] == interval[:, 1]
+    left_mask = np.isinf(interval[:, 0])
+    right_mask = np.isinf(interval[:, 1])
+    interval_mask = np.isfinite(interval).all(axis=1) & ~uncensored_mask
+
+    uncensored2 = interval[uncensored_mask, 0]
+    left2 = interval[left_mask, 1]
+    right2 = interval[right_mask, 0]
+    interval2 = interval[interval_mask]
+
+    return uncensored2, left2, right2, interval2
+
+
+def _validate_x_censored(x, censored):
+    x = np.asarray(x)
+    if x.ndim != 1:
+        raise ValueError('`x` must be one-dimensional.')
+    censored = np.asarray(censored)
+    if censored.ndim != 1:
+        raise ValueError('`censored` must be one-dimensional.')
+    if (~np.isfinite(x)).any():
+        raise ValueError('`x` must not contain nan or inf.')
+    if censored.size != x.size:
+        raise ValueError('`x` and `censored` must have the same length.')
+    return x, censored.astype(bool)
+
+
+class CensoredData:
+    """
+    Instances of this class represent censored data.
+
+    Instances may be passed to the ``fit`` method of continuous
+    univariate SciPy distributions for maximum likelihood estimation.
+    The *only* method of the univariate continuous distributions that
+    understands `CensoredData` is the ``fit`` method.  An instance of
+    `CensoredData` can not be passed to methods such as ``pdf`` and
+    ``cdf``.
+
+    An observation is said to be *censored* when the precise value is unknown,
+    but it has a known upper and/or lower bound.  The conventional terminology
+    is:
+
+    * left-censored: an observation is below a certain value but it is
+      unknown by how much.
+    * right-censored: an observation is above a certain value but it is
+      unknown by how much.
+    * interval-censored: an observation lies somewhere on an interval between
+      two values.
+
+    Left-, right-, and interval-censored data can be represented by
+    `CensoredData`.
+
+    For convenience, the class methods ``left_censored`` and
+    ``right_censored`` are provided to create a `CensoredData`
+    instance from a single one-dimensional array of measurements
+    and a corresponding boolean array to indicate which measurements
+    are censored.  The class method ``interval_censored`` accepts two
+    one-dimensional arrays that hold the lower and upper bounds of the
+    intervals.
+
+    Parameters
+    ----------
+    uncensored : array_like, 1D
+        Uncensored observations.
+    left : array_like, 1D
+        Left-censored observations.
+    right : array_like, 1D
+        Right-censored observations.
+    interval : array_like, 2D, with shape (m, 2)
+        Interval-censored observations.  Each row ``interval[k, :]``
+        represents the interval for the kth interval-censored observation.
+
+    Notes
+    -----
+    In the input array `interval`, the lower bound of the interval may
+    be ``-inf``, and the upper bound may be ``inf``, but at least one must be
+    finite. When the lower bound is ``-inf``, the row represents a left-
+    censored observation, and when the upper bound is ``inf``, the row
+    represents a right-censored observation.  If the length of an interval
+    is 0 (i.e. ``interval[k, 0] == interval[k, 1]``, the observation is
+    treated as uncensored.  So one can represent all the types of censored
+    and uncensored data in ``interval``, but it is generally more convenient
+    to use `uncensored`, `left` and `right` for uncensored, left-censored and
+    right-censored observations, respectively.
+
+    Examples
+    --------
+    In the most general case, a censored data set may contain values that
+    are left-censored, right-censored, interval-censored, and uncensored.
+    For example, here we create a data set with five observations.  Two
+    are uncensored (values 1 and 1.5), one is a left-censored observation
+    of 0, one is a right-censored observation of 10 and one is
+    interval-censored in the interval [2, 3].
+
+    >>> import numpy as np
+    >>> from scipy.stats import CensoredData
+    >>> data = CensoredData(uncensored=[1, 1.5], left=[0], right=[10],
+    ...                     interval=[[2, 3]])
+    >>> print(data)
+    CensoredData(5 values: 2 not censored, 1 left-censored,
+    1 right-censored, 1 interval-censored)
+
+    Equivalently,
+
+    >>> data = CensoredData(interval=[[1, 1],
+    ...                               [1.5, 1.5],
+    ...                               [-np.inf, 0],
+    ...                               [10, np.inf],
+    ...                               [2, 3]])
+    >>> print(data)
+    CensoredData(5 values: 2 not censored, 1 left-censored,
+    1 right-censored, 1 interval-censored)
+
+    A common case is to have a mix of uncensored observations and censored
+    observations that are all right-censored (or all left-censored). For
+    example, consider an experiment in which six devices are started at
+    various times and left running until they fail.  Assume that time is
+    measured in hours, and the experiment is stopped after 30 hours, even
+    if all the devices have not failed by that time.  We might end up with
+    data such as this::
+
+        Device  Start-time  Fail-time  Time-to-failure
+           1         0         13           13
+           2         2         24           22
+           3         5         22           17
+           4         8         23           15
+           5        10        ***          >20
+           6        12        ***          >18
+
+    Two of the devices had not failed when the experiment was stopped;
+    the observations of the time-to-failure for these two devices are
+    right-censored.  We can represent this data with
+
+    >>> data = CensoredData(uncensored=[13, 22, 17, 15], right=[20, 18])
+    >>> print(data)
+    CensoredData(6 values: 4 not censored, 2 right-censored)
+
+    Alternatively, we can use the method `CensoredData.right_censored` to
+    create a representation of this data.  The time-to-failure observations
+    are put the list ``ttf``.  The ``censored`` list indicates which values
+    in ``ttf`` are censored.
+
+    >>> ttf = [13, 22, 17, 15, 20, 18]
+    >>> censored = [False, False, False, False, True, True]
+
+    Pass these lists to `CensoredData.right_censored` to create an
+    instance of `CensoredData`.
+
+    >>> data = CensoredData.right_censored(ttf, censored)
+    >>> print(data)
+    CensoredData(6 values: 4 not censored, 2 right-censored)
+
+    If the input data is interval censored and already stored in two
+    arrays, one holding the low end of the intervals and another
+    holding the high ends, the class method ``interval_censored`` can
+    be used to create the `CensoredData` instance.
+
+    This example creates an instance with four interval-censored values.
+    The intervals are [10, 11], [0.5, 1], [2, 3], and [12.5, 13.5].
+
+    >>> a = [10, 0.5, 2, 12.5]  # Low ends of the intervals
+    >>> b = [11, 1.0, 3, 13.5]  # High ends of the intervals
+    >>> data = CensoredData.interval_censored(low=a, high=b)
+    >>> print(data)
+    CensoredData(4 values: 0 not censored, 4 interval-censored)
+
+    Finally, we create and censor some data from the `weibull_min`
+    distribution, and then fit `weibull_min` to that data. We'll assume
+    that the location parameter is known to be 0.
+
+    >>> from scipy.stats import weibull_min
+    >>> rng = np.random.default_rng()
+
+    Create the random data set.
+
+    >>> x = weibull_min.rvs(2.5, loc=0, scale=30, size=250, random_state=rng)
+    >>> x[x > 40] = 40  # Right-censor values greater or equal to 40.
+
+    Create the `CensoredData` instance with the `right_censored` method.
+    The censored values are those where the value is 40.
+
+    >>> data = CensoredData.right_censored(x, x == 40)
+    >>> print(data)
+    CensoredData(250 values: 215 not censored, 35 right-censored)
+
+    35 values have been right-censored.
+
+    Fit `weibull_min` to the censored data.  We expect to shape and scale
+    to be approximately 2.5 and 30, respectively.
+
+    >>> weibull_min.fit(data, floc=0)
+    (2.3575922823897315, 0, 30.40650074451254)
+
+    """
+
+    def __init__(self, uncensored=None, *, left=None, right=None,
+                 interval=None):
+        if uncensored is None:
+            uncensored = []
+        if left is None:
+            left = []
+        if right is None:
+            right = []
+        if interval is None:
+            interval = np.empty((0, 2))
+
+        _validate_1d(uncensored, 'uncensored')
+        _validate_1d(left, 'left')
+        _validate_1d(right, 'right')
+        uncensored2, left2, right2, interval2 = _validate_interval(interval)
+
+        self._uncensored = np.concatenate((uncensored, uncensored2))
+        self._left = np.concatenate((left, left2))
+        self._right = np.concatenate((right, right2))
+        # Note that by construction, the private attribute _interval
+        # will be a 2D array that contains only finite values representing
+        # intervals with nonzero but finite length.
