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.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/__init__.py

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+"""
+.. _statsrefmanual:
+
+==========================================
+Statistical functions (:mod:`scipy.stats`)
+==========================================
+
+.. currentmodule:: scipy.stats
+
+This module contains a large number of probability distributions,
+summary and frequency statistics, correlation functions and statistical
+tests, masked statistics, kernel density estimation, quasi-Monte Carlo
+functionality, and more.
+
+Statistics is a very large area, and there are topics that are out of scope
+for SciPy and are covered by other packages. Some of the most important ones
+are:
+
+- `statsmodels <https://www.statsmodels.org/stable/index.html>`__:
+  regression, linear models, time series analysis, extensions to topics
+  also covered by ``scipy.stats``.
+- `Pandas <https://pandas.pydata.org/>`__: tabular data, time series
+  functionality, interfaces to other statistical languages.
+- `PyMC <https://docs.pymc.io/>`__: Bayesian statistical
+  modeling, probabilistic machine learning.
+- `scikit-learn <https://scikit-learn.org/>`__: classification, regression,
+  model selection.
+- `Seaborn <https://seaborn.pydata.org/>`__: statistical data visualization.
+- `rpy2 <https://rpy2.github.io/>`__: Python to R bridge.
+
+
+Probability distributions
+=========================
+
+Each univariate distribution is an instance of a subclass of `rv_continuous`
+(`rv_discrete` for discrete distributions):
+
+.. autosummary::
+   :toctree: generated/
+
+   rv_continuous
+   rv_discrete
+   rv_histogram
+
+Continuous distributions
+------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   alpha             -- Alpha
+   anglit            -- Anglit
+   arcsine           -- Arcsine
+   argus             -- Argus
+   beta              -- Beta
+   betaprime         -- Beta Prime
+   bradford          -- Bradford
+   burr              -- Burr (Type III)
+   burr12            -- Burr (Type XII)
+   cauchy            -- Cauchy
+   chi               -- Chi
+   chi2              -- Chi-squared
+   cosine            -- Cosine
+   crystalball       -- Crystalball
+   dgamma            -- Double Gamma
+   dweibull          -- Double Weibull
+   erlang            -- Erlang
+   expon             -- Exponential
+   exponnorm         -- Exponentially Modified Normal
+   exponweib         -- Exponentiated Weibull
+   exponpow          -- Exponential Power
+   f                 -- F (Snecdor F)
+   fatiguelife       -- Fatigue Life (Birnbaum-Saunders)
+   fisk              -- Fisk
+   foldcauchy        -- Folded Cauchy
+   foldnorm          -- Folded Normal
+   genlogistic       -- Generalized Logistic
+   gennorm           -- Generalized normal
+   genpareto         -- Generalized Pareto
+   genexpon          -- Generalized Exponential
+   genextreme        -- Generalized Extreme Value
+   gausshyper        -- Gauss Hypergeometric
+   gamma             -- Gamma
+   gengamma          -- Generalized gamma
+   genhalflogistic   -- Generalized Half Logistic
+   genhyperbolic     -- Generalized Hyperbolic
+   geninvgauss       -- Generalized Inverse Gaussian
+   gibrat            -- Gibrat
+   gilbrat           -- Gilbrat
+   gompertz          -- Gompertz (Truncated Gumbel)
+   gumbel_r          -- Right Sided Gumbel, Log-Weibull, Fisher-Tippett, Extreme Value Type I
+   gumbel_l          -- Left Sided Gumbel, etc.
+   halfcauchy        -- Half Cauchy
+   halflogistic      -- Half Logistic
+   halfnorm          -- Half Normal
+   halfgennorm       -- Generalized Half Normal
+   hypsecant         -- Hyperbolic Secant
+   invgamma          -- Inverse Gamma
+   invgauss          -- Inverse Gaussian
+   invweibull        -- Inverse Weibull
+   johnsonsb         -- Johnson SB
+   johnsonsu         -- Johnson SU
+   kappa4            -- Kappa 4 parameter
+   kappa3            -- Kappa 3 parameter
+   ksone             -- Distribution of Kolmogorov-Smirnov one-sided test statistic
+   kstwo             -- Distribution of Kolmogorov-Smirnov two-sided test statistic
+   kstwobign         -- Limiting Distribution of scaled Kolmogorov-Smirnov two-sided test statistic.
+   laplace           -- Laplace
+   laplace_asymmetric    -- Asymmetric Laplace
+   levy              -- Levy
+   levy_l
+   levy_stable
+   logistic          -- Logistic
+   loggamma          -- Log-Gamma
+   loglaplace        -- Log-Laplace (Log Double Exponential)
+   lognorm           -- Log-Normal
+   loguniform        -- Log-Uniform
+   lomax             -- Lomax (Pareto of the second kind)
+   maxwell           -- Maxwell
+   mielke            -- Mielke's Beta-Kappa
+   moyal             -- Moyal
+   nakagami          -- Nakagami
+   ncx2              -- Non-central chi-squared
+   ncf               -- Non-central F
+   nct               -- Non-central Student's T
+   norm              -- Normal (Gaussian)
+   norminvgauss      -- Normal Inverse Gaussian
+   pareto            -- Pareto
+   pearson3          -- Pearson type III
+   powerlaw          -- Power-function
+   powerlognorm      -- Power log normal
+   powernorm         -- Power normal
+   rdist             -- R-distribution
+   rayleigh          -- Rayleigh
+   rice              -- Rice
+   recipinvgauss     -- Reciprocal Inverse Gaussian
+   semicircular      -- Semicircular
+   skewcauchy        -- Skew Cauchy
+   skewnorm          -- Skew normal
+   studentized_range    -- Studentized Range
+   t                 -- Student's T
+   trapezoid         -- Trapezoidal
+   triang            -- Triangular
+   truncexpon        -- Truncated Exponential
+   truncnorm         -- Truncated Normal
+   truncpareto       -- Truncated Pareto
+   truncweibull_min  -- Truncated minimum Weibull distribution
+   tukeylambda       -- Tukey-Lambda
+   uniform           -- Uniform
+   vonmises          -- Von-Mises (Circular)
+   vonmises_line     -- Von-Mises (Line)
+   wald              -- Wald
+   weibull_min       -- Minimum Weibull (see Frechet)
+   weibull_max       -- Maximum Weibull (see Frechet)
+   wrapcauchy        -- Wrapped Cauchy
+
+Multivariate distributions
+--------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   multivariate_normal    -- Multivariate normal distribution
+   matrix_normal          -- Matrix normal distribution
+   dirichlet              -- Dirichlet
+   wishart                -- Wishart
+   invwishart             -- Inverse Wishart
+   multinomial            -- Multinomial distribution
+   special_ortho_group    -- SO(N) group
+   ortho_group            -- O(N) group
+   unitary_group          -- U(N) group
+   random_correlation     -- random correlation matrices
+   multivariate_t         -- Multivariate t-distribution
+   multivariate_hypergeom -- Multivariate hypergeometric distribution
+   random_table           -- Distribution of random tables with given marginals
+   uniform_direction      -- Uniform distribution on S(N-1)
+
+`scipy.stats.multivariate_normal` methods accept instances
+of the following class to represent the covariance.
+
+.. autosummary::
+   :toctree: generated/
+
+   Covariance             -- Representation of a covariance matrix
+
+
+Discrete distributions
+----------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   bernoulli                -- Bernoulli
+   betabinom                -- Beta-Binomial
+   binom                    -- Binomial
+   boltzmann                -- Boltzmann (Truncated Discrete Exponential)
+   dlaplace                 -- Discrete Laplacian
+   geom                     -- Geometric
+   hypergeom                -- Hypergeometric
+   logser                   -- Logarithmic (Log-Series, Series)
+   nbinom                   -- Negative Binomial
+   nchypergeom_fisher       -- Fisher's Noncentral Hypergeometric
+   nchypergeom_wallenius    -- Wallenius's Noncentral Hypergeometric
+   nhypergeom               -- Negative Hypergeometric
+   planck                   -- Planck (Discrete Exponential)
+   poisson                  -- Poisson
+   randint                  -- Discrete Uniform
+   skellam                  -- Skellam
+   yulesimon                -- Yule-Simon
+   zipf                     -- Zipf (Zeta)
+   zipfian                  -- Zipfian
+
+An overview of statistical functions is given below.  Many of these functions
+have a similar version in `scipy.stats.mstats` which work for masked arrays.
+
+Summary statistics
+==================
+
+.. autosummary::
+   :toctree: generated/
+
+   describe          -- Descriptive statistics
+   gmean             -- Geometric mean
+   hmean             -- Harmonic mean
+   pmean             -- Power mean
+   kurtosis          -- Fisher or Pearson kurtosis
+   mode              -- Modal value
+   moment            -- Central moment
+   expectile         -- Expectile
+   skew              -- Skewness
+   kstat             --
+   kstatvar          --
+   tmean             -- Truncated arithmetic mean
+   tvar              -- Truncated variance
+   tmin              --
+   tmax              --
+   tstd              --
+   tsem              --
+   variation         -- Coefficient of variation
+   find_repeats
+   trim_mean
+   gstd              -- Geometric Standard Deviation
+   iqr
+   sem
+   bayes_mvs
+   mvsdist
+   entropy
+   differential_entropy
+   median_abs_deviation
+
+Frequency statistics
+====================
+
+.. autosummary::
+   :toctree: generated/
+
+   cumfreq
+   percentileofscore
+   scoreatpercentile
+   relfreq
+
+.. autosummary::
+   :toctree: generated/
+
+   binned_statistic     -- Compute a binned statistic for a set of data.
+   binned_statistic_2d  -- Compute a 2-D binned statistic for a set of data.
+   binned_statistic_dd  -- Compute a d-D binned statistic for a set of data.
+
+Correlation functions
+=====================
+
+.. autosummary::
+   :toctree: generated/
+
+   f_oneway
+   alexandergovern
+   pearsonr
+   spearmanr
+   pointbiserialr
+   kendalltau
+   weightedtau
+   somersd
+   linregress
+   siegelslopes
+   theilslopes
+   multiscale_graphcorr
+
+Statistical tests
+=================
+
+.. autosummary::
+   :toctree: generated/
+
+   ttest_1samp
+   ttest_ind
+   ttest_ind_from_stats
+   ttest_rel
+   chisquare
+   cramervonmises
+   cramervonmises_2samp
+   power_divergence
+   kstest
+   ks_1samp
+   ks_2samp
+   epps_singleton_2samp
+   mannwhitneyu
+   tiecorrect
+   rankdata
+   ranksums
+   wilcoxon
+   kruskal
+   friedmanchisquare
+   brunnermunzel
+   combine_pvalues
+   jarque_bera
+   page_trend_test
+   tukey_hsd
+   poisson_means_test
+
+.. autosummary::
+   :toctree: generated/
+
+   ansari
+   bartlett
+   levene
+   shapiro
+   anderson
+   anderson_ksamp
+   binom_test
+   binomtest
+   fligner
+   median_test
+   mood
+   skewtest
+   kurtosistest
+   normaltest
+   goodness_of_fit
+
+
+Quasi-Monte Carlo
+=================
+
+.. toctree::
+   :maxdepth: 4
+
+   stats.qmc
+
+Resampling Methods
+==================
+
+.. autosummary::
+   :toctree: generated/
+
+   bootstrap
+   permutation_test
+   monte_carlo_test
+
+Masked statistics functions
+===========================
+
+.. toctree::
+
+   stats.mstats
+
+
+Other statistical functionality
+===============================
+
+Transformations
+---------------
+
+.. autosummary::
+   :toctree: generated/
+
+   boxcox
+   boxcox_normmax
+   boxcox_llf
+   yeojohnson
+   yeojohnson_normmax
+   yeojohnson_llf
+   obrientransform
+   sigmaclip
+   trimboth
+   trim1
+   zmap
+   zscore
+   gzscore
+
+Statistical distances
+---------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   wasserstein_distance
+   energy_distance
+
+Sampling
+--------
+
+.. toctree::
+   :maxdepth: 4
+
+   stats.sampling
+
+Random variate generation / CDF Inversion
+-----------------------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   rvs_ratio_uniforms
+
+Distribution Fitting
+--------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   fit
+
+Directional statistical functions
+---------------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   directional_stats
+   circmean
+   circvar
+   circstd
+
+Contingency table functions
+---------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   chi2_contingency
+   contingency.crosstab
+   contingency.expected_freq
+   contingency.margins
+   contingency.relative_risk
+   contingency.association
+   contingency.odds_ratio
+   fisher_exact
+   barnard_exact
+   boschloo_exact
+
+Plot-tests
+----------
+
+.. autosummary::
+   :toctree: generated/
+
+   ppcc_max
+   ppcc_plot
+   probplot
+   boxcox_normplot
+   yeojohnson_normplot
+
+Univariate and multivariate kernel density estimation
+-----------------------------------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   gaussian_kde
+
+Warnings / Errors used in :mod:`scipy.stats`
+--------------------------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   DegenerateDataWarning
+   ConstantInputWarning
+   NearConstantInputWarning
+   FitError
+
+"""
+
+from ._warnings_errors import (ConstantInputWarning, NearConstantInputWarning,
+                               DegenerateDataWarning, FitError)
+from ._stats_py import *
+from ._variation import variation
+from .distributions import *
+from ._morestats import *
+from ._binomtest import binomtest
+from ._binned_statistic import *
+from ._kde import gaussian_kde
+from . import mstats
+from . import qmc
+from ._multivariate import *
+from . import contingency
+from .contingency import chi2_contingency
+from ._resampling import bootstrap, monte_carlo_test, permutation_test
+from ._entropy import *
+from ._hypotests import *
+from ._rvs_sampling import rvs_ratio_uniforms
+from ._page_trend_test import page_trend_test
+from ._mannwhitneyu import mannwhitneyu
+from ._fit import fit, goodness_of_fit
+from ._covariance import Covariance
+
+# Deprecated namespaces, to be removed in v2.0.0
+from . import (
+    biasedurn, kde, morestats, mstats_basic, mstats_extras, mvn, statlib, stats
+)
+
+__all__ = [s for s in dir() if not s.startswith("_")]  # Remove dunders.