+        self._interval = interval2
+
+    def __repr__(self):
+        uncensored_str = " ".join(np.array_repr(self._uncensored).split())
+        left_str = " ".join(np.array_repr(self._left).split())
+        right_str = " ".join(np.array_repr(self._right).split())
+        interval_str = " ".join(np.array_repr(self._interval).split())
+        return (f"CensoredData(uncensored={uncensored_str}, left={left_str}, "
+                f"right={right_str}, interval={interval_str})")
+
+    def __str__(self):
+        num_nc = len(self._uncensored)
+        num_lc = len(self._left)
+        num_rc = len(self._right)
+        num_ic = len(self._interval)
+        n = num_nc + num_lc + num_rc + num_ic
+        parts = [f'{num_nc} not censored']
+        if num_lc > 0:
+            parts.append(f'{num_lc} left-censored')
+        if num_rc > 0:
+            parts.append(f'{num_rc} right-censored')
+        if num_ic > 0:
+            parts.append(f'{num_ic} interval-censored')
+        return f'CensoredData({n} values: ' + ', '.join(parts) + ')'
+
+    # This is not a complete implementation of the arithmetic operators.
+    # All we need is subtracting a scalar and dividing by a scalar.
+
+    def __sub__(self, other):
+        return CensoredData(uncensored=self._uncensored - other,
+                            left=self._left - other,
+                            right=self._right - other,
+                            interval=self._interval - other)
+
+    def __truediv__(self, other):
+        return CensoredData(uncensored=self._uncensored / other,
+                            left=self._left / other,
+                            right=self._right / other,
+                            interval=self._interval / other)
+
+    def __len__(self):
+        """
+        The number of values (censored and not censored).
+        """
+        return (len(self._uncensored) + len(self._left) + len(self._right)
+                + len(self._interval))
+
+    def num_censored(self):
+        """
+        Number of censored values.
+        """
+        return len(self._left) + len(self._right) + len(self._interval)
+
+    @classmethod
+    def right_censored(cls, x, censored):
+        """
+        Create a `CensoredData` instance of right-censored data.
+
+        Parameters
+        ----------
+        x : array_like
+            `x` is the array of observed data or measurements.
+            `x` must be a one-dimensional sequence of finite numbers.
+        censored : array_like of bool
+            `censored` must be a one-dimensional sequence of boolean
+            values.  If ``censored[k]`` is True, the corresponding value
+            in `x` is right-censored.  That is, the value ``x[k]``
+            is the lower bound of the true (but unknown) value.
+
+        Returns
+        -------
+        data : `CensoredData`
+            An instance of `CensoredData` that represents the
+            collection of uncensored and right-censored values.
+
+        Examples
+        --------
+        >>> from scipy.stats import CensoredData
+
+        Two uncensored values (4 and 10) and two right-censored values
+        (24 and 25).
+
+        >>> data = CensoredData.right_censored([4, 10, 24, 25],
+        ...                                    [False, False, True, True])
+        >>> data
+        CensoredData(uncensored=array([ 4., 10.]),
+        left=array([], dtype=float64), right=array([24., 25.]),
+        interval=array([], shape=(0, 2), dtype=float64))
+        >>> print(data)
+        CensoredData(4 values: 2 not censored, 2 right-censored)
+        """
+        x, censored = _validate_x_censored(x, censored)
+        return cls(uncensored=x[~censored], right=x[censored])
+
+    @classmethod
+    def left_censored(cls, x, censored):
+        """
+        Create a `CensoredData` instance of left-censored data.
+
+        Parameters
+        ----------
+        x : array_like
+            `x` is the array of observed data or measurements.
+            `x` must be a one-dimensional sequence of finite numbers.
+        censored : array_like of bool
+            `censored` must be a one-dimensional sequence of boolean
+            values.  If ``censored[k]`` is True, the corresponding value
+            in `x` is left-censored.  That is, the value ``x[k]``
+            is the upper bound of the true (but unknown) value.
+
+        Returns
+        -------
+        data : `CensoredData`
+            An instance of `CensoredData` that represents the
+            collection of uncensored and left-censored values.
+
+        Examples
+        --------
+        >>> from scipy.stats import CensoredData
+
+        Two uncensored values (0.12 and 0.033) and two left-censored values
+        (both 1e-3).
+
+        >>> data = CensoredData.left_censored([0.12, 0.033, 1e-3, 1e-3],
+        ...                                   [False, False, True, True])
+        >>> data
+        CensoredData(uncensored=array([0.12 , 0.033]),
+        left=array([0.001, 0.001]), right=array([], dtype=float64),
+        interval=array([], shape=(0, 2), dtype=float64))
+        >>> print(data)
+        CensoredData(4 values: 2 not censored, 2 left-censored)
+        """
+        x, censored = _validate_x_censored(x, censored)
+        return cls(uncensored=x[~censored], left=x[censored])
+
+    @classmethod
+    def interval_censored(cls, low, high):
+        """
+        Create a `CensoredData` instance of interval-censored data.
+
+        This method is useful when all the data is interval-censored, and
+        the low and high ends of the intervals are already stored in
+        separate one-dimensional arrays.
+
+        Parameters
+        ----------
+        low : array_like
+            The one-dimensional array containing the low ends of the
+            intervals.
+        high : array_like
+            The one-dimensional array containing the high ends of the
+            intervals.
+
+        Returns
+        -------
+        data : `CensoredData`
+            An instance of `CensoredData` that represents the
+            collection of censored values.
+
+        Examples
+        --------
+        >>> import numpy as np
+        >>> from scipy.stats import CensoredData
+
+        ``a`` and ``b`` are the low and high ends of a collection of
+        interval-censored values.
+
+        >>> a = [0.5, 2.0, 3.0, 5.5]
+        >>> b = [1.0, 2.5, 3.5, 7.0]
+        >>> data = CensoredData.interval_censored(low=a, high=b)
+        >>> print(data)
+        CensoredData(4 values: 0 not censored, 4 interval-censored)
+        """
+        _validate_1d(low, 'low', allow_inf=True)
+        _validate_1d(high, 'high', allow_inf=True)
+        if len(low) != len(high):
+            raise ValueError('`low` and `high` must have the same length.')
+        interval = np.column_stack((low, high))
+        uncensored, left, right, interval = _validate_interval(interval)
+        return cls(uncensored=uncensored, left=left, right=right,
+                   interval=interval)
+
+    def _uncensor(self):
+        """
+        This function is used when a non-censored version of the data
+        is needed to create a rough estimate of the parameters of a
+        distribution via the method of moments or some similar method.
+        The data is "uncensored" by taking the given endpoints as the
+        data for the left- or right-censored data, and the mean for the
+        interval-censored data.
+        """
+        data = np.concatenate((self._uncensored, self._left, self._right,
+                               self._interval.mean(axis=1)))
+        return data
+
+    def _supported(self, a, b):
+        """
+        Return a subset of self containing the values that are in
+        (or overlap with) the interval (a, b).
+        """
+        uncensored = self._uncensored
+        uncensored = uncensored[(a < uncensored) & (uncensored < b)]
+        left = self._left
+        left = left[a < left]
+        right = self._right
+        right = right[right < b]
+        interval = self._interval
+        interval = interval[(a < interval[:, 1]) & (interval[:, 0] < b)]
+        return CensoredData(uncensored, left=left, right=right,
+                            interval=interval)

env-llmeval/lib/python3.10/site-packages/scipy/stats/_mannwhitneyu.py

@@ -0,0 +1,519 @@
+import numpy as np
+from collections import namedtuple
+from scipy import special
+from scipy import stats
+from scipy.stats._stats_py import _rankdata
+from ._axis_nan_policy import _axis_nan_policy_factory
+
+
+def _broadcast_concatenate(x, y, axis):
+    '''Broadcast then concatenate arrays, leaving concatenation axis last'''
+    x = np.moveaxis(x, axis, -1)
+    y = np.moveaxis(y, axis, -1)
+    z = np.broadcast(x[..., 0], y[..., 0])
+    x = np.broadcast_to(x, z.shape + (x.shape[-1],))
+    y = np.broadcast_to(y, z.shape + (y.shape[-1],))
+    z = np.concatenate((x, y), axis=-1)
+    return x, y, z
+
+
+class _MWU:
+    '''Distribution of MWU statistic under the null hypothesis'''
+    # Possible improvement: if m and n are small enough, use integer arithmetic
+
+    def __init__(self):
+        '''Minimal initializer'''
+        self._fmnks = -np.ones((1, 1, 1))
+        self._recursive = None
+
+    def pmf(self, k, m, n):
+
+        # In practice, `pmf` is never called with k > m*n/2.
+        # If it were, we'd exploit symmetry here:
+        # k = np.array(k, copy=True)
+        # k2 = m*n - k
+        # i = k2 < k
+        # k[i] = k2[i]
+
+        if (self._recursive is None and m <= 500 and n <= 500
+                or self._recursive):
+            return self.pmf_recursive(k, m, n)
+        else:
+            return self.pmf_iterative(k, m, n)
+
+    def pmf_recursive(self, k, m, n):
+        '''Probability mass function, recursive version'''
+        self._resize_fmnks(m, n, np.max(k))
+        # could loop over just the unique elements, but probably not worth
+        # the time to find them
+        for i in np.ravel(k):
+            self._f(m, n, i)
+        return self._fmnks[m, n, k] / special.binom(m + n, m)
+
+    def pmf_iterative(self, k, m, n):
+        '''Probability mass function, iterative version'''
+        fmnks = {}
+        for i in np.ravel(k):
+            fmnks = _mwu_f_iterative(m, n, i, fmnks)
+        return (np.array([fmnks[(m, n, ki)] for ki in k])
+                / special.binom(m + n, m))
+
+    def cdf(self, k, m, n):
+        '''Cumulative distribution function'''
+
+        # In practice, `cdf` is never called with k > m*n/2.
+        # If it were, we'd exploit symmetry here rather than in `sf`
+        pmfs = self.pmf(np.arange(0, np.max(k) + 1), m, n)
+        cdfs = np.cumsum(pmfs)
+        return cdfs[k]
+
+    def sf(self, k, m, n):
+        '''Survival function'''
+        # Note that both CDF and SF include the PMF at k. The p-value is
+        # calculated from the SF and should include the mass at k, so this
+        # is desirable
+
+        # Use the fact that the distribution is symmetric; i.e.
+        # _f(m, n, m*n-k) = _f(m, n, k), and sum from the left
+        kc = np.asarray(m*n - k)  # complement of k
+        i = k < kc
+        if np.any(i):
+            kc[i] = k[i]
+            cdfs = np.asarray(self.cdf(kc, m, n))
+            cdfs[i] = 1. - cdfs[i] + self.pmf(kc[i], m, n)
+        else:
+            cdfs = np.asarray(self.cdf(kc, m, n))
+        return cdfs[()]
+
+    def _resize_fmnks(self, m, n, k):
+        '''If necessary, expand the array that remembers PMF values'''
+        # could probably use `np.pad` but I'm not sure it would save code
+        shape_old = np.array(self._fmnks.shape)
+        shape_new = np.array((m+1, n+1, k+1))
+        if np.any(shape_new > shape_old):
+            shape = np.maximum(shape_old, shape_new)
+            fmnks = -np.ones(shape)             # create the new array
+            m0, n0, k0 = shape_old
+            fmnks[:m0, :n0, :k0] = self._fmnks  # copy remembered values
+            self._fmnks = fmnks
+
+    def _f(self, m, n, k):
+        '''Recursive implementation of function of [3] Theorem 2.5'''
+
+        # [3] Theorem 2.5 Line 1
+        if k < 0 or m < 0 or n < 0 or k > m*n:
+            return 0
+
+        # if already calculated, return the value
+        if self._fmnks[m, n, k] >= 0:
+            return self._fmnks[m, n, k]
+
+        if k == 0 and m >= 0 and n >= 0:  # [3] Theorem 2.5 Line 2
+            fmnk = 1
+        else:   # [3] Theorem 2.5 Line 3 / Equation 3
+            fmnk = self._f(m-1, n, k-n) + self._f(m, n-1, k)
+
+        self._fmnks[m, n, k] = fmnk  # remember result
+
+        return fmnk
+
+
+# Maintain state for faster repeat calls to mannwhitneyu w/ method='exact'
+_mwu_state = _MWU()
+
+
+def _mwu_f_iterative(m, n, k, fmnks):
+    '''Iterative implementation of function of [3] Theorem 2.5'''
+
+    def _base_case(m, n, k):
+        '''Base cases from recursive version'''
+
+        # if already calculated, return the value
+        if fmnks.get((m, n, k), -1) >= 0:
+            return fmnks[(m, n, k)]
+
+        # [3] Theorem 2.5 Line 1
+        elif k < 0 or m < 0 or n < 0 or k > m*n:
+            return 0
+
+        # [3] Theorem 2.5 Line 2
+        elif k == 0 and m >= 0 and n >= 0:
+            return 1
+
+        return None
+
+    stack = [(m, n, k)]
+    fmnk = None
+
+    while stack:
+        # Popping only if necessary would save a tiny bit of time, but NWI.
+        m, n, k = stack.pop()
+
+        # If we're at a base case, continue (stack unwinds)
+        fmnk = _base_case(m, n, k)
+        if fmnk is not None:
+            fmnks[(m, n, k)] = fmnk
+            continue
+
+        # If both terms are base cases, continue (stack unwinds)
+        f1 = _base_case(m-1, n, k-n)
+        f2 = _base_case(m, n-1, k)
+        if f1 is not None and f2 is not None:
+            # [3] Theorem 2.5 Line 3 / Equation 3
+            fmnk = f1 + f2
+            fmnks[(m, n, k)] = fmnk
+            continue
+
+        # recurse deeper
+        stack.append((m, n, k))
+        if f1 is None:
+            stack.append((m-1, n, k-n))
+        if f2 is None:
+            stack.append((m, n-1, k))
+
+    return fmnks
+
+
+def _get_mwu_z(U, n1, n2, t, axis=0, continuity=True):
+    '''Standardized MWU statistic'''
+    # Follows mannwhitneyu [2]
+    mu = n1 * n2 / 2
+    n = n1 + n2
+
+    # Tie correction according to [2], "Normal approximation and tie correction"
+    # "A more computationally-efficient form..."
+    tie_term = (t**3 - t).sum(axis=-1)
+    s = np.sqrt(n1*n2/12 * ((n + 1) - tie_term/(n*(n-1))))
+
+    numerator = U - mu
+
+    # Continuity correction.
+    # Because SF is always used to calculate the p-value, we can always
+    # _subtract_ 0.5 for the continuity correction. This always increases the
+    # p-value to account for the rest of the probability mass _at_ q = U.
+    if continuity:
+        numerator -= 0.5
+
+    # no problem evaluating the norm SF at an infinity
+    with np.errstate(divide='ignore', invalid='ignore'):
+        z = numerator / s
+    return z
+
+
+def _mwu_input_validation(x, y, use_continuity, alternative, axis, method):
+    ''' Input validation and standardization for mannwhitneyu '''
+    # Would use np.asarray_chkfinite, but infs are OK
+    x, y = np.atleast_1d(x), np.atleast_1d(y)
+    if np.isnan(x).any() or np.isnan(y).any():
+        raise ValueError('`x` and `y` must not contain NaNs.')
+    if np.size(x) == 0 or np.size(y) == 0:
+        raise ValueError('`x` and `y` must be of nonzero size.')
+
+    bools = {True, False}
+    if use_continuity not in bools:
+        raise ValueError(f'`use_continuity` must be one of {bools}.')
+
+    alternatives = {"two-sided", "less", "greater"}
+    alternative = alternative.lower()
+    if alternative not in alternatives:
+        raise ValueError(f'`alternative` must be one of {alternatives}.')
+
+    axis_int = int(axis)
+    if axis != axis_int:
+        raise ValueError('`axis` must be an integer.')
+
+    if not isinstance(method, stats.PermutationMethod):
+        methods = {"asymptotic", "exact", "auto"}
+        method = method.lower()
+        if method not in methods:
+            raise ValueError(f'`method` must be one of {methods}.')
+
+    return x, y, use_continuity, alternative, axis_int, method
+
+
+def _mwu_choose_method(n1, n2, ties):
+    """Choose method 'asymptotic' or 'exact' depending on input size, ties"""
+
+    # if both inputs are large, asymptotic is OK
+    if n1 > 8 and n2 > 8:
+        return "asymptotic"
+
+    # if there are any ties, asymptotic is preferred
+    if ties:
+        return "asymptotic"
+
+    return "exact"
+
+
+MannwhitneyuResult = namedtuple('MannwhitneyuResult', ('statistic', 'pvalue'))
+
+
+@_axis_nan_policy_factory(MannwhitneyuResult, n_samples=2)
+def mannwhitneyu(x, y, use_continuity=True, alternative="two-sided",
+                 axis=0, method="auto"):
+    r'''Perform the Mann-Whitney U rank test on two independent samples.
+
+    The Mann-Whitney U test is a nonparametric test of the null hypothesis
+    that the distribution underlying sample `x` is the same as the
+    distribution underlying sample `y`. It is often used as a test of
+    difference in location between distributions.
+
+    Parameters
+    ----------
+    x, y : array-like
+        N-d arrays of samples. The arrays must be broadcastable except along
+        the dimension given by `axis`.
+    use_continuity : bool, optional
+            Whether a continuity correction (1/2) should be applied.