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_axis_nan_policy.py

@@ -0,0 +1,605 @@
+# Many scipy.stats functions support `axis` and `nan_policy` parameters.
+# When the two are combined, it can be tricky to get all the behavior just
+# right. This file contains utility functions useful for scipy.stats functions
+# that support `axis` and `nan_policy`, including a decorator that
+# automatically adds `axis` and `nan_policy` arguments to a function.
+
+import numpy as np
+from functools import wraps
+from scipy._lib._docscrape import FunctionDoc, Parameter
+from scipy._lib._util import _contains_nan
+import inspect
+
+
+def _broadcast_arrays(arrays, axis=None):
+    """
+    Broadcast shapes of arrays, ignoring incompatibility of specified axes
+    """
+    new_shapes = _broadcast_array_shapes(arrays, axis=axis)
+    if axis is None:
+        new_shapes = [new_shapes]*len(arrays)
+    return [np.broadcast_to(array, new_shape)
+            for array, new_shape in zip(arrays, new_shapes)]
+
+
+def _broadcast_array_shapes(arrays, axis=None):
+    """
+    Broadcast shapes of arrays, ignoring incompatibility of specified axes
+    """
+    shapes = [np.asarray(arr).shape for arr in arrays]
+    return _broadcast_shapes(shapes, axis)
+
+
+def _broadcast_shapes(shapes, axis=None):
+    """
+    Broadcast shapes, ignoring incompatibility of specified axes
+    """
+    if not shapes:
+        return shapes
+
+    # input validation
+    if axis is not None:
+        axis = np.atleast_1d(axis)
+        axis_int = axis.astype(int)
+        if not np.array_equal(axis_int, axis):
+            raise np.AxisError('`axis` must be an integer, a '
+                               'tuple of integers, or `None`.')
+        axis = axis_int
+
+    # First, ensure all shapes have same number of dimensions by prepending 1s.
+    n_dims = max([len(shape) for shape in shapes])
+    new_shapes = np.ones((len(shapes), n_dims), dtype=int)
+    for row, shape in zip(new_shapes, shapes):
+        row[len(row)-len(shape):] = shape  # can't use negative indices (-0:)
+
+    # Remove the shape elements of the axes to be ignored, but remember them.
+    if axis is not None:
+        axis[axis < 0] = n_dims + axis[axis < 0]
+        axis = np.sort(axis)
+        if axis[-1] >= n_dims or axis[0] < 0:
+            message = (f"`axis` is out of bounds "
+                       f"for array of dimension {n_dims}")
+            raise np.AxisError(message)
+
+        if len(np.unique(axis)) != len(axis):
+            raise np.AxisError("`axis` must contain only distinct elements")
+
+        removed_shapes = new_shapes[:, axis]
+        new_shapes = np.delete(new_shapes, axis, axis=1)
+
+    # If arrays are broadcastable, shape elements that are 1 may be replaced
+    # with a corresponding non-1 shape element. Assuming arrays are
+    # broadcastable, that final shape element can be found with:
+    new_shape = np.max(new_shapes, axis=0)
+    # except in case of an empty array:
+    new_shape *= new_shapes.all(axis=0)
+
+    # Among all arrays, there can only be one unique non-1 shape element.
+    # Therefore, if any non-1 shape element does not match what we found
+    # above, the arrays must not be broadcastable after all.
+    if np.any(~((new_shapes == 1) | (new_shapes == new_shape))):
+        raise ValueError("Array shapes are incompatible for broadcasting.")
+
+    if axis is not None:
+        # Add back the shape elements that were ignored
+        new_axis = axis - np.arange(len(axis))
+        new_shapes = [tuple(np.insert(new_shape, new_axis, removed_shape))
+                      for removed_shape in removed_shapes]
+        return new_shapes
+    else:
+        return tuple(new_shape)
+
+
+def _broadcast_array_shapes_remove_axis(arrays, axis=None):
+    """
+    Broadcast shapes of arrays, dropping specified axes
+
+    Given a sequence of arrays `arrays` and an integer or tuple `axis`, find
+    the shape of the broadcast result after consuming/dropping `axis`.
+    In other words, return output shape of a typical hypothesis test on
+    `arrays` vectorized along `axis`.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> a = np.zeros((5, 2, 1))
+    >>> b = np.zeros((9, 3))
+    >>> _broadcast_array_shapes((a, b), 1)
+    (5, 3)
+    """
+    # Note that here, `axis=None` means do not consume/drop any axes - _not_
+    # ravel arrays before broadcasting.
+    shapes = [arr.shape for arr in arrays]
+    return _broadcast_shapes_remove_axis(shapes, axis)
+
+
+def _broadcast_shapes_remove_axis(shapes, axis=None):
+    """
+    Broadcast shapes, dropping specified axes
+
+    Same as _broadcast_array_shapes, but given a sequence
+    of array shapes `shapes` instead of the arrays themselves.
+    """
+    shapes = _broadcast_shapes(shapes, axis)
+    shape = shapes[0]
+    if axis is not None:
+        shape = np.delete(shape, axis)
+    return tuple(shape)
+
+
+def _broadcast_concatenate(arrays, axis):
+    """Concatenate arrays along an axis with broadcasting."""
+    arrays = _broadcast_arrays(arrays, axis)
+    res = np.concatenate(arrays, axis=axis)
+    return res
+
+
+# TODO: add support for `axis` tuples
+def _remove_nans(samples, paired):
+    "Remove nans from paired or unpaired 1D samples"
+    # potential optimization: don't copy arrays that don't contain nans
+    if not paired:
+        return [sample[~np.isnan(sample)] for sample in samples]
+
+    # for paired samples, we need to remove the whole pair when any part
+    # has a nan
+    nans = np.isnan(samples[0])
+    for sample in samples[1:]:
+        nans = nans | np.isnan(sample)
+    not_nans = ~nans
+    return [sample[not_nans] for sample in samples]
+
+
+def _remove_sentinel(samples, paired, sentinel):
+    "Remove sentinel values from paired or unpaired 1D samples"
+    # could consolidate with `_remove_nans`, but it's not quite as simple as
+    # passing `sentinel=np.nan` because `(np.nan == np.nan) is False`
+
+    # potential optimization: don't copy arrays that don't contain sentinel
+    if not paired:
+        return [sample[sample != sentinel] for sample in samples]
+
+    # for paired samples, we need to remove the whole pair when any part
+    # has a nan
+    sentinels = (samples[0] == sentinel)
+    for sample in samples[1:]:
+        sentinels = sentinels | (sample == sentinel)
+    not_sentinels = ~sentinels
+    return [sample[not_sentinels] for sample in samples]
+
+
+def _masked_arrays_2_sentinel_arrays(samples):
+    # masked arrays in `samples` are converted to regular arrays, and values
+    # corresponding with masked elements are replaced with a sentinel value
+
+    # return without modifying arrays if none have a mask
+    has_mask = False
+    for sample in samples:
+        mask = getattr(sample, 'mask', False)
+        has_mask = has_mask or np.any(mask)
+    if not has_mask:
+        return samples, None  # None means there is no sentinel value
+
+    # Choose a sentinel value. We can't use `np.nan`, because sentinel (masked)
+    # values are always omitted, but there are different nan policies.
+    dtype = np.result_type(*samples)
+    dtype = dtype if np.issubdtype(dtype, np.number) else np.float64
+    for i in range(len(samples)):
+        # Things get more complicated if the arrays are of different types.
+        # We could have different sentinel values for each array, but
+        # the purpose of this code is convenience, not efficiency.
+        samples[i] = samples[i].astype(dtype, copy=False)
+
+    inexact = np.issubdtype(dtype, np.inexact)
+    info = np.finfo if inexact else np.iinfo
+    max_possible, min_possible = info(dtype).max, info(dtype).min
+    nextafter = np.nextafter if inexact else (lambda x, _: x - 1)
+
+    sentinel = max_possible
+    # For simplicity, min_possible/np.infs are not candidate sentinel values
+    while sentinel > min_possible:
+        for sample in samples:
+            if np.any(sample == sentinel):  # choose a new sentinel value
+                sentinel = nextafter(sentinel, -np.inf)
+                break
+        else:  # when sentinel value is OK, break the while loop
+            break
+    else:
+        message = ("This function replaces masked elements with sentinel "
+                   "values, but the data contains all distinct values of this "
+                   "data type. Consider promoting the dtype to `np.float64`.")
+        raise ValueError(message)
+
+    # replace masked elements with sentinel value
+    out_samples = []
+    for sample in samples:
+        mask = getattr(sample, 'mask', None)
+        if mask is not None:  # turn all masked arrays into sentinel arrays
+            mask = np.broadcast_to(mask, sample.shape)
+            sample = sample.data.copy() if np.any(mask) else sample.data
+            sample = np.asarray(sample)  # `sample.data` could be a memoryview?
+            sample[mask] = sentinel
+        out_samples.append(sample)
+
+    return out_samples, sentinel
+
+
+def _check_empty_inputs(samples, axis):
+    """
+    Check for empty sample; return appropriate output for a vectorized hypotest
+    """
+    # if none of the samples are empty, we need to perform the test
+    if not any((sample.size == 0 for sample in samples)):
+        return None
+    # otherwise, the statistic and p-value will be either empty arrays or
+    # arrays with NaNs. Produce the appropriate array and return it.
+    output_shape = _broadcast_array_shapes_remove_axis(samples, axis)
+    output = np.ones(output_shape) * np.nan
+    return output
+
+
+def _add_reduced_axes(res, reduced_axes, keepdims):
+    """
+    Add reduced axes back to all the arrays in the result object
+    if keepdims = True.
+    """
+    return ([np.expand_dims(output, reduced_axes) for output in res]
+            if keepdims else res)
+
+
+# Standard docstring / signature entries for `axis`, `nan_policy`, `keepdims`
+_name = 'axis'
+_desc = (
+    """If an int, the axis of the input along which to compute the statistic.
+The statistic of each axis-slice (e.g. row) of the input will appear in a
+corresponding element of the output.
+If ``None``, the input will be raveled before computing the statistic."""
+    .split('\n'))
+
+
+def _get_axis_params(default_axis=0, _name=_name, _desc=_desc):  # bind NOW
+    _type = f"int or None, default: {default_axis}"
+    _axis_parameter_doc = Parameter(_name, _type, _desc)
+    _axis_parameter = inspect.Parameter(_name,
+                                        inspect.Parameter.KEYWORD_ONLY,
+                                        default=default_axis)
+    return _axis_parameter_doc, _axis_parameter
+
+
+_name = 'nan_policy'
+_type = "{'propagate', 'omit', 'raise'}"
+_desc = (
+    """Defines how to handle input NaNs.
+
+- ``propagate``: if a NaN is present in the axis slice (e.g. row) along
+  which the  statistic is computed, the corresponding entry of the output
+  will be NaN.
+- ``omit``: NaNs will be omitted when performing the calculation.
+  If insufficient data remains in the axis slice along which the
+  statistic is computed, the corresponding entry of the output will be
+  NaN.
+- ``raise``: if a NaN is present, a ``ValueError`` will be raised."""
+    .split('\n'))
+_nan_policy_parameter_doc = Parameter(_name, _type, _desc)
+_nan_policy_parameter = inspect.Parameter(_name,
+                                          inspect.Parameter.KEYWORD_ONLY,
+                                          default='propagate')
+
+_name = 'keepdims'
+_type = "bool, default: False"
+_desc = (
+    """If this is set to True, the axes which are reduced are left
+in the result as dimensions with size one. With this option,
+the result will broadcast correctly against the input array."""
+    .split('\n'))
+_keepdims_parameter_doc = Parameter(_name, _type, _desc)
+_keepdims_parameter = inspect.Parameter(_name,
+                                        inspect.Parameter.KEYWORD_ONLY,
+                                        default=False)
+
+_standard_note_addition = (
+    """\nBeginning in SciPy 1.9, ``np.matrix`` inputs (not recommended for new
+code) are converted to ``np.ndarray`` before the calculation is performed. In
+this case, the output will be a scalar or ``np.ndarray`` of appropriate shape
+rather than a 2D ``np.matrix``. Similarly, while masked elements of masked
+arrays are ignored, the output will be a scalar or ``np.ndarray`` rather than a
+masked array with ``mask=False``.""").split('\n')
+
+
+def _axis_nan_policy_factory(tuple_to_result, default_axis=0,
+                             n_samples=1, paired=False,
+                             result_to_tuple=None, too_small=0,
+                             n_outputs=2, kwd_samples=[]):
+    """Factory for a wrapper that adds axis/nan_policy params to a function.
+
+    Parameters
+    ----------
+    tuple_to_result : callable
+        Callable that returns an object of the type returned by the function
+        being wrapped (e.g. the namedtuple or dataclass returned by a
+        statistical test) provided the separate components (e.g. statistic,
+        pvalue).
+    default_axis : int, default: 0
+        The default value of the axis argument. Standard is 0 except when
+        backwards compatibility demands otherwise (e.g. `None`).
+    n_samples : int or callable, default: 1
+        The number of data samples accepted by the function
+        (e.g. `mannwhitneyu`), a callable that accepts a dictionary of
+        parameters passed into the function and returns the number of data
+        samples (e.g. `wilcoxon`), or `None` to indicate an arbitrary number
+        of samples (e.g. `kruskal`).
+    paired : {False, True}
+        Whether the function being wrapped treats the samples as paired (i.e.
+        corresponding elements of each sample should be considered as different
+        components of the same sample.)
+    result_to_tuple : callable, optional
+        Function that unpacks the results of the function being wrapped into
+        a tuple. This is essentially the inverse of `tuple_to_result`. Default
+        is `None`, which is appropriate for statistical tests that return a
+        statistic, pvalue tuple (rather than, e.g., a non-iterable datalass).
+    too_small : int, default: 0
+        The largest unnacceptably small sample for the function being wrapped.
+        For example, some functions require samples of size two or more or they
+        raise an error. This argument prevents the error from being raised when
+        input is not 1D and instead places a NaN in the corresponding element
+        of the result.
+    n_outputs : int or callable, default: 2
+        The number of outputs produced by the function given 1d sample(s). For
+        example, hypothesis tests that return a namedtuple or result object
+        with attributes ``statistic`` and ``pvalue`` use the default
+        ``n_outputs=2``; summary statistics with scalar output use
+        ``n_outputs=1``. Alternatively, may be a callable that accepts a
+        dictionary of arguments passed into the wrapped function and returns
+        the number of outputs corresponding with those arguments.
+    kwd_samples : sequence, default: []
+        The names of keyword parameters that should be treated as samples. For
+        example, `gmean` accepts as its first argument a sample `a` but
+        also `weights` as a fourth, optional keyword argument. In this case, we
+        use `n_samples=1` and kwd_samples=['weights'].
+    """
+
+    if result_to_tuple is None:
+        def result_to_tuple(res):
+            return res
+
+    def is_too_small(samples):
+        for sample in samples:
+            if len(sample) <= too_small:
+                return True
+        return False
+
+    def axis_nan_policy_decorator(hypotest_fun_in):
+        @wraps(hypotest_fun_in)
+        def axis_nan_policy_wrapper(*args, _no_deco=False, **kwds):
+
+            if _no_deco:  # for testing, decorator does nothing
+                return hypotest_fun_in(*args, **kwds)
+
+            # We need to be flexible about whether position or keyword
+            # arguments are used, but we need to make sure users don't pass
+            # both for the same parameter. To complicate matters, some
+            # functions accept samples with *args, and some functions already
+            # accept `axis` and `nan_policy` as positional arguments.
+            # The strategy is to make sure that there is no duplication
+            # between `args` and `kwds`, combine the two into `kwds`, then
+            # the samples, `nan_policy`, and `axis` from `kwds`, as they are
+            # dealt with separately.
+
+            # Check for intersection between positional and keyword args
+            params = list(inspect.signature(hypotest_fun_in).parameters)
+            if n_samples is None:
+                # Give unique names to each positional sample argument
+                # Note that *args can't be provided as a keyword argument
+                params = [f"arg{i}" for i in range(len(args))] + params[1:]
+
+            d_args = dict(zip(params, args))
+            intersection = set(d_args) & set(kwds)
+            if intersection:
+                message = (f"{hypotest_fun_in.__name__}() got multiple values "
+                           f"for argument '{list(intersection)[0]}'")
+                raise TypeError(message)
+
+            # Consolidate other positional and keyword args into `kwds`
+            kwds.update(d_args)
+
+            # rename avoids UnboundLocalError
+            if callable(n_samples):
+                # Future refactoring idea: no need for callable n_samples.
+                # Just replace `n_samples` and `kwd_samples` with a single
+                # list of the names of all samples, and treat all of them
+                # as `kwd_samples` are treated below.
+                n_samp = n_samples(kwds)
+            else:
+                n_samp = n_samples or len(args)
+
+            # get the number of outputs
+            n_out = n_outputs  # rename to avoid UnboundLocalError
+            if callable(n_out):
+                n_out = n_out(kwds)
+
+            # If necessary, rearrange function signature: accept other samples
+            # as positional args right after the first n_samp args
+            kwd_samp = [name for name in kwd_samples
+                        if kwds.get(name, None) is not None]
+            n_kwd_samp = len(kwd_samp)
+            if not kwd_samp:
+                hypotest_fun_out = hypotest_fun_in
+            else:
+                def hypotest_fun_out(*samples, **kwds):
+                    new_kwds = dict(zip(kwd_samp, samples[n_samp:]))
+                    kwds.update(new_kwds)
+                    return hypotest_fun_in(*samples[:n_samp], **kwds)
+
+            # Extract the things we need here
+            samples = [np.atleast_1d(kwds.pop(param))
+                       for param in (params[:n_samp] + kwd_samp)]
+            vectorized = True if 'axis' in params else False
+            axis = kwds.pop('axis', default_axis)
+            nan_policy = kwds.pop('nan_policy', 'propagate')
+            keepdims = kwds.pop("keepdims", False)
+            del args  # avoid the possibility of passing both `args` and `kwds`
+
+            # convert masked arrays to regular arrays with sentinel values
+            samples, sentinel = _masked_arrays_2_sentinel_arrays(samples)
+
+            # standardize to always work along last axis
+            reduced_axes = axis
+            if axis is None:
+                if samples:
+                    # when axis=None, take the maximum of all dimensions since
+                    # all the dimensions are reduced.
+                    n_dims = np.max([sample.ndim for sample in samples])
+                    reduced_axes = tuple(range(n_dims))
+                samples = [np.asarray(sample.ravel()) for sample in samples]
+            else:
+                samples = _broadcast_arrays(samples, axis=axis)
+                axis = np.atleast_1d(axis)
+                n_axes = len(axis)
+                # move all axes in `axis` to the end to be raveled
+                samples = [np.moveaxis(sample, axis, range(-len(axis), 0))
+                           for sample in samples]
+                shapes = [sample.shape for sample in samples]
+                # New shape is unchanged for all axes _not_ in `axis`
+                # At the end, we append the product of the shapes of the axes
+                # in `axis`. Appending -1 doesn't work for zero-size arrays!
+                new_shapes = [shape[:-n_axes] + (np.prod(shape[-n_axes:]),)
+                              for shape in shapes]
+                samples = [sample.reshape(new_shape)
+                           for sample, new_shape in zip(samples, new_shapes)]
+            axis = -1  # work over the last axis
+
+            # if axis is not needed, just handle nan_policy and return
+            ndims = np.array([sample.ndim for sample in samples])
+            if np.all(ndims <= 1):
+                # Addresses nan_policy == "raise"
+                contains_nans = []
+                for sample in samples:
+                    contains_nan, _ = _contains_nan(sample, nan_policy)
+                    contains_nans.append(contains_nan)
+
+                # Addresses nan_policy == "propagate"
+                # Consider adding option to let function propagate nans, but
+                # currently the hypothesis tests this is applied to do not
+                # propagate nans in a sensible way
+                if any(contains_nans) and nan_policy == 'propagate':
+                    res = np.full(n_out, np.nan)
+                    res = _add_reduced_axes(res, reduced_axes, keepdims)
+                    return tuple_to_result(*res)
+
+                # Addresses nan_policy == "omit"
+                if any(contains_nans) and nan_policy == 'omit':
+                    # consider passing in contains_nans
+                    samples = _remove_nans(samples, paired)
+
+                # ideally, this is what the behavior would be:
+                # if is_too_small(samples):
+                #     return tuple_to_result(np.nan, np.nan)
+                # but some existing functions raise exceptions, and changing
+                # behavior of those would break backward compatibility.
+
+                if sentinel:
+                    samples = _remove_sentinel(samples, paired, sentinel)
+                res = hypotest_fun_out(*samples, **kwds)
+                res = result_to_tuple(res)
+                res = _add_reduced_axes(res, reduced_axes, keepdims)
+                return tuple_to_result(*res)
+
+            # check for empty input
+            # ideally, move this to the top, but some existing functions raise
+            # exceptions for empty input, so overriding it would break
+            # backward compatibility.
+            empty_output = _check_empty_inputs(samples, axis)
+            if empty_output is not None:
+                res = [empty_output.copy() for i in range(n_out)]
+                res = _add_reduced_axes(res, reduced_axes, keepdims)
+                return tuple_to_result(*res)
+
+            # otherwise, concatenate all samples along axis, remembering where
+            # each separate sample begins
+            lengths = np.array([sample.shape[axis] for sample in samples])
+            split_indices = np.cumsum(lengths)
+            x = _broadcast_concatenate(samples, axis)
+
+            # Addresses nan_policy == "raise"
+            contains_nan, _ = _contains_nan(x, nan_policy)
+
+            if vectorized and not contains_nan and not sentinel:
+                res = hypotest_fun_out(*samples, axis=axis, **kwds)
+                res = result_to_tuple(res)
+                res = _add_reduced_axes(res, reduced_axes, keepdims)
+                return tuple_to_result(*res)
+
+            # Addresses nan_policy == "omit"
+            if contains_nan and nan_policy == 'omit':
+                def hypotest_fun(x):
+                    samples = np.split(x, split_indices)[:n_samp+n_kwd_samp]
+                    samples = _remove_nans(samples, paired)
+                    if sentinel:
+                        samples = _remove_sentinel(samples, paired, sentinel)
+                    if is_too_small(samples):
+                        return np.full(n_out, np.nan)
+                    return result_to_tuple(hypotest_fun_out(*samples, **kwds))
+
+            # Addresses nan_policy == "propagate"
+            elif contains_nan and nan_policy == 'propagate':
+                def hypotest_fun(x):
+                    if np.isnan(x).any():
+                        return np.full(n_out, np.nan)
+
+                    samples = np.split(x, split_indices)[:n_samp+n_kwd_samp]
+                    if sentinel:
+                        samples = _remove_sentinel(samples, paired, sentinel)
+                    if is_too_small(samples):
+                        return np.full(n_out, np.nan)
+                    return result_to_tuple(hypotest_fun_out(*samples, **kwds))
+
+            else:
+                def hypotest_fun(x):
+                    samples = np.split(x, split_indices)[:n_samp+n_kwd_samp]
+                    if sentinel:
+                        samples = _remove_sentinel(samples, paired, sentinel)
+                    if is_too_small(samples):
+                        return np.full(n_out, np.nan)
+                    return result_to_tuple(hypotest_fun_out(*samples, **kwds))
+
+            x = np.moveaxis(x, axis, 0)
+            res = np.apply_along_axis(hypotest_fun, axis=0, arr=x)
+            res = _add_reduced_axes(res, reduced_axes, keepdims)
+            return tuple_to_result(*res)
+
+        _axis_parameter_doc, _axis_parameter = _get_axis_params(default_axis)
+        doc = FunctionDoc(axis_nan_policy_wrapper)
+        parameter_names = [param.name for param in doc['Parameters']]
+        if 'axis' in parameter_names:
+            doc['Parameters'][parameter_names.index('axis')] = (
+                _axis_parameter_doc)
+        else:
+            doc['Parameters'].append(_axis_parameter_doc)
+        if 'nan_policy' in parameter_names:
+            doc['Parameters'][parameter_names.index('nan_policy')] = (
+                _nan_policy_parameter_doc)
+        else:
+            doc['Parameters'].append(_nan_policy_parameter_doc)
+        if 'keepdims' in parameter_names:
+            doc['Parameters'][parameter_names.index('keepdims')] = (
+                _keepdims_parameter_doc)
+        else:
+            doc['Parameters'].append(_keepdims_parameter_doc)
+        doc['Notes'] += _standard_note_addition
+        doc = str(doc).split("\n", 1)[1]  # remove signature
+        axis_nan_policy_wrapper.__doc__ = str(doc)
+
+        sig = inspect.signature(axis_nan_policy_wrapper)
+        parameters = sig.parameters
+        parameter_list = list(parameters.values())
+        if 'axis' not in parameters:
+            parameter_list.append(_axis_parameter)
+        if 'nan_policy' not in parameters:
+            parameter_list.append(_nan_policy_parameter)
+        if 'keepdims' not in parameters:
+            parameter_list.append(_keepdims_parameter)
+        sig = sig.replace(parameters=parameter_list)
+        axis_nan_policy_wrapper.__signature__ = sig
+
+        return axis_nan_policy_wrapper
+    return axis_nan_policy_decorator

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_biasedurn.pxd

@@ -0,0 +1,27 @@
+# Declare the class with cdef
+cdef extern from "biasedurn/stocc.h" nogil:
+    cdef cppclass CFishersNCHypergeometric:
+        CFishersNCHypergeometric(int, int, int, double, double) except +
+        int mode()
+        double mean()
+        double variance()
+        double probability(int x)
+        double moments(double * mean, double * var)
+
+    cdef cppclass CWalleniusNCHypergeometric:
+        CWalleniusNCHypergeometric() except +
+        CWalleniusNCHypergeometric(int, int, int, double, double) except +
+        int mode()
+        double mean()
+        double variance()
+        double probability(int x)
+        double moments(double * mean, double * var)
+
+    cdef cppclass StochasticLib3:
+        StochasticLib3(int seed) except +
+        double Random() except +
+        void SetAccuracy(double accur)
+        int FishersNCHyp (int n, int m, int N, double odds) except +
+        int WalleniusNCHyp (int n, int m, int N, double odds) except +
+        double(*next_double)()
+        double(*next_normal)(const double m, const double s)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_binned_statistic.py

@@ -0,0 +1,795 @@
+import builtins
+import numpy as np
+from numpy.testing import suppress_warnings
+from operator import index
+from collections import namedtuple
+
+__all__ = ['binned_statistic',
+           'binned_statistic_2d',
+           'binned_statistic_dd']
+
+
+BinnedStatisticResult = namedtuple('BinnedStatisticResult',
+                                   ('statistic', 'bin_edges', 'binnumber'))
+
+
+def binned_statistic(x, values, statistic='mean',
+                     bins=10, range=None):
+    """
+    Compute a binned statistic for one or more sets of data.