+            Default is True when `method` is ``'asymptotic'``; has no effect
+            otherwise.
+    alternative : {'two-sided', 'less', 'greater'}, optional
+        Defines the alternative hypothesis. Default is 'two-sided'.
+        Let *F(u)* and *G(u)* be the cumulative distribution functions of the
+        distributions underlying `x` and `y`, respectively. Then the following
+        alternative hypotheses are available:
+
+        * 'two-sided': the distributions are not equal, i.e. *F(u) ≠ G(u)* for
+          at least one *u*.
+        * 'less': the distribution underlying `x` is stochastically less
+          than the distribution underlying `y`, i.e. *F(u) > G(u)* for all *u*.
+        * 'greater': the distribution underlying `x` is stochastically greater
+          than the distribution underlying `y`, i.e. *F(u) < G(u)* for all *u*.
+
+        Note that the mathematical expressions in the alternative hypotheses
+        above describe the CDFs of the underlying distributions. The directions
+        of the inequalities appear inconsistent with the natural language
+        description at first glance, but they are not. For example, suppose
+        *X* and *Y* are random variables that follow distributions with CDFs
+        *F* and *G*, respectively. If *F(u) > G(u)* for all *u*, samples drawn
+        from *X* tend to be less than those drawn from *Y*.
+
+        Under a more restrictive set of assumptions, the alternative hypotheses
+        can be expressed in terms of the locations of the distributions;
+        see [5] section 5.1.
+    axis : int, optional
+        Axis along which to perform the test. Default is 0.
+    method : {'auto', 'asymptotic', 'exact'} or `PermutationMethod` instance, optional
+        Selects the method used to calculate the *p*-value.
+        Default is 'auto'. The following options are available.
+
+        * ``'asymptotic'``: compares the standardized test statistic
+          against the normal distribution, correcting for ties.
+        * ``'exact'``: computes the exact *p*-value by comparing the observed
+          :math:`U` statistic against the exact distribution of the :math:`U`
+          statistic under the null hypothesis. No correction is made for ties.
+        * ``'auto'``: chooses ``'exact'`` when the size of one of the samples
+          is less than or equal to 8 and there are no ties;
+          chooses ``'asymptotic'`` otherwise.
+        * `PermutationMethod` instance. In this case, the p-value
+          is computed using `permutation_test` with the provided
+          configuration options and other appropriate settings.
+
+    Returns
+    -------
+    res : MannwhitneyuResult
+        An object containing attributes:
+
+        statistic : float
+            The Mann-Whitney U statistic corresponding with sample `x`. See
+            Notes for the test statistic corresponding with sample `y`.
+        pvalue : float
+            The associated *p*-value for the chosen `alternative`.
+
+    Notes
+    -----
+    If ``U1`` is the statistic corresponding with sample `x`, then the
+    statistic corresponding with sample `y` is
+    ``U2 = x.shape[axis] * y.shape[axis] - U1``.
+
+    `mannwhitneyu` is for independent samples. For related / paired samples,
+    consider `scipy.stats.wilcoxon`.
+
+    `method` ``'exact'`` is recommended when there are no ties and when either
+    sample size is less than 8 [1]_. The implementation follows the recurrence
+    relation originally proposed in [1]_ as it is described in [3]_.
+    Note that the exact method is *not* corrected for ties, but
+    `mannwhitneyu` will not raise errors or warnings if there are ties in the
+    data. If there are ties and either samples is small (fewer than ~10
+    observations), consider passing an instance of `PermutationMethod`
+    as the `method` to perform a permutation test.
+
+    The Mann-Whitney U test is a non-parametric version of the t-test for
+    independent samples. When the means of samples from the populations
+    are normally distributed, consider `scipy.stats.ttest_ind`.
+
+    See Also
+    --------
+    scipy.stats.wilcoxon, scipy.stats.ranksums, scipy.stats.ttest_ind
+
+    References
+    ----------
+    .. [1] H.B. Mann and D.R. Whitney, "On a test of whether one of two random
+           variables is stochastically larger than the other", The Annals of
+           Mathematical Statistics, Vol. 18, pp. 50-60, 1947.
+    .. [2] Mann-Whitney U Test, Wikipedia,
+           http://en.wikipedia.org/wiki/Mann-Whitney_U_test
+    .. [3] A. Di Bucchianico, "Combinatorics, computer algebra, and the
+           Wilcoxon-Mann-Whitney test", Journal of Statistical Planning and
+           Inference, Vol. 79, pp. 349-364, 1999.
+    .. [4] Rosie Shier, "Statistics: 2.3 The Mann-Whitney U Test", Mathematics
+           Learning Support Centre, 2004.
+    .. [5] Michael P. Fay and Michael A. Proschan. "Wilcoxon-Mann-Whitney
+           or t-test? On assumptions for hypothesis tests and multiple \
+           interpretations of decision rules." Statistics surveys, Vol. 4, pp.
+           1-39, 2010. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857732/
+
+    Examples
+    --------
+    We follow the example from [4]_: nine randomly sampled young adults were
+    diagnosed with type II diabetes at the ages below.
+
+    >>> males = [19, 22, 16, 29, 24]
+    >>> females = [20, 11, 17, 12]
+
+    We use the Mann-Whitney U test to assess whether there is a statistically
+    significant difference in the diagnosis age of males and females.
+    The null hypothesis is that the distribution of male diagnosis ages is
+    the same as the distribution of female diagnosis ages. We decide
+    that a confidence level of 95% is required to reject the null hypothesis
+    in favor of the alternative that the distributions are different.
+    Since the number of samples is very small and there are no ties in the
+    data, we can compare the observed test statistic against the *exact*
+    distribution of the test statistic under the null hypothesis.
+
+    >>> from scipy.stats import mannwhitneyu
+    >>> U1, p = mannwhitneyu(males, females, method="exact")
+    >>> print(U1)
+    17.0
+
+    `mannwhitneyu` always reports the statistic associated with the first
+    sample, which, in this case, is males. This agrees with :math:`U_M = 17`
+    reported in [4]_. The statistic associated with the second statistic
+    can be calculated:
+
+    >>> nx, ny = len(males), len(females)
+    >>> U2 = nx*ny - U1
+    >>> print(U2)
+    3.0
+
+    This agrees with :math:`U_F = 3` reported in [4]_. The two-sided
+    *p*-value can be calculated from either statistic, and the value produced
+    by `mannwhitneyu` agrees with :math:`p = 0.11` reported in [4]_.
+
+    >>> print(p)
+    0.1111111111111111
+
+    The exact distribution of the test statistic is asymptotically normal, so
+    the example continues by comparing the exact *p*-value against the
+    *p*-value produced using the normal approximation.
+
+    >>> _, pnorm = mannwhitneyu(males, females, method="asymptotic")
+    >>> print(pnorm)
+    0.11134688653314041
+
+    Here `mannwhitneyu`'s reported *p*-value appears to conflict with the
+    value :math:`p = 0.09` given in [4]_. The reason is that [4]_
+    does not apply the continuity correction performed by `mannwhitneyu`;
+    `mannwhitneyu` reduces the distance between the test statistic and the
+    mean :math:`\mu = n_x n_y / 2` by 0.5 to correct for the fact that the
+    discrete statistic is being compared against a continuous distribution.
+    Here, the :math:`U` statistic used is less than the mean, so we reduce
+    the distance by adding 0.5 in the numerator.
+
+    >>> import numpy as np
+    >>> from scipy.stats import norm
+    >>> U = min(U1, U2)
+    >>> N = nx + ny
+    >>> z = (U - nx*ny/2 + 0.5) / np.sqrt(nx*ny * (N + 1)/ 12)
+    >>> p = 2 * norm.cdf(z)  # use CDF to get p-value from smaller statistic
+    >>> print(p)
+    0.11134688653314041
+
+    If desired, we can disable the continuity correction to get a result
+    that agrees with that reported in [4]_.
+
+    >>> _, pnorm = mannwhitneyu(males, females, use_continuity=False,
+    ...                         method="asymptotic")
+    >>> print(pnorm)
+    0.0864107329737
+
+    Regardless of whether we perform an exact or asymptotic test, the
+    probability of the test statistic being as extreme or more extreme by
+    chance exceeds 5%, so we do not consider the results statistically
+    significant.
+
+    Suppose that, before seeing the data, we had hypothesized that females
+    would tend to be diagnosed at a younger age than males.
+    In that case, it would be natural to provide the female ages as the
+    first input, and we would have performed a one-sided test using
+    ``alternative = 'less'``: females are diagnosed at an age that is
+    stochastically less than that of males.