+
+    This is a generalization of a histogram function.  A histogram divides
+    the space into bins, and returns the count of the number of points in
+    each bin.  This function allows the computation of the sum, mean, median,
+    or other statistic of the values (or set of values) within each bin.
+
+    Parameters
+    ----------
+    x : (N,) array_like
+        A sequence of values to be binned.
+    values : (N,) array_like or list of (N,) array_like
+        The data on which the statistic will be computed.  This must be
+        the same shape as `x`, or a set of sequences - each the same shape as
+        `x`.  If `values` is a set of sequences, the statistic will be computed
+        on each independently.
+    statistic : string or callable, optional
+        The statistic to compute (default is 'mean').
+        The following statistics are available:
+
+          * 'mean' : compute the mean of values for points within each bin.
+            Empty bins will be represented by NaN.
+          * 'std' : compute the standard deviation within each bin. This
+            is implicitly calculated with ddof=0.
+          * 'median' : compute the median of values for points within each
+            bin. Empty bins will be represented by NaN.
+          * 'count' : compute the count of points within each bin.  This is
+            identical to an unweighted histogram.  `values` array is not
+            referenced.
+          * 'sum' : compute the sum of values for points within each bin.
+            This is identical to a weighted histogram.
+          * 'min' : compute the minimum of values for points within each bin.
+            Empty bins will be represented by NaN.
+          * 'max' : compute the maximum of values for point within each bin.
+            Empty bins will be represented by NaN.
+          * function : a user-defined function which takes a 1D array of
+            values, and outputs a single numerical statistic. This function
+            will be called on the values in each bin.  Empty bins will be
+            represented by function([]), or NaN if this returns an error.
+
+    bins : int or sequence of scalars, optional
+        If `bins` is an int, it defines the number of equal-width bins in the
+        given range (10 by default).  If `bins` is a sequence, it defines the
+        bin edges, including the rightmost edge, allowing for non-uniform bin
+        widths.  Values in `x` that are smaller than lowest bin edge are
+        assigned to bin number 0, values beyond the highest bin are assigned to
+        ``bins[-1]``.  If the bin edges are specified, the number of bins will
+        be, (nx = len(bins)-1).
+    range : (float, float) or [(float, float)], optional
+        The lower and upper range of the bins.  If not provided, range
+        is simply ``(x.min(), x.max())``.  Values outside the range are
+        ignored.
+
+    Returns
+    -------
+    statistic : array
+        The values of the selected statistic in each bin.
+    bin_edges : array of dtype float
+        Return the bin edges ``(length(statistic)+1)``.
+    binnumber: 1-D ndarray of ints
+        Indices of the bins (corresponding to `bin_edges`) in which each value
+        of `x` belongs.  Same length as `values`.  A binnumber of `i` means the
+        corresponding value is between (bin_edges[i-1], bin_edges[i]).
+
+    See Also
+    --------
+    numpy.digitize, numpy.histogram, binned_statistic_2d, binned_statistic_dd
+
+    Notes
+    -----
+    All but the last (righthand-most) bin is half-open.  In other words, if
+    `bins` is ``[1, 2, 3, 4]``, then the first bin is ``[1, 2)`` (including 1,
+    but excluding 2) and the second ``[2, 3)``.  The last bin, however, is
+    ``[3, 4]``, which *includes* 4.
+
+    .. versionadded:: 0.11.0
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy import stats
+    >>> import matplotlib.pyplot as plt
+
+    First some basic examples:
+
+    Create two evenly spaced bins in the range of the given sample, and sum the
+    corresponding values in each of those bins:
+
+    >>> values = [1.0, 1.0, 2.0, 1.5, 3.0]
+    >>> stats.binned_statistic([1, 1, 2, 5, 7], values, 'sum', bins=2)
+    BinnedStatisticResult(statistic=array([4. , 4.5]),
+            bin_edges=array([1., 4., 7.]), binnumber=array([1, 1, 1, 2, 2]))
+
+    Multiple arrays of values can also be passed.  The statistic is calculated
+    on each set independently:
+
+    >>> values = [[1.0, 1.0, 2.0, 1.5, 3.0], [2.0, 2.0, 4.0, 3.0, 6.0]]
+    >>> stats.binned_statistic([1, 1, 2, 5, 7], values, 'sum', bins=2)
+    BinnedStatisticResult(statistic=array([[4. , 4.5],
+           [8. , 9. ]]), bin_edges=array([1., 4., 7.]),
+           binnumber=array([1, 1, 1, 2, 2]))
+
+    >>> stats.binned_statistic([1, 2, 1, 2, 4], np.arange(5), statistic='mean',
+    ...                        bins=3)
+    BinnedStatisticResult(statistic=array([1., 2., 4.]),
+            bin_edges=array([1., 2., 3., 4.]),
+            binnumber=array([1, 2, 1, 2, 3]))
+
+    As a second example, we now generate some random data of sailing boat speed
+    as a function of wind speed, and then determine how fast our boat is for
+    certain wind speeds:
+
+    >>> rng = np.random.default_rng()
+    >>> windspeed = 8 * rng.random(500)
+    >>> boatspeed = .3 * windspeed**.5 + .2 * rng.random(500)
+    >>> bin_means, bin_edges, binnumber = stats.binned_statistic(windspeed,
+    ...                 boatspeed, statistic='median', bins=[1,2,3,4,5,6,7])
+    >>> plt.figure()
+    >>> plt.plot(windspeed, boatspeed, 'b.', label='raw data')
+    >>> plt.hlines(bin_means, bin_edges[:-1], bin_edges[1:], colors='g', lw=5,
+    ...            label='binned statistic of data')
+    >>> plt.legend()
+
+    Now we can use ``binnumber`` to select all datapoints with a windspeed
+    below 1:
+
+    >>> low_boatspeed = boatspeed[binnumber == 0]
+
+    As a final example, we will use ``bin_edges`` and ``binnumber`` to make a
+    plot of a distribution that shows the mean and distribution around that
+    mean per bin, on top of a regular histogram and the probability
+    distribution function:
+
+    >>> x = np.linspace(0, 5, num=500)
+    >>> x_pdf = stats.maxwell.pdf(x)
+    >>> samples = stats.maxwell.rvs(size=10000)
+
+    >>> bin_means, bin_edges, binnumber = stats.binned_statistic(x, x_pdf,
+    ...         statistic='mean', bins=25)
+    >>> bin_width = (bin_edges[1] - bin_edges[0])
+    >>> bin_centers = bin_edges[1:] - bin_width/2
+
+    >>> plt.figure()
+    >>> plt.hist(samples, bins=50, density=True, histtype='stepfilled',
+    ...          alpha=0.2, label='histogram of data')
+    >>> plt.plot(x, x_pdf, 'r-', label='analytical pdf')
+    >>> plt.hlines(bin_means, bin_edges[:-1], bin_edges[1:], colors='g', lw=2,
+    ...            label='binned statistic of data')
+    >>> plt.plot((binnumber - 0.5) * bin_width, x_pdf, 'g.', alpha=0.5)
+    >>> plt.legend(fontsize=10)
+    >>> plt.show()
+
+    """
+    try:
+        N = len(bins)
+    except TypeError:
+        N = 1
+
+    if N != 1:
+        bins = [np.asarray(bins, float)]
+
+    if range is not None:
+        if len(range) == 2:
+            range = [range]
+
+    medians, edges, binnumbers = binned_statistic_dd(
+        [x], values, statistic, bins, range)
+
+    return BinnedStatisticResult(medians, edges[0], binnumbers)
+
+
+BinnedStatistic2dResult = namedtuple('BinnedStatistic2dResult',
+                                     ('statistic', 'x_edge', 'y_edge',
+                                      'binnumber'))
+
+
+def binned_statistic_2d(x, y, values, statistic='mean',
+                        bins=10, range=None, expand_binnumbers=False):
+    """
+    Compute a bidimensional binned statistic for one or more sets of data.
+
+    This is a generalization of a histogram2d function.  A histogram divides
+    the space into bins, and returns the count of the number of points in
+    each bin.  This function allows the computation of the sum, mean, median,
+    or other statistic of the values (or set of values) within each bin.
+
+    Parameters
+    ----------
+    x : (N,) array_like
+        A sequence of values to be binned along the first dimension.
+    y : (N,) array_like
+        A sequence of values to be binned along the second dimension.
+    values : (N,) array_like or list of (N,) array_like
+        The data on which the statistic will be computed.  This must be
+        the same shape as `x`, or a list of sequences - each with the same
+        shape as `x`.  If `values` is such a list, the statistic will be
+        computed on each independently.
+    statistic : string or callable, optional
+        The statistic to compute (default is 'mean').
+        The following statistics are available:
+
+          * 'mean' : compute the mean of values for points within each bin.
+            Empty bins will be represented by NaN.
+          * 'std' : compute the standard deviation within each bin. This
+            is implicitly calculated with ddof=0.
+          * 'median' : compute the median of values for points within each
+            bin. Empty bins will be represented by NaN.
+          * 'count' : compute the count of points within each bin.  This is
+            identical to an unweighted histogram.  `values` array is not
+            referenced.
+          * 'sum' : compute the sum of values for points within each bin.
+            This is identical to a weighted histogram.
+          * 'min' : compute the minimum of values for points within each bin.
+            Empty bins will be represented by NaN.
+          * 'max' : compute the maximum of values for point within each bin.
+            Empty bins will be represented by NaN.
+          * function : a user-defined function which takes a 1D array of
+            values, and outputs a single numerical statistic. This function
+            will be called on the values in each bin.  Empty bins will be
+            represented by function([]), or NaN if this returns an error.
+
+    bins : int or [int, int] or array_like or [array, array], optional
+        The bin specification:
+
+          * the number of bins for the two dimensions (nx = ny = bins),
+          * the number of bins in each dimension (nx, ny = bins),
+          * the bin edges for the two dimensions (x_edge = y_edge = bins),
+          * the bin edges in each dimension (x_edge, y_edge = bins).
+
+        If the bin edges are specified, the number of bins will be,
+        (nx = len(x_edge)-1, ny = len(y_edge)-1).
+
+    range : (2,2) array_like, optional
+        The leftmost and rightmost edges of the bins along each dimension
+        (if not specified explicitly in the `bins` parameters):
+        [[xmin, xmax], [ymin, ymax]]. All values outside of this range will be
+        considered outliers and not tallied in the histogram.
+    expand_binnumbers : bool, optional
+        'False' (default): the returned `binnumber` is a shape (N,) array of
+        linearized bin indices.
+        'True': the returned `binnumber` is 'unraveled' into a shape (2,N)
+        ndarray, where each row gives the bin numbers in the corresponding
+        dimension.
+        See the `binnumber` returned value, and the `Examples` section.
+
+        .. versionadded:: 0.17.0
+
+    Returns
+    -------
+    statistic : (nx, ny) ndarray
+        The values of the selected statistic in each two-dimensional bin.
+    x_edge : (nx + 1) ndarray
+        The bin edges along the first dimension.
+    y_edge : (ny + 1) ndarray
+        The bin edges along the second dimension.
+    binnumber : (N,) array of ints or (2,N) ndarray of ints
+        This assigns to each element of `sample` an integer that represents the
+        bin in which this observation falls.  The representation depends on the
+        `expand_binnumbers` argument.  See `Notes` for details.
+
+
+    See Also
+    --------
+    numpy.digitize, numpy.histogram2d, binned_statistic, binned_statistic_dd
+
+    Notes
+    -----
+    Binedges:
+    All but the last (righthand-most) bin is half-open.  In other words, if
+    `bins` is ``[1, 2, 3, 4]``, then the first bin is ``[1, 2)`` (including 1,
+    but excluding 2) and the second ``[2, 3)``.  The last bin, however, is
+    ``[3, 4]``, which *includes* 4.
+
+    `binnumber`:
+    This returned argument assigns to each element of `sample` an integer that
+    represents the bin in which it belongs.  The representation depends on the
+    `expand_binnumbers` argument. If 'False' (default): The returned
+    `binnumber` is a shape (N,) array of linearized indices mapping each
+    element of `sample` to its corresponding bin (using row-major ordering).
+    Note that the returned linearized bin indices are used for an array with
+    extra bins on the outer binedges to capture values outside of the defined
+    bin bounds.
+    If 'True': The returned `binnumber` is a shape (2,N) ndarray where
+    each row indicates bin placements for each dimension respectively.  In each
+    dimension, a binnumber of `i` means the corresponding value is between
+    (D_edge[i-1], D_edge[i]), where 'D' is either 'x' or 'y'.
+
+    .. versionadded:: 0.11.0
+
+    Examples
+    --------
+    >>> from scipy import stats
+
+    Calculate the counts with explicit bin-edges:
+
+    >>> x = [0.1, 0.1, 0.1, 0.6]
+    >>> y = [2.1, 2.6, 2.1, 2.1]
+    >>> binx = [0.0, 0.5, 1.0]
+    >>> biny = [2.0, 2.5, 3.0]
+    >>> ret = stats.binned_statistic_2d(x, y, None, 'count', bins=[binx, biny])
+    >>> ret.statistic
+    array([[2., 1.],
+           [1., 0.]])
+
+    The bin in which each sample is placed is given by the `binnumber`
+    returned parameter.  By default, these are the linearized bin indices:
+
+    >>> ret.binnumber
+    array([5, 6, 5, 9])
+
+    The bin indices can also be expanded into separate entries for each
+    dimension using the `expand_binnumbers` parameter:
+
+    >>> ret = stats.binned_statistic_2d(x, y, None, 'count', bins=[binx, biny],
+    ...                                 expand_binnumbers=True)
+    >>> ret.binnumber
+    array([[1, 1, 1, 2],
+           [1, 2, 1, 1]])
+
+    Which shows that the first three elements belong in the xbin 1, and the
+    fourth into xbin 2; and so on for y.
+
+    """
+
+    # This code is based on np.histogram2d
+    try:
+        N = len(bins)
+    except TypeError:
+        N = 1
+
+    if N != 1 and N != 2:
+        xedges = yedges = np.asarray(bins, float)
+        bins = [xedges, yedges]
+
+    medians, edges, binnumbers = binned_statistic_dd(
+        [x, y], values, statistic, bins, range,
+        expand_binnumbers=expand_binnumbers)
+
+    return BinnedStatistic2dResult(medians, edges[0], edges[1], binnumbers)
+
+
+BinnedStatisticddResult = namedtuple('BinnedStatisticddResult',
+                                     ('statistic', 'bin_edges',
+                                      'binnumber'))
+
+
+def _bincount(x, weights):
+    if np.iscomplexobj(weights):
+        a = np.bincount(x, np.real(weights))
+        b = np.bincount(x, np.imag(weights))
+        z = a + b*1j
+
+    else:
+        z = np.bincount(x, weights)
+    return z
+
+
+def binned_statistic_dd(sample, values, statistic='mean',
+                        bins=10, range=None, expand_binnumbers=False,
+                        binned_statistic_result=None):
+    """
+    Compute a multidimensional binned statistic for a set of data.
+
+    This is a generalization of a histogramdd function.  A histogram divides
+    the space into bins, and returns the count of the number of points in
+    each bin.  This function allows the computation of the sum, mean, median,
+    or other statistic of the values within each bin.
+
+    Parameters
+    ----------
+    sample : array_like
+        Data to histogram passed as a sequence of N arrays of length D, or
+        as an (N,D) array.
+    values : (N,) array_like or list of (N,) array_like
+        The data on which the statistic will be computed.  This must be
+        the same shape as `sample`, or a list of sequences - each with the
+        same shape as `sample`.  If `values` is such a list, the statistic
+        will be computed on each independently.
+    statistic : string or callable, optional
+        The statistic to compute (default is 'mean').
+        The following statistics are available:
+
+          * 'mean' : compute the mean of values for points within each bin.
+            Empty bins will be represented by NaN.
+          * 'median' : compute the median of values for points within each
+            bin. Empty bins will be represented by NaN.
+          * 'count' : compute the count of points within each bin.  This is
+            identical to an unweighted histogram.  `values` array is not
+            referenced.
+          * 'sum' : compute the sum of values for points within each bin.
+            This is identical to a weighted histogram.
+          * 'std' : compute the standard deviation within each bin. This
+            is implicitly calculated with ddof=0. If the number of values
+            within a given bin is 0 or 1, the computed standard deviation value
+            will be 0 for the bin.
+          * 'min' : compute the minimum of values for points within each bin.
+            Empty bins will be represented by NaN.
+          * 'max' : compute the maximum of values for point within each bin.
+            Empty bins will be represented by NaN.
+          * function : a user-defined function which takes a 1D array of
+            values, and outputs a single numerical statistic. This function
+            will be called on the values in each bin.  Empty bins will be
+            represented by function([]), or NaN if this returns an error.
+
+    bins : sequence or positive int, optional
+        The bin specification must be in one of the following forms:
+
+          * A sequence of arrays describing the bin edges along each dimension.
+          * The number of bins for each dimension (nx, ny, ... = bins).
+          * The number of bins for all dimensions (nx = ny = ... = bins).
+    range : sequence, optional
+        A sequence of lower and upper bin edges to be used if the edges are
+        not given explicitly in `bins`. Defaults to the minimum and maximum
+        values along each dimension.
+    expand_binnumbers : bool, optional
+        'False' (default): the returned `binnumber` is a shape (N,) array of
+        linearized bin indices.
+        'True': the returned `binnumber` is 'unraveled' into a shape (D,N)
+        ndarray, where each row gives the bin numbers in the corresponding
+        dimension.
+        See the `binnumber` returned value, and the `Examples` section of
+        `binned_statistic_2d`.
+    binned_statistic_result : binnedStatisticddResult
+        Result of a previous call to the function in order to reuse bin edges
+        and bin numbers with new values and/or a different statistic.
+        To reuse bin numbers, `expand_binnumbers` must have been set to False
+        (the default)
+
+        .. versionadded:: 0.17.0
+
+    Returns
+    -------
+    statistic : ndarray, shape(nx1, nx2, nx3,...)
+        The values of the selected statistic in each two-dimensional bin.
+    bin_edges : list of ndarrays
+        A list of D arrays describing the (nxi + 1) bin edges for each
+        dimension.
+    binnumber : (N,) array of ints or (D,N) ndarray of ints
+        This assigns to each element of `sample` an integer that represents the
+        bin in which this observation falls.  The representation depends on the
+        `expand_binnumbers` argument.  See `Notes` for details.
+
+
+    See Also
+    --------
+    numpy.digitize, numpy.histogramdd, binned_statistic, binned_statistic_2d
+
+    Notes
+    -----
+    Binedges:
+    All but the last (righthand-most) bin is half-open in each dimension.  In
+    other words, if `bins` is ``[1, 2, 3, 4]``, then the first bin is
+    ``[1, 2)`` (including 1, but excluding 2) and the second ``[2, 3)``.  The
+    last bin, however, is ``[3, 4]``, which *includes* 4.
+
+    `binnumber`:
+    This returned argument assigns to each element of `sample` an integer that
+    represents the bin in which it belongs.  The representation depends on the
+    `expand_binnumbers` argument. If 'False' (default): The returned
+    `binnumber` is a shape (N,) array of linearized indices mapping each
+    element of `sample` to its corresponding bin (using row-major ordering).
+    If 'True': The returned `binnumber` is a shape (D,N) ndarray where
+    each row indicates bin placements for each dimension respectively.  In each
+    dimension, a binnumber of `i` means the corresponding value is between
+    (bin_edges[D][i-1], bin_edges[D][i]), for each dimension 'D'.
+
+    .. versionadded:: 0.11.0
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy import stats
+    >>> import matplotlib.pyplot as plt
+    >>> from mpl_toolkits.mplot3d import Axes3D
+
+    Take an array of 600 (x, y) coordinates as an example.
+    `binned_statistic_dd` can handle arrays of higher dimension `D`. But a plot
+    of dimension `D+1` is required.
+
+    >>> mu = np.array([0., 1.])
+    >>> sigma = np.array([[1., -0.5],[-0.5, 1.5]])
+    >>> multinormal = stats.multivariate_normal(mu, sigma)
+    >>> data = multinormal.rvs(size=600, random_state=235412)
+    >>> data.shape
+    (600, 2)
+
+    Create bins and count how many arrays fall in each bin:
+
+    >>> N = 60
+    >>> x = np.linspace(-3, 3, N)
+    >>> y = np.linspace(-3, 4, N)
+    >>> ret = stats.binned_statistic_dd(data, np.arange(600), bins=[x, y],
+    ...                                 statistic='count')
+    >>> bincounts = ret.statistic
+
+    Set the volume and the location of bars:
+
+    >>> dx = x[1] - x[0]
+    >>> dy = y[1] - y[0]
+    >>> x, y = np.meshgrid(x[:-1]+dx/2, y[:-1]+dy/2)
+    >>> z = 0
+
+    >>> bincounts = bincounts.ravel()
+    >>> x = x.ravel()
+    >>> y = y.ravel()
+
+    >>> fig = plt.figure()
+    >>> ax = fig.add_subplot(111, projection='3d')
+    >>> with np.errstate(divide='ignore'):   # silence random axes3d warning
+    ...     ax.bar3d(x, y, z, dx, dy, bincounts)
+
+    Reuse bin numbers and bin edges with new values:
+
+    >>> ret2 = stats.binned_statistic_dd(data, -np.arange(600),
+    ...                                  binned_statistic_result=ret,
+    ...                                  statistic='mean')
+    """
+    known_stats = ['mean', 'median', 'count', 'sum', 'std', 'min', 'max']
+    if not callable(statistic) and statistic not in known_stats:
+        raise ValueError('invalid statistic %r' % (statistic,))
+
+    try:
+        bins = index(bins)
+    except TypeError:
+        # bins is not an integer
+        pass
+    # If bins was an integer-like object, now it is an actual Python int.
+
+    # NOTE: for _bin_edges(), see e.g. gh-11365
+    if isinstance(bins, int) and not np.isfinite(sample).all():
+        raise ValueError('%r contains non-finite values.' % (sample,))
+
+    # `Ndim` is the number of dimensions (e.g. `2` for `binned_statistic_2d`)
+    # `Dlen` is the length of elements along each dimension.
+    # This code is based on np.histogramdd
+    try:
+        # `sample` is an ND-array.
+        Dlen, Ndim = sample.shape
+    except (AttributeError, ValueError):
+        # `sample` is a sequence of 1D arrays.
+        sample = np.atleast_2d(sample).T
+        Dlen, Ndim = sample.shape
+
+    # Store initial shape of `values` to preserve it in the output
+    values = np.asarray(values)
+    input_shape = list(values.shape)
+    # Make sure that `values` is 2D to iterate over rows
+    values = np.atleast_2d(values)
+    Vdim, Vlen = values.shape
+
+    # Make sure `values` match `sample`
+    if statistic != 'count' and Vlen != Dlen:
+        raise AttributeError('The number of `values` elements must match the '
+                             'length of each `sample` dimension.')
+
+    try:
+        M = len(bins)
+        if M != Ndim:
+            raise AttributeError('The dimension of bins must be equal '
+                                 'to the dimension of the sample x.')
+    except TypeError:
+        bins = Ndim * [bins]
+
+    if binned_statistic_result is None:
+        nbin, edges, dedges = _bin_edges(sample, bins, range)
+        binnumbers = _bin_numbers(sample, nbin, edges, dedges)
+    else:
+        edges = binned_statistic_result.bin_edges
+        nbin = np.array([len(edges[i]) + 1 for i in builtins.range(Ndim)])
+        # +1 for outlier bins
+        dedges = [np.diff(edges[i]) for i in builtins.range(Ndim)]
+        binnumbers = binned_statistic_result.binnumber
+
+    # Avoid overflow with double precision. Complex `values` -> `complex128`.
+    result_type = np.result_type(values, np.float64)
+    result = np.empty([Vdim, nbin.prod()], dtype=result_type)
+
+    if statistic in {'mean', np.mean}:
+        result.fill(np.nan)
+        flatcount = _bincount(binnumbers, None)
+        a = flatcount.nonzero()
+        for vv in builtins.range(Vdim):
+            flatsum = _bincount(binnumbers, values[vv])
+            result[vv, a] = flatsum[a] / flatcount[a]
+    elif statistic in {'std', np.std}:
+        result.fill(np.nan)
+        flatcount = _bincount(binnumbers, None)
+        a = flatcount.nonzero()
+        for vv in builtins.range(Vdim):
+            flatsum = _bincount(binnumbers, values[vv])
+            delta = values[vv] - flatsum[binnumbers] / flatcount[binnumbers]
+            std = np.sqrt(
+                _bincount(binnumbers, delta*np.conj(delta))[a] / flatcount[a]
+            )
+            result[vv, a] = std
+        result = np.real(result)
+    elif statistic == 'count':
+        result = np.empty([Vdim, nbin.prod()], dtype=np.float64)
+        result.fill(0)
+        flatcount = _bincount(binnumbers, None)
+        a = np.arange(len(flatcount))
+        result[:, a] = flatcount[np.newaxis, :]
+    elif statistic in {'sum', np.sum}:
+        result.fill(0)
+        for vv in builtins.range(Vdim):
+            flatsum = _bincount(binnumbers, values[vv])
+            a = np.arange(len(flatsum))
+            result[vv, a] = flatsum
+    elif statistic in {'median', np.median}:
+        result.fill(np.nan)
+        for vv in builtins.range(Vdim):
+            i = np.lexsort((values[vv], binnumbers))
+            _, j, counts = np.unique(binnumbers[i],
+                                     return_index=True, return_counts=True)
+            mid = j + (counts - 1) / 2
+            mid_a = values[vv, i][np.floor(mid).astype(int)]
+            mid_b = values[vv, i][np.ceil(mid).astype(int)]
+            medians = (mid_a + mid_b) / 2
+            result[vv, binnumbers[i][j]] = medians
+    elif statistic in {'min', np.min}:
+        result.fill(np.nan)
+        for vv in builtins.range(Vdim):
+            i = np.argsort(values[vv])[::-1]  # Reversed so the min is last
+            result[vv, binnumbers[i]] = values[vv, i]
+    elif statistic in {'max', np.max}:
+        result.fill(np.nan)
+        for vv in builtins.range(Vdim):
+            i = np.argsort(values[vv])
+            result[vv, binnumbers[i]] = values[vv, i]
+    elif callable(statistic):
+        with np.errstate(invalid='ignore'), suppress_warnings() as sup:
+            sup.filter(RuntimeWarning)
+            try:
+                null = statistic([])
+            except Exception:
+                null = np.nan
+        if np.iscomplexobj(null):
+            result = result.astype(np.complex128)
+        result.fill(null)
+        try:
+            _calc_binned_statistic(
+                Vdim, binnumbers, result, values, statistic
+            )
+        except ValueError:
+            result = result.astype(np.complex128)
+            _calc_binned_statistic(
+                Vdim, binnumbers, result, values, statistic
+            )
+
+    # Shape into a proper matrix
+    result = result.reshape(np.append(Vdim, nbin))
+
+    # Remove outliers (indices 0 and -1 for each bin-dimension).