+
+    >>> res = mannwhitneyu(females, males, alternative="less", method="exact")
+    >>> print(res)
+    MannwhitneyuResult(statistic=3.0, pvalue=0.05555555555555555)
+
+    Again, the probability of getting a sufficiently low value of the
+    test statistic by chance under the null hypothesis is greater than 5%,
+    so we do not reject the null hypothesis in favor of our alternative.
+
+    If it is reasonable to assume that the means of samples from the
+    populations are normally distributed, we could have used a t-test to
+    perform the analysis.
+
+    >>> from scipy.stats import ttest_ind
+    >>> res = ttest_ind(females, males, alternative="less")
+    >>> print(res)
+    Ttest_indResult(statistic=-2.239334696520584, pvalue=0.030068441095757924)
+
+    Under this assumption, the *p*-value would be low enough to reject the
+    null hypothesis in favor of the alternative.
+
+    '''
+
+    x, y, use_continuity, alternative, axis_int, method = (
+        _mwu_input_validation(x, y, use_continuity, alternative, axis, method))
+
+    x, y, xy = _broadcast_concatenate(x, y, axis)
+
+    n1, n2 = x.shape[-1], y.shape[-1]
+
+    # Follows [2]
+    ranks, t = _rankdata(xy, 'average', return_ties=True)  # method 2, step 1
+    R1 = ranks[..., :n1].sum(axis=-1)                      # method 2, step 2
+    U1 = R1 - n1*(n1+1)/2                                  # method 2, step 3
+    U2 = n1 * n2 - U1                                      # as U1 + U2 = n1 * n2
+
+    if alternative == "greater":
+        U, f = U1, 1  # U is the statistic to use for p-value, f is a factor
+    elif alternative == "less":
+        U, f = U2, 1  # Due to symmetry, use SF of U2 rather than CDF of U1
+    else:
+        U, f = np.maximum(U1, U2), 2  # multiply SF by two for two-sided test
+
+    if method == "auto":
+        method = _mwu_choose_method(n1, n2, np.any(t > 1))
+
+    if method == "exact":
+        p = _mwu_state.sf(U.astype(int), min(n1, n2), max(n1, n2))
+    elif method == "asymptotic":
+        z = _get_mwu_z(U, n1, n2, t, continuity=use_continuity)
+        p = stats.norm.sf(z)
+    else:  # `PermutationMethod` instance (already validated)
+        def statistic(x, y, axis):
+            return mannwhitneyu(x, y, use_continuity=use_continuity,
+                                alternative=alternative, axis=axis,
+                                method="asymptotic").statistic
+
+        res = stats.permutation_test((x, y), statistic, axis=axis,
+                                     **method._asdict(), alternative=alternative)
+        p = res.pvalue
+        f = 1
+
+    p *= f
+
+    # Ensure that test statistic is not greater than 1
+    # This could happen for exact test when U = m*n/2
+    p = np.clip(p, 0, 1)
+
+    return MannwhitneyuResult(U1, p)

env-llmeval/lib/python3.10/site-packages/scipy/stats/_rvs_sampling.py

@@ -0,0 +1,56 @@
+import warnings
+from scipy.stats.sampling import RatioUniforms
+
+def rvs_ratio_uniforms(pdf, umax, vmin, vmax, size=1, c=0, random_state=None):
+    """
+    Generate random samples from a probability density function using the
+    ratio-of-uniforms method.
+
+    .. deprecated:: 1.12.0
+        `rvs_ratio_uniforms` is deprecated in favour of
+        `scipy.stats.sampling.RatioUniforms` from version 1.12.0 and will
+        be removed in SciPy 1.15.0
+
+    Parameters
+    ----------
+    pdf : callable
+        A function with signature `pdf(x)` that is proportional to the
+        probability density function of the distribution.
+    umax : float
+        The upper bound of the bounding rectangle in the u-direction.
+    vmin : float
+        The lower bound of the bounding rectangle in the v-direction.
+    vmax : float
+        The upper bound of the bounding rectangle in the v-direction.
+    size : int or tuple of ints, optional
+        Defining number of random variates (default is 1).
+    c : float, optional.
+        Shift parameter of ratio-of-uniforms method, see Notes. Default is 0.
+    random_state : {None, int, `numpy.random.Generator`,
+                    `numpy.random.RandomState`}, optional
+
+        If `seed` is None (or `np.random`), the `numpy.random.RandomState`
+        singleton is used.
+        If `seed` is an int, a new ``RandomState`` instance is used,
+        seeded with `seed`.
+        If `seed` is already a ``Generator`` or ``RandomState`` instance then
+        that instance is used.
+
+    Returns
+    -------
+    rvs : ndarray
+        The random variates distributed according to the probability
+        distribution defined by the pdf.
+
+    Notes
+    -----
+    Please refer to `scipy.stats.sampling.RatioUniforms` for the documentation.
+    """
+    warnings.warn("Please use `RatioUniforms` from the "
+                  "`scipy.stats.sampling` namespace. The "
+                  "`scipy.stats.rvs_ratio_uniforms` namespace is deprecated "
+                  "and will be removed in SciPy 1.15.0",
+                  category=DeprecationWarning, stacklevel=2)
+    gen = RatioUniforms(pdf, umax=umax, vmin=vmin, vmax=vmax,
+                        c=c, random_state=random_state)
+    return gen.rvs(size)

env-llmeval/lib/python3.10/site-packages/scipy/stats/contingency.py

@@ -0,0 +1,468 @@
+"""
+Contingency table functions (:mod:`scipy.stats.contingency`)
+============================================================
+
+Functions for creating and analyzing contingency tables.
+
+.. currentmodule:: scipy.stats.contingency
+
+.. autosummary::
+   :toctree: generated/
+
+   chi2_contingency
+   relative_risk
+   odds_ratio
+   crosstab
+   association
+
+   expected_freq
+   margins
+
+"""
+
+
+from functools import reduce
+import math
+import numpy as np
+from ._stats_py import power_divergence
+from ._relative_risk import relative_risk
+from ._crosstab import crosstab
+from ._odds_ratio import odds_ratio
+from scipy._lib._bunch import _make_tuple_bunch
+
+
+__all__ = ['margins', 'expected_freq', 'chi2_contingency', 'crosstab',
+           'association', 'relative_risk', 'odds_ratio']
+
+
+def margins(a):
+    """Return a list of the marginal sums of the array `a`.
+
+    Parameters
+    ----------
+    a : ndarray
+        The array for which to compute the marginal sums.
+
+    Returns
+    -------
+    margsums : list of ndarrays
+        A list of length `a.ndim`.  `margsums[k]` is the result
+        of summing `a` over all axes except `k`; it has the same
+        number of dimensions as `a`, but the length of each axis
+        except axis `k` will be 1.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.stats.contingency import margins
+
+    >>> a = np.arange(12).reshape(2, 6)
+    >>> a
+    array([[ 0,  1,  2,  3,  4,  5],
+           [ 6,  7,  8,  9, 10, 11]])
+    >>> m0, m1 = margins(a)
+    >>> m0
+    array([[15],
+           [51]])
+    >>> m1
+    array([[ 6,  8, 10, 12, 14, 16]])
+
+    >>> b = np.arange(24).reshape(2,3,4)
+    >>> m0, m1, m2 = margins(b)
+    >>> m0
+    array([[[ 66]],
+           [[210]]])
+    >>> m1
+    array([[[ 60],
+            [ 92],
+            [124]]])
+    >>> m2
+    array([[[60, 66, 72, 78]]])
+    """
+    margsums = []
+    ranged = list(range(a.ndim))
+    for k in ranged:
+        marg = np.apply_over_axes(np.sum, a, [j for j in ranged if j != k])
+        margsums.append(marg)
+    return margsums
+
+
+def expected_freq(observed):
+    """
+    Compute the expected frequencies from a contingency table.
+
+    Given an n-dimensional contingency table of observed frequencies,
+    compute the expected frequencies for the table based on the marginal
+    sums under the assumption that the groups associated with each
+    dimension are independent.
+
+    Parameters
+    ----------
+    observed : array_like
+        The table of observed frequencies.  (While this function can handle
+        a 1-D array, that case is trivial.  Generally `observed` is at
+        least 2-D.)
+
+    Returns
+    -------
+    expected : ndarray of float64
+        The expected frequencies, based on the marginal sums of the table.
+        Same shape as `observed`.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.stats.contingency import expected_freq
+    >>> observed = np.array([[10, 10, 20],[20, 20, 20]])
+    >>> expected_freq(observed)
+    array([[ 12.,  12.,  16.],
+           [ 18.,  18.,  24.]])
+
+    """
+    # Typically `observed` is an integer array. If `observed` has a large
+    # number of dimensions or holds large values, some of the following
+    # computations may overflow, so we first switch to floating point.
+    observed = np.asarray(observed, dtype=np.float64)
+
+    # Create a list of the marginal sums.