+    core = tuple([slice(None)] + Ndim * [slice(1, -1)])
+    result = result[core]
+
+    # Unravel binnumbers into an ndarray, each row the bins for each dimension
+    if expand_binnumbers and Ndim > 1:
+        binnumbers = np.asarray(np.unravel_index(binnumbers, nbin))
+
+    if np.any(result.shape[1:] != nbin - 2):
+        raise RuntimeError('Internal Shape Error')
+
+    # Reshape to have output (`result`) match input (`values`) shape
+    result = result.reshape(input_shape[:-1] + list(nbin-2))
+
+    return BinnedStatisticddResult(result, edges, binnumbers)
+
+
+def _calc_binned_statistic(Vdim, bin_numbers, result, values, stat_func):
+    unique_bin_numbers = np.unique(bin_numbers)
+    for vv in builtins.range(Vdim):
+        bin_map = _create_binned_data(bin_numbers, unique_bin_numbers,
+                                      values, vv)
+        for i in unique_bin_numbers:
+            stat = stat_func(np.array(bin_map[i]))
+            if np.iscomplexobj(stat) and not np.iscomplexobj(result):
+                raise ValueError("The statistic function returns complex ")
+            result[vv, i] = stat
+
+
+def _create_binned_data(bin_numbers, unique_bin_numbers, values, vv):
+    """ Create hashmap of bin ids to values in bins
+    key: bin number
+    value: list of binned data
+    """
+    bin_map = dict()
+    for i in unique_bin_numbers:
+        bin_map[i] = []
+    for i in builtins.range(len(bin_numbers)):
+        bin_map[bin_numbers[i]].append(values[vv, i])
+    return bin_map
+
+
+def _bin_edges(sample, bins=None, range=None):
+    """ Create edge arrays
+    """
+    Dlen, Ndim = sample.shape
+
+    nbin = np.empty(Ndim, int)    # Number of bins in each dimension
+    edges = Ndim * [None]         # Bin edges for each dim (will be 2D array)
+    dedges = Ndim * [None]        # Spacing between edges (will be 2D array)
+
+    # Select range for each dimension
+    # Used only if number of bins is given.
+    if range is None:
+        smin = np.atleast_1d(np.array(sample.min(axis=0), float))
+        smax = np.atleast_1d(np.array(sample.max(axis=0), float))
+    else:
+        if len(range) != Ndim:
+            raise ValueError(
+                f"range given for {len(range)} dimensions; {Ndim} required")
+        smin = np.empty(Ndim)
+        smax = np.empty(Ndim)
+        for i in builtins.range(Ndim):
+            if range[i][1] < range[i][0]:
+                raise ValueError(
+                    "In {}range, start must be <= stop".format(
+                        f"dimension {i + 1} of " if Ndim > 1 else ""))
+            smin[i], smax[i] = range[i]
+
+    # Make sure the bins have a finite width.
+    for i in builtins.range(len(smin)):
+        if smin[i] == smax[i]:
+            smin[i] = smin[i] - .5
+            smax[i] = smax[i] + .5
+
+    # Preserve sample floating point precision in bin edges
+    edges_dtype = (sample.dtype if np.issubdtype(sample.dtype, np.floating)
+                   else float)
+
+    # Create edge arrays
+    for i in builtins.range(Ndim):
+        if np.isscalar(bins[i]):
+            nbin[i] = bins[i] + 2  # +2 for outlier bins
+            edges[i] = np.linspace(smin[i], smax[i], nbin[i] - 1,
+                                   dtype=edges_dtype)
+        else:
+            edges[i] = np.asarray(bins[i], edges_dtype)
+            nbin[i] = len(edges[i]) + 1  # +1 for outlier bins
+        dedges[i] = np.diff(edges[i])
+
+    nbin = np.asarray(nbin)
+
+    return nbin, edges, dedges
+
+
+def _bin_numbers(sample, nbin, edges, dedges):
+    """Compute the bin number each sample falls into, in each dimension
+    """
+    Dlen, Ndim = sample.shape
+
+    sampBin = [
+        np.digitize(sample[:, i], edges[i])
+        for i in range(Ndim)
+    ]
+
+    # Using `digitize`, values that fall on an edge are put in the right bin.
+    # For the rightmost bin, we want values equal to the right
+    # edge to be counted in the last bin, and not as an outlier.
+    for i in range(Ndim):
+        # Find the rounding precision
+        dedges_min = dedges[i].min()
+        if dedges_min == 0:
+            raise ValueError('The smallest edge difference is numerically 0.')
+        decimal = int(-np.log10(dedges_min)) + 6
+        # Find which points are on the rightmost edge.
+        on_edge = np.where((sample[:, i] >= edges[i][-1]) &
+                           (np.around(sample[:, i], decimal) ==
+                            np.around(edges[i][-1], decimal)))[0]
+        # Shift these points one bin to the left.
+        sampBin[i][on_edge] -= 1
+
+    # Compute the sample indices in the flattened statistic matrix.
+    binnumbers = np.ravel_multi_index(sampBin, nbin)
+
+    return binnumbers

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_binomtest.py

@@ -0,0 +1,375 @@
+from math import sqrt
+import numpy as np
+from scipy._lib._util import _validate_int
+from scipy.optimize import brentq
+from scipy.special import ndtri
+from ._discrete_distns import binom
+from ._common import ConfidenceInterval
+
+
+class BinomTestResult:
+    """
+    Result of `scipy.stats.binomtest`.
+
+    Attributes
+    ----------
+    k : int
+        The number of successes (copied from `binomtest` input).
+    n : int
+        The number of trials (copied from `binomtest` input).
+    alternative : str
+        Indicates the alternative hypothesis specified in the input
+        to `binomtest`.  It will be one of ``'two-sided'``, ``'greater'``,
+        or ``'less'``.
+    statistic: float
+        The estimate of the proportion of successes.
+    pvalue : float
+        The p-value of the hypothesis test.
+
+    """
+    def __init__(self, k, n, alternative, statistic, pvalue):
+        self.k = k
+        self.n = n
+        self.alternative = alternative
+        self.statistic = statistic
+        self.pvalue = pvalue
+
+        # add alias for backward compatibility
+        self.proportion_estimate = statistic
+
+    def __repr__(self):
+        s = ("BinomTestResult("
+             f"k={self.k}, "
+             f"n={self.n}, "
+             f"alternative={self.alternative!r}, "
+             f"statistic={self.statistic}, "
+             f"pvalue={self.pvalue})")
+        return s
+
+    def proportion_ci(self, confidence_level=0.95, method='exact'):
+        """
+        Compute the confidence interval for ``statistic``.
+
+        Parameters
+        ----------
+        confidence_level : float, optional
+            Confidence level for the computed confidence interval
+            of the estimated proportion. Default is 0.95.
+        method : {'exact', 'wilson', 'wilsoncc'}, optional
+            Selects the method used to compute the confidence interval
+            for the estimate of the proportion:
+
+            'exact' :
+                Use the Clopper-Pearson exact method [1]_.
+            'wilson' :
+                Wilson's method, without continuity correction ([2]_, [3]_).
+            'wilsoncc' :
+                Wilson's method, with continuity correction ([2]_, [3]_).
+
+            Default is ``'exact'``.
+
+        Returns
+        -------
+        ci : ``ConfidenceInterval`` object
+            The object has attributes ``low`` and ``high`` that hold the
+            lower and upper bounds of the confidence interval.
+
+        References
+        ----------
+        .. [1] C. J. Clopper and E. S. Pearson, The use of confidence or
+               fiducial limits illustrated in the case of the binomial,
+               Biometrika, Vol. 26, No. 4, pp 404-413 (Dec. 1934).
+        .. [2] E. B. Wilson, Probable inference, the law of succession, and
+               statistical inference, J. Amer. Stat. Assoc., 22, pp 209-212
+               (1927).
+        .. [3] Robert G. Newcombe, Two-sided confidence intervals for the
+               single proportion: comparison of seven methods, Statistics
+               in Medicine, 17, pp 857-872 (1998).
+
+        Examples
+        --------
+        >>> from scipy.stats import binomtest
+        >>> result = binomtest(k=7, n=50, p=0.1)
+        >>> result.statistic
+        0.14
+        >>> result.proportion_ci()
+        ConfidenceInterval(low=0.05819170033997342, high=0.26739600249700846)
+        """
+        if method not in ('exact', 'wilson', 'wilsoncc'):
+            raise ValueError("method must be one of 'exact', 'wilson' or "
+                             "'wilsoncc'.")
+        if not (0 <= confidence_level <= 1):
+            raise ValueError('confidence_level must be in the interval '
+                             '[0, 1].')
+        if method == 'exact':
+            low, high = _binom_exact_conf_int(self.k, self.n,
+                                              confidence_level,
+                                              self.alternative)
+        else:
+            # method is 'wilson' or 'wilsoncc'
+            low, high = _binom_wilson_conf_int(self.k, self.n,
+                                               confidence_level,
+                                               self.alternative,
+                                               correction=method == 'wilsoncc')
+        return ConfidenceInterval(low=low, high=high)
+
+
+def _findp(func):
+    try:
+        p = brentq(func, 0, 1)
+    except RuntimeError:
+        raise RuntimeError('numerical solver failed to converge when '
+                           'computing the confidence limits') from None
+    except ValueError as exc:
+        raise ValueError('brentq raised a ValueError; report this to the '
+                         'SciPy developers') from exc
+    return p
+
+
+def _binom_exact_conf_int(k, n, confidence_level, alternative):
+    """
+    Compute the estimate and confidence interval for the binomial test.
+
+    Returns proportion, prop_low, prop_high
+    """
+    if alternative == 'two-sided':
+        alpha = (1 - confidence_level) / 2
+        if k == 0:
+            plow = 0.0
+        else:
+            plow = _findp(lambda p: binom.sf(k-1, n, p) - alpha)
+        if k == n:
+            phigh = 1.0
+        else:
+            phigh = _findp(lambda p: binom.cdf(k, n, p) - alpha)
+    elif alternative == 'less':
+        alpha = 1 - confidence_level
+        plow = 0.0
+        if k == n:
+            phigh = 1.0
+        else:
+            phigh = _findp(lambda p: binom.cdf(k, n, p) - alpha)
+    elif alternative == 'greater':
+        alpha = 1 - confidence_level
+        if k == 0:
+            plow = 0.0
+        else:
+            plow = _findp(lambda p: binom.sf(k-1, n, p) - alpha)
+        phigh = 1.0
+    return plow, phigh
+
+
+def _binom_wilson_conf_int(k, n, confidence_level, alternative, correction):
+    # This function assumes that the arguments have already been validated.
+    # In particular, `alternative` must be one of 'two-sided', 'less' or
+    # 'greater'.
+    p = k / n
+    if alternative == 'two-sided':
+        z = ndtri(0.5 + 0.5*confidence_level)
+    else:
+        z = ndtri(confidence_level)
+
+    # For reference, the formulas implemented here are from
+    # Newcombe (1998) (ref. [3] in the proportion_ci docstring).
+    denom = 2*(n + z**2)
+    center = (2*n*p + z**2)/denom
+    q = 1 - p
+    if correction:
+        if alternative == 'less' or k == 0:
+            lo = 0.0
+        else:
+            dlo = (1 + z*sqrt(z**2 - 2 - 1/n + 4*p*(n*q + 1))) / denom
+            lo = center - dlo
+        if alternative == 'greater' or k == n:
+            hi = 1.0
+        else:
+            dhi = (1 + z*sqrt(z**2 + 2 - 1/n + 4*p*(n*q - 1))) / denom
+            hi = center + dhi
+    else:
+        delta = z/denom * sqrt(4*n*p*q + z**2)
+        if alternative == 'less' or k == 0:
+            lo = 0.0
+        else:
+            lo = center - delta
+        if alternative == 'greater' or k == n:
+            hi = 1.0
+        else:
+            hi = center + delta
+
+    return lo, hi
+
+
+def binomtest(k, n, p=0.5, alternative='two-sided'):
+    """
+    Perform a test that the probability of success is p.
+
+    The binomial test [1]_ is a test of the null hypothesis that the
+    probability of success in a Bernoulli experiment is `p`.
+
+    Details of the test can be found in many texts on statistics, such
+    as section 24.5 of [2]_.
+
+    Parameters
+    ----------
+    k : int
+        The number of successes.
+    n : int
+        The number of trials.
+    p : float, optional
+        The hypothesized probability of success, i.e. the expected
+        proportion of successes.  The value must be in the interval
+        ``0 <= p <= 1``. The default value is ``p = 0.5``.
+    alternative : {'two-sided', 'greater', 'less'}, optional
+        Indicates the alternative hypothesis. The default value is
+        'two-sided'.
+
+    Returns
+    -------
+    result : `~scipy.stats._result_classes.BinomTestResult` instance
+        The return value is an object with the following attributes:
+
+        k : int
+            The number of successes (copied from `binomtest` input).
+        n : int
+            The number of trials (copied from `binomtest` input).
+        alternative : str
+            Indicates the alternative hypothesis specified in the input
+            to `binomtest`.  It will be one of ``'two-sided'``, ``'greater'``,
+            or ``'less'``.
+        statistic : float
+            The estimate of the proportion of successes.
+        pvalue : float
+            The p-value of the hypothesis test.
+
+        The object has the following methods:
+
+        proportion_ci(confidence_level=0.95, method='exact') :
+            Compute the confidence interval for ``statistic``.
+
+    Notes
+    -----
+    .. versionadded:: 1.7.0
+
+    References
+    ----------
+    .. [1] Binomial test, https://en.wikipedia.org/wiki/Binomial_test
+    .. [2] Jerrold H. Zar, Biostatistical Analysis (fifth edition),
+           Prentice Hall, Upper Saddle River, New Jersey USA (2010)
+
+    Examples
+    --------
+    >>> from scipy.stats import binomtest
+
+    A car manufacturer claims that no more than 10% of their cars are unsafe.
+    15 cars are inspected for safety, 3 were found to be unsafe. Test the
+    manufacturer's claim:
+
+    >>> result = binomtest(3, n=15, p=0.1, alternative='greater')
+    >>> result.pvalue
+    0.18406106910639114
+
+    The null hypothesis cannot be rejected at the 5% level of significance
+    because the returned p-value is greater than the critical value of 5%.
+
+    The test statistic is equal to the estimated proportion, which is simply
+    ``3/15``:
+
+    >>> result.statistic
+    0.2
+
+    We can use the `proportion_ci()` method of the result to compute the
+    confidence interval of the estimate:
+
+    >>> result.proportion_ci(confidence_level=0.95)
+    ConfidenceInterval(low=0.05684686759024681, high=1.0)
+
+    """
+    k = _validate_int(k, 'k', minimum=0)
+    n = _validate_int(n, 'n', minimum=1)
+    if k > n:
+        raise ValueError('k must not be greater than n.')
+
+    if not (0 <= p <= 1):
+        raise ValueError("p must be in range [0,1]")
+
+    if alternative not in ('two-sided', 'less', 'greater'):
+        raise ValueError("alternative not recognized; \n"
+                         "must be 'two-sided', 'less' or 'greater'")
+    if alternative == 'less':
+        pval = binom.cdf(k, n, p)
+    elif alternative == 'greater':
+        pval = binom.sf(k-1, n, p)
+    else:
+        # alternative is 'two-sided'
+        d = binom.pmf(k, n, p)
+        rerr = 1 + 1e-7
+        if k == p * n:
+            # special case as shortcut, would also be handled by `else` below
+            pval = 1.
+        elif k < p * n:
+            ix = _binary_search_for_binom_tst(lambda x1: -binom.pmf(x1, n, p),
+                                              -d*rerr, np.ceil(p * n), n)
+            # y is the number of terms between mode and n that are <= d*rerr.
+            # ix gave us the first term where a(ix) <= d*rerr < a(ix-1)
+            # if the first equality doesn't hold, y=n-ix. Otherwise, we
+            # need to include ix as well as the equality holds. Note that
+            # the equality will hold in very very rare situations due to rerr.
+            y = n - ix + int(d*rerr == binom.pmf(ix, n, p))
+            pval = binom.cdf(k, n, p) + binom.sf(n - y, n, p)
+        else:
+            ix = _binary_search_for_binom_tst(lambda x1: binom.pmf(x1, n, p),
+                                              d*rerr, 0, np.floor(p * n))
+            # y is the number of terms between 0 and mode that are <= d*rerr.
+            # we need to add a 1 to account for the 0 index.
+            # For comparing this with old behavior, see
+            # tst_binary_srch_for_binom_tst method in test_morestats.
+            y = ix + 1
+            pval = binom.cdf(y-1, n, p) + binom.sf(k-1, n, p)
+
+        pval = min(1.0, pval)
+
+    result = BinomTestResult(k=k, n=n, alternative=alternative,
+                             statistic=k/n, pvalue=pval)
+    return result
+
+
+def _binary_search_for_binom_tst(a, d, lo, hi):
+    """
+    Conducts an implicit binary search on a function specified by `a`.
+
+    Meant to be used on the binomial PMF for the case of two-sided tests
+    to obtain the value on the other side of the mode where the tail
+    probability should be computed. The values on either side of
+    the mode are always in order, meaning binary search is applicable.
+
+    Parameters
+    ----------
+    a : callable
+      The function over which to perform binary search. Its values
+      for inputs lo and hi should be in ascending order.
+    d : float
+      The value to search.
+    lo : int
+      The lower end of range to search.
+    hi : int
+      The higher end of the range to search.
+
+    Returns
+    -------
+    int
+      The index, i between lo and hi
+      such that a(i)<=d<a(i+1)
+    """
+    while lo < hi:
+        mid = lo + (hi-lo)//2
+        midval = a(mid)
+        if midval < d:
+            lo = mid+1
+        elif midval > d:
+            hi = mid-1
+        else:
+            return mid
+    if a(lo) <= d:
+        return lo
+    else:
+        return lo-1

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_boost/__init__.py

@@ -0,0 +1,53 @@
+from scipy.stats._boost.beta_ufunc import (
+    _beta_pdf, _beta_cdf, _beta_sf, _beta_ppf,
+    _beta_isf, _beta_mean, _beta_variance,
+    _beta_skewness, _beta_kurtosis_excess,
+)
+
+from scipy.stats._boost.binom_ufunc import (
+    _binom_pdf, _binom_cdf, _binom_sf, _binom_ppf,
+    _binom_isf, _binom_mean, _binom_variance,
+    _binom_skewness, _binom_kurtosis_excess,
+)
+
+from scipy.stats._boost.nbinom_ufunc import (
+    _nbinom_pdf, _nbinom_cdf, _nbinom_sf, _nbinom_ppf,
+    _nbinom_isf, _nbinom_mean, _nbinom_variance,
+    _nbinom_skewness, _nbinom_kurtosis_excess,
+)
+
+from scipy.stats._boost.hypergeom_ufunc import (
+    _hypergeom_pdf, _hypergeom_cdf, _hypergeom_sf, _hypergeom_ppf,
+    _hypergeom_isf, _hypergeom_mean, _hypergeom_variance,
+    _hypergeom_skewness, _hypergeom_kurtosis_excess,
+)
+
+from scipy.stats._boost.ncf_ufunc import (
+    _ncf_pdf, _ncf_cdf, _ncf_sf, _ncf_ppf,
+    _ncf_isf, _ncf_mean, _ncf_variance,
+    _ncf_skewness, _ncf_kurtosis_excess,
+)
+
+from scipy.stats._boost.ncx2_ufunc import (
+    _ncx2_pdf, _ncx2_cdf, _ncx2_sf, _ncx2_ppf,
+    _ncx2_isf, _ncx2_mean, _ncx2_variance,
+    _ncx2_skewness, _ncx2_kurtosis_excess,
+)
+
+from scipy.stats._boost.nct_ufunc import (
+    _nct_pdf, _nct_cdf, _nct_sf, _nct_ppf,
+    _nct_isf, _nct_mean, _nct_variance,
+    _nct_skewness, _nct_kurtosis_excess,
+)
+
+from scipy.stats._boost.skewnorm_ufunc import (
+    _skewnorm_pdf, _skewnorm_cdf, _skewnorm_sf, _skewnorm_ppf,
+    _skewnorm_isf, _skewnorm_mean, _skewnorm_variance,
+    _skewnorm_skewness, _skewnorm_kurtosis_excess,
+)
+
+from scipy.stats._boost.invgauss_ufunc import (
+    _invgauss_pdf, _invgauss_cdf, _invgauss_sf, _invgauss_ppf,
+    _invgauss_isf, _invgauss_mean, _invgauss_variance,
+    _invgauss_skewness, _invgauss_kurtosis_excess,
+)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_common.py

@@ -0,0 +1,6 @@
+
+from collections import namedtuple
+
+
+ConfidenceInterval = namedtuple("ConfidenceInterval", ["low", "high"])
+ConfidenceInterval. __doc__ = "Class for confidence intervals."

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_constants.py

@@ -0,0 +1,34 @@
+"""
+Statistics-related constants.
+
+"""
+import numpy as np
+
+
+# The smallest representable positive number such that 1.0 + _EPS != 1.0.
+_EPS = np.finfo(float).eps
+
+# The largest [in magnitude] usable floating value.
+_XMAX = np.finfo(float).max
+
+# The log of the largest usable floating value; useful for knowing
+# when exp(something) will overflow
+_LOGXMAX = np.log(_XMAX)
+
+# The smallest [in magnitude] usable floating value.
+_XMIN = np.finfo(float).tiny
+
+# -special.psi(1)
+_EULER = 0.577215664901532860606512090082402431042
+
+# special.zeta(3, 1)  Apery's constant
+_ZETA3 = 1.202056903159594285399738161511449990765
+
+# sqrt(pi)
+_SQRT_PI = 1.772453850905516027298167483341145182798
+
+# sqrt(2/pi)
+_SQRT_2_OVER_PI = 0.7978845608028654
+
+# log(sqrt(2/pi))
+_LOG_SQRT_2_OVER_PI = -0.22579135264472744

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_covariance.py

@@ -0,0 +1,629 @@
+from functools import cached_property
+
+import numpy as np
+from scipy import linalg
+from scipy.stats import _multivariate
+
+
+__all__ = ["Covariance"]
+
+
+class Covariance:
+    """
+    Representation of a covariance matrix
+
+    Calculations involving covariance matrices (e.g. data whitening,
+    multivariate normal function evaluation) are often performed more
+    efficiently using a decomposition of the covariance matrix instead of the
+    covariance metrix itself. This class allows the user to construct an
+    object representing a covariance matrix using any of several
+    decompositions and perform calculations using a common interface.
+
+    .. note::
+
+        The `Covariance` class cannot be instantiated directly. Instead, use
+        one of the factory methods (e.g. `Covariance.from_diagonal`).
+
+    Examples
+    --------
+    The `Covariance` class is is used by calling one of its
+    factory methods to create a `Covariance` object, then pass that
+    representation of the `Covariance` matrix as a shape parameter of a
+    multivariate distribution.
+
+    For instance, the multivariate normal distribution can accept an array
+    representing a covariance matrix:
+
+    >>> from scipy import stats
+    >>> import numpy as np
+    >>> d = [1, 2, 3]
+    >>> A = np.diag(d)  # a diagonal covariance matrix
+    >>> x = [4, -2, 5]  # a point of interest
+    >>> dist = stats.multivariate_normal(mean=[0, 0, 0], cov=A)
+    >>> dist.pdf(x)
+    4.9595685102808205e-08
+
+    but the calculations are performed in a very generic way that does not
+    take advantage of any special properties of the covariance matrix. Because
+    our covariance matrix is diagonal, we can use ``Covariance.from_diagonal``
+    to create an object representing the covariance matrix, and
+    `multivariate_normal` can use this to compute the probability density
+    function more efficiently.
+
+    >>> cov = stats.Covariance.from_diagonal(d)
+    >>> dist = stats.multivariate_normal(mean=[0, 0, 0], cov=cov)
+    >>> dist.pdf(x)
+    4.9595685102808205e-08
+
+    """
+    def __init__(self):
+        message = ("The `Covariance` class cannot be instantiated directly. "
+                   "Please use one of the factory methods "
+                   "(e.g. `Covariance.from_diagonal`).")
+        raise NotImplementedError(message)
+
+    @staticmethod
+    def from_diagonal(diagonal):
+        r"""
+        Return a representation of a covariance matrix from its diagonal.
+
+        Parameters
+        ----------
+        diagonal : array_like
+            The diagonal elements of a diagonal matrix.
+
+        Notes
+        -----
+        Let the diagonal elements of a diagonal covariance matrix :math:`D` be
+        stored in the vector :math:`d`.
+
+        When all elements of :math:`d` are strictly positive, whitening of a
+        data point :math:`x` is performed by computing
+        :math:`x \cdot d^{-1/2}`, where the inverse square root can be taken
+        element-wise.
+        :math:`\log\det{D}` is calculated as :math:`-2 \sum(\log{d})`,
+        where the :math:`\log` operation is performed element-wise.
+
+        This `Covariance` class supports singular covariance matrices. When
+        computing ``_log_pdet``, non-positive elements of :math:`d` are
+        ignored. Whitening is not well defined when the point to be whitened
+        does not lie in the span of the columns of the covariance matrix. The
+        convention taken here is to treat the inverse square root of
+        non-positive elements of :math:`d` as zeros.
+
+        Examples
+        --------
+        Prepare a symmetric positive definite covariance matrix ``A`` and a
+        data point ``x``.
+
+        >>> import numpy as np
+        >>> from scipy import stats
+        >>> rng = np.random.default_rng()
+        >>> n = 5
+        >>> A = np.diag(rng.random(n))
+        >>> x = rng.random(size=n)
+
+        Extract the diagonal from ``A`` and create the `Covariance` object.
+
+        >>> d = np.diag(A)
+        >>> cov = stats.Covariance.from_diagonal(d)
+
+        Compare the functionality of the `Covariance` object against a
+        reference implementations.
+
+        >>> res = cov.whiten(x)
+        >>> ref = np.diag(d**-0.5) @ x
+        >>> np.allclose(res, ref)
+        True
+        >>> res = cov.log_pdet
+        >>> ref = np.linalg.slogdet(A)[-1]
+        >>> np.allclose(res, ref)
+        True
+
+        """
+        return CovViaDiagonal(diagonal)
+
+    @staticmethod
+    def from_precision(precision, covariance=None):
+        r"""
+        Return a representation of a covariance from its precision matrix.
+
+        Parameters
+        ----------
+        precision : array_like
+            The precision matrix; that is, the inverse of a square, symmetric,
+            positive definite covariance matrix.
+        covariance : array_like, optional
+            The square, symmetric, positive definite covariance matrix. If not
+            provided, this may need to be calculated (e.g. to evaluate the
+            cumulative distribution function of
+            `scipy.stats.multivariate_normal`) by inverting `precision`.
+
+        Notes
+        -----
+        Let the covariance matrix be :math:`A`, its precision matrix be
+        :math:`P = A^{-1}`, and :math:`L` be the lower Cholesky factor such
+        that :math:`L L^T = P`.
+        Whitening of a data point :math:`x` is performed by computing
+        :math:`x^T L`. :math:`\log\det{A}` is calculated as
+        :math:`-2tr(\log{L})`, where the :math:`\log` operation is performed
+        element-wise.