+    margsums = margins(observed)
+
+    # Create the array of expected frequencies.  The shapes of the
+    # marginal sums returned by apply_over_axes() are just what we
+    # need for broadcasting in the following product.
+    d = observed.ndim
+    expected = reduce(np.multiply, margsums) / observed.sum() ** (d - 1)
+    return expected
+
+
+Chi2ContingencyResult = _make_tuple_bunch(
+    'Chi2ContingencyResult',
+    ['statistic', 'pvalue', 'dof', 'expected_freq'], []
+)
+
+
+def chi2_contingency(observed, correction=True, lambda_=None):
+    """Chi-square test of independence of variables in a contingency table.
+
+    This function computes the chi-square statistic and p-value for the
+    hypothesis test of independence of the observed frequencies in the
+    contingency table [1]_ `observed`.  The expected frequencies are computed
+    based on the marginal sums under the assumption of independence; see
+    `scipy.stats.contingency.expected_freq`.  The number of degrees of
+    freedom is (expressed using numpy functions and attributes)::
+
+        dof = observed.size - sum(observed.shape) + observed.ndim - 1
+
+
+    Parameters
+    ----------
+    observed : array_like
+        The contingency table. The table contains the observed frequencies
+        (i.e. number of occurrences) in each category.  In the two-dimensional
+        case, the table is often described as an "R x C table".
+    correction : bool, optional
+        If True, *and* the degrees of freedom is 1, apply Yates' correction
+        for continuity.  The effect of the correction is to adjust each
+        observed value by 0.5 towards the corresponding expected value.
+    lambda_ : float or str, optional
+        By default, the statistic computed in this test is Pearson's
+        chi-squared statistic [2]_.  `lambda_` allows a statistic from the
+        Cressie-Read power divergence family [3]_ to be used instead.  See
+        `scipy.stats.power_divergence` for details.
+
+    Returns
+    -------
+    res : Chi2ContingencyResult
+        An object containing attributes:
+
+        statistic : float
+            The test statistic.
+        pvalue : float
+            The p-value of the test.
+        dof : int
+            The degrees of freedom.
+        expected_freq : ndarray, same shape as `observed`
+            The expected frequencies, based on the marginal sums of the table.
+
+    See Also
+    --------
+    scipy.stats.contingency.expected_freq
+    scipy.stats.fisher_exact
+    scipy.stats.chisquare
+    scipy.stats.power_divergence
+    scipy.stats.barnard_exact
+    scipy.stats.boschloo_exact
+
+    Notes
+    -----
+    An often quoted guideline for the validity of this calculation is that
+    the test should be used only if the observed and expected frequencies
+    in each cell are at least 5.
+
+    This is a test for the independence of different categories of a
+    population. The test is only meaningful when the dimension of
+    `observed` is two or more.  Applying the test to a one-dimensional
+    table will always result in `expected` equal to `observed` and a
+    chi-square statistic equal to 0.
+
+    This function does not handle masked arrays, because the calculation
+    does not make sense with missing values.
+
+    Like `scipy.stats.chisquare`, this function computes a chi-square
+    statistic; the convenience this function provides is to figure out the
+    expected frequencies and degrees of freedom from the given contingency
+    table. If these were already known, and if the Yates' correction was not
+    required, one could use `scipy.stats.chisquare`.  That is, if one calls::
+
+        res = chi2_contingency(obs, correction=False)
+
+    then the following is true::
+
+        (res.statistic, res.pvalue) == stats.chisquare(obs.ravel(),
+                                                       f_exp=ex.ravel(),
+                                                       ddof=obs.size - 1 - dof)
+
+    The `lambda_` argument was added in version 0.13.0 of scipy.
+
+    References
+    ----------
+    .. [1] "Contingency table",
+           https://en.wikipedia.org/wiki/Contingency_table
+    .. [2] "Pearson's chi-squared test",
+           https://en.wikipedia.org/wiki/Pearson%27s_chi-squared_test
+    .. [3] Cressie, N. and Read, T. R. C., "Multinomial Goodness-of-Fit
+           Tests", J. Royal Stat. Soc. Series B, Vol. 46, No. 3 (1984),
+           pp. 440-464.
+    .. [4] Berger, Jeffrey S. et al. "Aspirin for the Primary Prevention of
+           Cardiovascular Events in Women and Men: A Sex-Specific
+           Meta-analysis of Randomized Controlled Trials."
+           JAMA, 295(3):306-313, :doi:`10.1001/jama.295.3.306`, 2006.
+
+    Examples
+    --------
+    In [4]_, the use of aspirin to prevent cardiovascular events in women
+    and men was investigated. The study notably concluded:
+
+        ...aspirin therapy reduced the risk of a composite of
+        cardiovascular events due to its effect on reducing the risk of
+        ischemic stroke in women [...]
+
+    The article lists studies of various cardiovascular events. Let's
+    focus on the ischemic stoke in women.
+
+    The following table summarizes the results of the experiment in which
+    participants took aspirin or a placebo on a regular basis for several
+    years. Cases of ischemic stroke were recorded::
+
+                          Aspirin   Control/Placebo
+        Ischemic stroke     176           230
+        No stroke         21035         21018
+
+    Is there evidence that the aspirin reduces the risk of ischemic stroke?
+    We begin by formulating a null hypothesis :math:`H_0`:
+
+        The effect of aspirin is equivalent to that of placebo.
+
+    Let's assess the plausibility of this hypothesis with
+    a chi-square test.
+
+    >>> import numpy as np
+    >>> from scipy.stats import chi2_contingency
+    >>> table = np.array([[176, 230], [21035, 21018]])
+    >>> res = chi2_contingency(table)
+    >>> res.statistic
+    6.892569132546561
+    >>> res.pvalue
+    0.008655478161175739
+
+    Using a significance level of 5%, we would reject the null hypothesis in
+    favor of the alternative hypothesis: "the effect of aspirin
+    is not equivalent to the effect of placebo".
+    Because `scipy.stats.contingency.chi2_contingency` performs a two-sided
+    test, the alternative hypothesis does not indicate the direction of the
+    effect. We can use `stats.contingency.odds_ratio` to support the
+    conclusion that aspirin *reduces* the risk of ischemic stroke.
+
+    Below are further examples showing how larger contingency tables can be
+    tested.
+
+    A two-way example (2 x 3):
+
+    >>> obs = np.array([[10, 10, 20], [20, 20, 20]])
+    >>> res = chi2_contingency(obs)
+    >>> res.statistic
+    2.7777777777777777
+    >>> res.pvalue
+    0.24935220877729619
+    >>> res.dof
+    2
+    >>> res.expected_freq
+    array([[ 12.,  12.,  16.],
+           [ 18.,  18.,  24.]])
+
+    Perform the test using the log-likelihood ratio (i.e. the "G-test")
+    instead of Pearson's chi-squared statistic.
+
+    >>> res = chi2_contingency(obs, lambda_="log-likelihood")
+    >>> res.statistic
+    2.7688587616781319
+    >>> res.pvalue
+    0.25046668010954165
+
+    A four-way example (2 x 2 x 2 x 2):
+
+    >>> obs = np.array(
+    ...     [[[[12, 17],
+    ...        [11, 16]],
+    ...       [[11, 12],
+    ...        [15, 16]]],
+    ...      [[[23, 15],
+    ...        [30, 22]],
+    ...       [[14, 17],
+    ...        [15, 16]]]])
+    >>> res = chi2_contingency(obs)
+    >>> res.statistic
+    8.7584514426741897
+    >>> res.pvalue
+    0.64417725029295503
+    """
+    observed = np.asarray(observed)
+    if np.any(observed < 0):
+        raise ValueError("All values in `observed` must be nonnegative.")
+    if observed.size == 0:
+        raise ValueError("No data; `observed` has size 0.")
+
+    expected = expected_freq(observed)
+    if np.any(expected == 0):
+        # Include one of the positions where expected is zero in
+        # the exception message.
+        zeropos = list(zip(*np.nonzero(expected == 0)))[0]
+        raise ValueError("The internally computed table of expected "
+                         f"frequencies has a zero element at {zeropos}.")
+
+    # The degrees of freedom
+    dof = expected.size - sum(expected.shape) + expected.ndim - 1
+
+    if dof == 0:
+        # Degenerate case; this occurs when `observed` is 1D (or, more
+        # generally, when it has only one nontrivial dimension).  In this
+        # case, we also have observed == expected, so chi2 is 0.
+        chi2 = 0.0
+        p = 1.0
+    else:
+        if dof == 1 and correction:
+            # Adjust `observed` according to Yates' correction for continuity.
+            # Magnitude of correction no bigger than difference; see gh-13875
+            diff = expected - observed
+            direction = np.sign(diff)
+            magnitude = np.minimum(0.5, np.abs(diff))
+            observed = observed + magnitude * direction
+
+        chi2, p = power_divergence(observed, expected,
+                                   ddof=observed.size - 1 - dof, axis=None,
+                                   lambda_=lambda_)
+
+    return Chi2ContingencyResult(chi2, p, dof, expected)
+
+
+def association(observed, method="cramer", correction=False, lambda_=None):
+    """Calculates degree of association between two nominal variables.
+
+    The function provides the option for computing one of three measures of
+    association between two nominal variables from the data given in a 2d
+    contingency table: Tschuprow's T, Pearson's Contingency Coefficient
+    and Cramer's V.
+
+    Parameters
+    ----------
+    observed : array-like
+        The array of observed values
+    method : {"cramer", "tschuprow", "pearson"} (default = "cramer")
+        The association test statistic.
+    correction : bool, optional
+        Inherited from `scipy.stats.contingency.chi2_contingency()`
+    lambda_ : float or str, optional
+        Inherited from `scipy.stats.contingency.chi2_contingency()`
+
+    Returns
+    -------
+    statistic : float
+        Value of the test statistic
+
+    Notes
+    -----
+    Cramer's V, Tschuprow's T and Pearson's Contingency Coefficient, all
+    measure the degree to which two nominal or ordinal variables are related,
+    or the level of their association. This differs from correlation, although
+    many often mistakenly consider them equivalent. Correlation measures in
+    what way two variables are related, whereas, association measures how
+    related the variables are. As such, association does not subsume
+    independent variables, and is rather a test of independence. A value of
+    1.0 indicates perfect association, and 0.0 means the variables have no
+    association.
+
+    Both the Cramer's V and Tschuprow's T are extensions of the phi
+    coefficient.  Moreover, due to the close relationship between the
+    Cramer's V and Tschuprow's T the returned values can often be similar
+    or even equivalent.  They are likely to diverge more as the array shape
+    diverges from a 2x2.
+
+    References
+    ----------
+    .. [1] "Tschuprow's T",
+           https://en.wikipedia.org/wiki/Tschuprow's_T
+    .. [2] Tschuprow, A. A. (1939)
+           Principles of the Mathematical Theory of Correlation;
+           translated by M. Kantorowitsch. W. Hodge & Co.
+    .. [3] "Cramer's V", https://en.wikipedia.org/wiki/Cramer's_V
+    .. [4] "Nominal Association: Phi and Cramer's V",
+           http://www.people.vcu.edu/~pdattalo/702SuppRead/MeasAssoc/NominalAssoc.html
+    .. [5] Gingrich, Paul, "Association Between Variables",
+           http://uregina.ca/~gingrich/ch11a.pdf
+
+    Examples
+    --------
+    An example with a 4x2 contingency table:
+
+    >>> import numpy as np
+    >>> from scipy.stats.contingency import association
+    >>> obs4x2 = np.array([[100, 150], [203, 322], [420, 700], [320, 210]])
+
+    Pearson's contingency coefficient
+
+    >>> association(obs4x2, method="pearson")
+    0.18303298140595667
+
+    Cramer's V
+
+    >>> association(obs4x2, method="cramer")
+    0.18617813077483678
+
+    Tschuprow's T
+
+    >>> association(obs4x2, method="tschuprow")
+    0.14146478765062995
+    """
+    arr = np.asarray(observed)
+    if not np.issubdtype(arr.dtype, np.integer):
+        raise ValueError("`observed` must be an integer array.")
+
+    if len(arr.shape) != 2:
+        raise ValueError("method only accepts 2d arrays")
+
+    chi2_stat = chi2_contingency(arr, correction=correction,
+                                 lambda_=lambda_)
+
+    phi2 = chi2_stat.statistic / arr.sum()
+    n_rows, n_cols = arr.shape
+    if method == "cramer":
+        value = phi2 / min(n_cols - 1, n_rows - 1)
+    elif method == "tschuprow":
+        value = phi2 / math.sqrt((n_rows - 1) * (n_cols - 1))
+    elif method == 'pearson':
+        value = phi2 / (1 + phi2)
+    else:
+        raise ValueError("Invalid argument value: 'method' argument must "
+                         "be 'cramer', 'tschuprow', or 'pearson'")
+
+    return math.sqrt(value)

env-llmeval/lib/python3.10/site-packages/scipy/stats/kde.py

@@ -0,0 +1,23 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.stats` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'gaussian_kde', 'linalg', 'logsumexp', 'check_random_state',
+    'atleast_2d', 'reshape', 'newaxis', 'exp', 'ravel', 'power',
+    'atleast_1d', 'squeeze', 'sum', 'transpose', 'cov',
+    'gaussian_kernel_estimate'
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="stats", module="kde",
+                                   private_modules=["_kde"], all=__all__,
+                                   attribute=name)

env-llmeval/lib/python3.10/site-packages/scipy/stats/qmc.py

@@ -0,0 +1,235 @@
+r"""
+====================================================
+Quasi-Monte Carlo submodule (:mod:`scipy.stats.qmc`)
+====================================================
+
+.. currentmodule:: scipy.stats.qmc
+
+This module provides Quasi-Monte Carlo generators and associated helper
+functions.
+
+
+Quasi-Monte Carlo
+=================
+
+Engines
+-------
+
+.. autosummary::
+   :toctree: generated/
+
+   QMCEngine
+   Sobol
+   Halton
+   LatinHypercube
+   PoissonDisk
+   MultinomialQMC
+   MultivariateNormalQMC
+
+Helpers
+-------
+
+.. autosummary::
+   :toctree: generated/
+
+   discrepancy
+   geometric_discrepancy
+   update_discrepancy
+   scale
+
+
+Introduction to Quasi-Monte Carlo
+=================================
+
+Quasi-Monte Carlo (QMC) methods [1]_, [2]_, [3]_ provide an
+:math:`n \times d` array of numbers in :math:`[0,1]`. They can be used in
+place of :math:`n` points from the :math:`U[0,1]^{d}` distribution. Compared to
+random points, QMC points are designed to have fewer gaps and clumps. This is
+quantified by discrepancy measures [4]_. From the Koksma-Hlawka
+inequality [5]_ we know that low discrepancy reduces a bound on
+integration error. Averaging a function :math:`f` over :math:`n` QMC points
+can achieve an integration error close to :math:`O(n^{-1})` for well
+behaved functions [2]_.
+
+Most QMC constructions are designed for special values of :math:`n`
+such as powers of 2 or large primes. Changing the sample
+size by even one can degrade their performance, even their
+rate of convergence [6]_. For instance :math:`n=100` points may give less
+accuracy than :math:`n=64` if the method was designed for :math:`n=2^m`.
+
+Some QMC constructions are extensible in :math:`n`: we can find
+another special sample size :math:`n' > n` and often an infinite
+sequence of increasing special sample sizes. Some QMC
+constructions are extensible in :math:`d`: we can increase the dimension,
+possibly to some upper bound, and typically without requiring
+special values of :math:`d`. Some QMC methods are extensible in
+both :math:`n` and :math:`d`.
+
+QMC points are deterministic. That makes it hard to estimate the accuracy of
+integrals estimated by averages over QMC points. Randomized QMC (RQMC) [7]_
+points are constructed so that each point is individually :math:`U[0,1]^{d}`
+while collectively the :math:`n` points retain their low discrepancy.
+One can make :math:`R` independent replications of RQMC points to
+see how stable a computation is. From :math:`R` independent values,
+a t-test (or bootstrap t-test [8]_) then gives approximate confidence
+intervals on the mean value. Some RQMC methods produce a
+root mean squared error that is actually :math:`o(1/n)` and smaller than
+the rate seen in unrandomized QMC. An intuitive explanation is
+that the error is a sum of many small ones and random errors
+cancel in a way that deterministic ones do not. RQMC also
+has advantages on integrands that are singular or, for other
+reasons, fail to be Riemann integrable.
+
+(R)QMC cannot beat Bahkvalov's curse of dimension (see [9]_). For
+any random or deterministic method, there are worst case functions
+that will give it poor performance in high dimensions. A worst
+case function for QMC might be 0 at all n points but very
+large elsewhere. Worst case analyses get very pessimistic
+in high dimensions. (R)QMC can bring a great improvement over
+MC when the functions on which it is used are not worst case.
+For instance (R)QMC can be especially effective on integrands
+that are well approximated by sums of functions of
+some small number of their input variables at a time [10]_, [11]_.
+That property is often a surprising finding about those functions.
+
+Also, to see an improvement over IID MC, (R)QMC requires a bit of smoothness of
+the integrand, roughly the mixed first order derivative in each direction,
+:math:`\partial^d f/\partial x_1 \cdots \partial x_d`, must be integral.
+For instance, a function that is 1 inside the hypersphere and 0 outside of it
+has infinite variation in the sense of Hardy and Krause for any dimension
+:math:`d = 2`.
+
+Scrambled nets are a kind of RQMC that have some valuable robustness
+properties [12]_. If the integrand is square integrable, they give variance
+:math:`var_{SNET} = o(1/n)`. There is a finite upper bound on
+:math:`var_{SNET} / var_{MC}` that holds simultaneously for every square
+integrable integrand. Scrambled nets satisfy a strong law of large numbers
+for :math:`f` in :math:`L^p` when :math:`p>1`. In some
+special cases there is a central limit theorem [13]_. For smooth enough
+integrands they can achieve RMSE nearly :math:`O(n^{-3})`. See [12]_
+for references about these properties.
+
+The main kinds of QMC methods are lattice rules [14]_ and digital
+nets and sequences [2]_, [15]_. The theories meet up in polynomial
+lattice rules [16]_ which can produce digital nets. Lattice rules
+require some form of search for good constructions. For digital
+nets there are widely used default constructions.
+
+The most widely used QMC methods are Sobol' sequences [17]_.
+These are digital nets. They are extensible in both :math:`n` and :math:`d`.
+They can be scrambled. The special sample sizes are powers
+of 2. Another popular method are Halton sequences [18]_.
+The constructions resemble those of digital nets. The earlier
+dimensions have much better equidistribution properties than
+later ones. There are essentially no special sample sizes.
+They are not thought to be as accurate as Sobol' sequences.
+They can be scrambled. The nets of Faure [19]_ are also widely
+used. All dimensions are equally good, but the special sample
+sizes grow rapidly with dimension :math:`d`. They can be scrambled.
+The nets of Niederreiter and Xing [20]_ have the best asymptotic
+properties but have not shown good empirical performance [21]_.
+
+Higher order digital nets are formed by a digit interleaving process
+in the digits of the constructed points. They can achieve higher
+levels of asymptotic accuracy given higher smoothness conditions on :math:`f`
+and they can be scrambled [22]_. There is little or no empirical work
+showing the improved rate to be attained.
+
+Using QMC is like using the entire period of a small random
+number generator. The constructions are similar and so
+therefore are the computational costs [23]_.
+
+(R)QMC is sometimes improved by passing the points through
+a baker's transformation (tent function) prior to using them.
+That function has the form :math:`1-2|x-1/2|`. As :math:`x` goes from 0 to
+1, this function goes from 0 to 1 and then back. It is very
+useful to produce a periodic function for lattice rules [14]_,
+and sometimes it improves the convergence rate [24]_.
+
+It is not straightforward to apply QMC methods to Markov
+chain Monte Carlo (MCMC).  We can think of MCMC as using
+:math:`n=1` point in :math:`[0,1]^{d}` for very large :math:`d`, with
+ergodic results corresponding to :math:`d \to \infty`. One proposal is
+in [25]_ and under strong conditions an improved rate of convergence
+has been shown [26]_.
+
+Returning to Sobol' points: there are many versions depending
+on what are called direction numbers. Those are the result of
+searches and are tabulated. A very widely used set of direction
+numbers come from [27]_. It is extensible in dimension up to
+:math:`d=21201`.
+
+References
+----------
+.. [1] Owen, Art B. "Monte Carlo Book: the Quasi-Monte Carlo parts." 2019.
+.. [2] Niederreiter, Harald. "Random number generation and quasi-Monte Carlo
+   methods." Society for Industrial and Applied Mathematics, 1992.
+.. [3] Dick, Josef, Frances Y. Kuo, and Ian H. Sloan. "High-dimensional
+   integration: the quasi-Monte Carlo way." Acta Numerica no. 22: 133, 2013.
+.. [4] Aho, A. V., C. Aistleitner, T. Anderson, K. Appel, V. Arnol'd, N.
+   Aronszajn, D. Asotsky et al. "W. Chen et al.(eds.), "A Panorama of
+   Discrepancy Theory", Sringer International Publishing,
+   Switzerland: 679, 2014.
+.. [5] Hickernell, Fred J. "Koksma-Hlawka Inequality." Wiley StatsRef:
+   Statistics Reference Online, 2014.
+.. [6] Owen, Art B. "On dropping the first Sobol' point." :arxiv:`2008.08051`,
+   2020.
+.. [7] L'Ecuyer, Pierre, and Christiane Lemieux. "Recent advances in randomized
+   quasi-Monte Carlo methods." In Modeling uncertainty, pp. 419-474. Springer,
+   New York, NY, 2002.
+.. [8] DiCiccio, Thomas J., and Bradley Efron. "Bootstrap confidence
+   intervals." Statistical science: 189-212, 1996.
+.. [9] Dimov, Ivan T. "Monte Carlo methods for applied scientists." World
+   Scientific, 2008.
+.. [10] Caflisch, Russel E., William J. Morokoff, and Art B. Owen. "Valuation
+   of mortgage backed securities using Brownian bridges to reduce effective
+   dimension." Journal of Computational Finance: no. 1 27-46, 1997.
+.. [11] Sloan, Ian H., and Henryk Wozniakowski. "When are quasi-Monte Carlo
+   algorithms efficient for high dimensional integrals?." Journal of Complexity
+   14, no. 1 (1998): 1-33.
+.. [12] Owen, Art B., and Daniel Rudolf, "A strong law of large numbers for
+   scrambled net integration." SIAM Review, to appear.
+.. [13] Loh, Wei-Liem. "On the asymptotic distribution of scrambled net
+   quadrature." The Annals of Statistics 31, no. 4: 1282-1324, 2003.
+.. [14] Sloan, Ian H. and S. Joe. "Lattice methods for multiple integration."
+   Oxford University Press, 1994.
+.. [15] Dick, Josef, and Friedrich Pillichshammer. "Digital nets and sequences:
+   discrepancy theory and quasi-Monte Carlo integration." Cambridge University
+   Press, 2010.
+.. [16] Dick, Josef, F. Kuo, Friedrich Pillichshammer, and I. Sloan.
+   "Construction algorithms for polynomial lattice rules for multivariate
+   integration." Mathematics of computation 74, no. 252: 1895-1921, 2005.
+.. [17] Sobol', Il'ya Meerovich. "On the distribution of points in a cube and
+   the approximate evaluation of integrals." Zhurnal Vychislitel'noi Matematiki
+   i Matematicheskoi Fiziki 7, no. 4: 784-802, 1967.
+.. [18] Halton, John H. "On the efficiency of certain quasi-random sequences of
+   points in evaluating multi-dimensional integrals." Numerische Mathematik 2,
+   no. 1: 84-90, 1960.
+.. [19] Faure, Henri. "Discrepance de suites associees a un systeme de
+   numeration (en dimension s)." Acta arithmetica 41, no. 4: 337-351, 1982.
+.. [20] Niederreiter, Harold, and Chaoping Xing. "Low-discrepancy sequences and
+   global function fields with many rational places." Finite Fields and their
+   applications 2, no. 3: 241-273, 1996.
+.. [21] Hong, Hee Sun, and Fred J. Hickernell. "Algorithm 823: Implementing
+   scrambled digital sequences." ACM Transactions on Mathematical Software
+   (TOMS) 29, no. 2: 95-109, 2003.
+.. [22] Dick, Josef. "Higher order scrambled digital nets achieve the optimal
+   rate of the root mean square error for smooth integrands." The Annals of
+   Statistics 39, no. 3: 1372-1398, 2011.
+.. [23] Niederreiter, Harald. "Multidimensional numerical integration using
+   pseudorandom numbers." In Stochastic Programming 84 Part I, pp. 17-38.
+   Springer, Berlin, Heidelberg, 1986.
+.. [24] Hickernell, Fred J. "Obtaining O (N-2+e) Convergence for Lattice
+   Quadrature Rules." In Monte Carlo and Quasi-Monte Carlo Methods 2000,
+   pp. 274-289. Springer, Berlin, Heidelberg, 2002.
+.. [25] Owen, Art B., and Seth D. Tribble. "A quasi-Monte Carlo Metropolis
+   algorithm." Proceedings of the National Academy of Sciences 102,
+   no. 25: 8844-8849, 2005.
+.. [26] Chen, Su. "Consistency and convergence rate of Markov chain quasi Monte
+   Carlo with examples." PhD diss., Stanford University, 2011.
+.. [27] Joe, Stephen, and Frances Y. Kuo. "Constructing Sobol sequences with
+   better two-dimensional projections." SIAM Journal on Scientific Computing
+   30, no. 5: 2635-2654, 2008.
+
+"""
+from ._qmc import *  # noqa: F403