+
+        This `Covariance` class does not support singular covariance matrices
+        because the precision matrix does not exist for a singular covariance
+        matrix.
+
+        Examples
+        --------
+        Prepare a symmetric positive definite precision matrix ``P`` and a
+        data point ``x``. (If the precision matrix is not already available,
+        consider the other factory methods of the `Covariance` class.)
+
+        >>> import numpy as np
+        >>> from scipy import stats
+        >>> rng = np.random.default_rng()
+        >>> n = 5
+        >>> P = rng.random(size=(n, n))
+        >>> P = P @ P.T  # a precision matrix must be positive definite
+        >>> x = rng.random(size=n)
+
+        Create the `Covariance` object.
+
+        >>> cov = stats.Covariance.from_precision(P)
+
+        Compare the functionality of the `Covariance` object against
+        reference implementations.
+
+        >>> res = cov.whiten(x)
+        >>> ref = x @ np.linalg.cholesky(P)
+        >>> np.allclose(res, ref)
+        True
+        >>> res = cov.log_pdet
+        >>> ref = -np.linalg.slogdet(P)[-1]
+        >>> np.allclose(res, ref)
+        True
+
+        """
+        return CovViaPrecision(precision, covariance)
+
+    @staticmethod
+    def from_cholesky(cholesky):
+        r"""
+        Representation of a covariance provided via the (lower) Cholesky factor
+
+        Parameters
+        ----------
+        cholesky : array_like
+            The lower triangular Cholesky factor of the covariance matrix.
+
+        Notes
+        -----
+        Let the covariance matrix be :math:`A`and :math:`L` be the lower
+        Cholesky factor such that :math:`L L^T = A`.
+        Whitening of a data point :math:`x` is performed by computing
+        :math:`L^{-1} x`. :math:`\log\det{A}` is calculated as
+        :math:`2tr(\log{L})`, where the :math:`\log` operation is performed
+        element-wise.
+
+        This `Covariance` class does not support singular covariance matrices
+        because the Cholesky decomposition does not exist for a singular
+        covariance matrix.
+
+        Examples
+        --------
+        Prepare a symmetric positive definite covariance matrix ``A`` and a
+        data point ``x``.
+
+        >>> import numpy as np
+        >>> from scipy import stats
+        >>> rng = np.random.default_rng()
+        >>> n = 5
+        >>> A = rng.random(size=(n, n))
+        >>> A = A @ A.T  # make the covariance symmetric positive definite
+        >>> x = rng.random(size=n)
+
+        Perform the Cholesky decomposition of ``A`` and create the
+        `Covariance` object.
+
+        >>> L = np.linalg.cholesky(A)
+        >>> cov = stats.Covariance.from_cholesky(L)
+
+        Compare the functionality of the `Covariance` object against
+        reference implementation.
+
+        >>> from scipy.linalg import solve_triangular
+        >>> res = cov.whiten(x)
+        >>> ref = solve_triangular(L, x, lower=True)
+        >>> np.allclose(res, ref)
+        True
+        >>> res = cov.log_pdet
+        >>> ref = np.linalg.slogdet(A)[-1]
+        >>> np.allclose(res, ref)
+        True
+
+        """
+        return CovViaCholesky(cholesky)
+
+    @staticmethod
+    def from_eigendecomposition(eigendecomposition):
+        r"""
+        Representation of a covariance provided via eigendecomposition
+
+        Parameters
+        ----------
+        eigendecomposition : sequence
+            A sequence (nominally a tuple) containing the eigenvalue and
+            eigenvector arrays as computed by `scipy.linalg.eigh` or
+            `numpy.linalg.eigh`.
+
+        Notes
+        -----
+        Let the covariance matrix be :math:`A`, let :math:`V` be matrix of
+        eigenvectors, and let :math:`W` be the diagonal matrix of eigenvalues
+        such that `V W V^T = A`.
+
+        When all of the eigenvalues are strictly positive, whitening of a
+        data point :math:`x` is performed by computing
+        :math:`x^T (V W^{-1/2})`, where the inverse square root can be taken
+        element-wise.
+        :math:`\log\det{A}` is calculated as  :math:`tr(\log{W})`,
+        where the :math:`\log` operation is performed element-wise.
+
+        This `Covariance` class supports singular covariance matrices. When
+        computing ``_log_pdet``, non-positive eigenvalues are ignored.
+        Whitening is not well defined when the point to be whitened
+        does not lie in the span of the columns of the covariance matrix. The
+        convention taken here is to treat the inverse square root of
+        non-positive eigenvalues as zeros.
+
+        Examples
+        --------
+        Prepare a symmetric positive definite covariance matrix ``A`` and a
+        data point ``x``.
+
+        >>> import numpy as np
+        >>> from scipy import stats
+        >>> rng = np.random.default_rng()
+        >>> n = 5
+        >>> A = rng.random(size=(n, n))
+        >>> A = A @ A.T  # make the covariance symmetric positive definite
+        >>> x = rng.random(size=n)
+
+        Perform the eigendecomposition of ``A`` and create the `Covariance`
+        object.
+
+        >>> w, v = np.linalg.eigh(A)
+        >>> cov = stats.Covariance.from_eigendecomposition((w, v))
+
+        Compare the functionality of the `Covariance` object against
+        reference implementations.
+
+        >>> res = cov.whiten(x)
+        >>> ref = x @ (v @ np.diag(w**-0.5))
+        >>> np.allclose(res, ref)
+        True
+        >>> res = cov.log_pdet
+        >>> ref = np.linalg.slogdet(A)[-1]
+        >>> np.allclose(res, ref)
+        True
+
+        """
+        return CovViaEigendecomposition(eigendecomposition)
+
+    def whiten(self, x):
+        """
+        Perform a whitening transformation on data.
+
+        "Whitening" ("white" as in "white noise", in which each frequency has
+        equal magnitude) transforms a set of random variables into a new set of
+        random variables with unit-diagonal covariance. When a whitening
+        transform is applied to a sample of points distributed according to
+        a multivariate normal distribution with zero mean, the covariance of
+        the transformed sample is approximately the identity matrix.
+
+        Parameters
+        ----------
+        x : array_like
+            An array of points. The last dimension must correspond with the
+            dimensionality of the space, i.e., the number of columns in the
+            covariance matrix.
+
+        Returns
+        -------
+        x_ : array_like
+            The transformed array of points.
+
+        References
+        ----------
+        .. [1] "Whitening Transformation". Wikipedia.
+               https://en.wikipedia.org/wiki/Whitening_transformation
+        .. [2] Novak, Lukas, and Miroslav Vorechovsky. "Generalization of
+               coloring linear transformation". Transactions of VSB 18.2
+               (2018): 31-35. :doi:`10.31490/tces-2018-0013`
+
+        Examples
+        --------
+        >>> import numpy as np
+        >>> from scipy import stats
+        >>> rng = np.random.default_rng()
+        >>> n = 3
+        >>> A = rng.random(size=(n, n))
+        >>> cov_array = A @ A.T  # make matrix symmetric positive definite
+        >>> precision = np.linalg.inv(cov_array)
+        >>> cov_object = stats.Covariance.from_precision(precision)
+        >>> x = rng.multivariate_normal(np.zeros(n), cov_array, size=(10000))
+        >>> x_ = cov_object.whiten(x)
+        >>> np.cov(x_, rowvar=False)  # near-identity covariance
+        array([[0.97862122, 0.00893147, 0.02430451],
+               [0.00893147, 0.96719062, 0.02201312],
+               [0.02430451, 0.02201312, 0.99206881]])
+
+        """
+        return self._whiten(np.asarray(x))
+
+    def colorize(self, x):
+        """
+        Perform a colorizing transformation on data.
+
+        "Colorizing" ("color" as in "colored noise", in which different
+        frequencies may have different magnitudes) transforms a set of
+        uncorrelated random variables into a new set of random variables with
+        the desired covariance. When a coloring transform is applied to a
+        sample of points distributed according to a multivariate normal
+        distribution with identity covariance and zero mean, the covariance of
+        the transformed sample is approximately the covariance matrix used
+        in the coloring transform.
+
+        Parameters
+        ----------
+        x : array_like
+            An array of points. The last dimension must correspond with the
+            dimensionality of the space, i.e., the number of columns in the
+            covariance matrix.
+
+        Returns
+        -------
+        x_ : array_like
+            The transformed array of points.
+
+        References
+        ----------
+        .. [1] "Whitening Transformation". Wikipedia.
+               https://en.wikipedia.org/wiki/Whitening_transformation
+        .. [2] Novak, Lukas, and Miroslav Vorechovsky. "Generalization of
+               coloring linear transformation". Transactions of VSB 18.2
+               (2018): 31-35. :doi:`10.31490/tces-2018-0013`
+
+        Examples
+        --------
+        >>> import numpy as np
+        >>> from scipy import stats
+        >>> rng = np.random.default_rng(1638083107694713882823079058616272161)
+        >>> n = 3
+        >>> A = rng.random(size=(n, n))
+        >>> cov_array = A @ A.T  # make matrix symmetric positive definite
+        >>> cholesky = np.linalg.cholesky(cov_array)
+        >>> cov_object = stats.Covariance.from_cholesky(cholesky)
+        >>> x = rng.multivariate_normal(np.zeros(n), np.eye(n), size=(10000))
+        >>> x_ = cov_object.colorize(x)
+        >>> cov_data = np.cov(x_, rowvar=False)
+        >>> np.allclose(cov_data, cov_array, rtol=3e-2)
+        True
+        """
+        return self._colorize(np.asarray(x))
+
+    @property
+    def log_pdet(self):
+        """
+        Log of the pseudo-determinant of the covariance matrix
+        """
+        return np.array(self._log_pdet, dtype=float)[()]
+
+    @property
+    def rank(self):
+        """
+        Rank of the covariance matrix
+        """
+        return np.array(self._rank, dtype=int)[()]
+
+    @property
+    def covariance(self):
+        """
+        Explicit representation of the covariance matrix
+        """
+        return self._covariance
+
+    @property
+    def shape(self):
+        """
+        Shape of the covariance array
+        """
+        return self._shape
+
+    def _validate_matrix(self, A, name):
+        A = np.atleast_2d(A)
+        m, n = A.shape[-2:]
+        if m != n or A.ndim != 2 or not (np.issubdtype(A.dtype, np.integer) or
+                                         np.issubdtype(A.dtype, np.floating)):
+            message = (f"The input `{name}` must be a square, "
+                       "two-dimensional array of real numbers.")
+            raise ValueError(message)
+        return A
+
+    def _validate_vector(self, A, name):
+        A = np.atleast_1d(A)
+        if A.ndim != 1 or not (np.issubdtype(A.dtype, np.integer) or
+                               np.issubdtype(A.dtype, np.floating)):
+            message = (f"The input `{name}` must be a one-dimensional array "
+                       "of real numbers.")
+            raise ValueError(message)
+        return A
+
+
+class CovViaPrecision(Covariance):
+
+    def __init__(self, precision, covariance=None):
+        precision = self._validate_matrix(precision, 'precision')
+        if covariance is not None:
+            covariance = self._validate_matrix(covariance, 'covariance')
+            message = "`precision.shape` must equal `covariance.shape`."
+            if precision.shape != covariance.shape:
+                raise ValueError(message)
+
+        self._chol_P = np.linalg.cholesky(precision)
+        self._log_pdet = -2*np.log(np.diag(self._chol_P)).sum(axis=-1)
+        self._rank = precision.shape[-1]  # must be full rank if invertible
+        self._precision = precision
+        self._cov_matrix = covariance
+        self._shape = precision.shape
+        self._allow_singular = False
+
+    def _whiten(self, x):
+        return x @ self._chol_P
+
+    @cached_property
+    def _covariance(self):
+        n = self._shape[-1]
+        return (linalg.cho_solve((self._chol_P, True), np.eye(n))
+                if self._cov_matrix is None else self._cov_matrix)
+
+    def _colorize(self, x):
+        return linalg.solve_triangular(self._chol_P.T, x.T, lower=False).T
+
+
+def _dot_diag(x, d):
+    # If d were a full diagonal matrix, x @ d would always do what we want.
+    # Special treatment is needed for n-dimensional `d` in which each row
+    # includes only the diagonal elements of a covariance matrix.
+    return x * d if x.ndim < 2 else x * np.expand_dims(d, -2)
+
+
+class CovViaDiagonal(Covariance):
+
+    def __init__(self, diagonal):
+        diagonal = self._validate_vector(diagonal, 'diagonal')
+
+        i_zero = diagonal <= 0
+        positive_diagonal = np.array(diagonal, dtype=np.float64)
+
+        positive_diagonal[i_zero] = 1  # ones don't affect determinant
+        self._log_pdet = np.sum(np.log(positive_diagonal), axis=-1)
+
+        psuedo_reciprocals = 1 / np.sqrt(positive_diagonal)
+        psuedo_reciprocals[i_zero] = 0
+
+        self._sqrt_diagonal = np.sqrt(diagonal)
+        self._LP = psuedo_reciprocals
+        self._rank = positive_diagonal.shape[-1] - i_zero.sum(axis=-1)
+        self._covariance = np.apply_along_axis(np.diag, -1, diagonal)
+        self._i_zero = i_zero
+        self._shape = self._covariance.shape
+        self._allow_singular = True
+
+    def _whiten(self, x):
+        return _dot_diag(x, self._LP)
+
+    def _colorize(self, x):
+        return _dot_diag(x, self._sqrt_diagonal)
+
+    def _support_mask(self, x):
+        """
+        Check whether x lies in the support of the distribution.
+        """
+        return ~np.any(_dot_diag(x, self._i_zero), axis=-1)
+
+
+class CovViaCholesky(Covariance):
+
+    def __init__(self, cholesky):
+        L = self._validate_matrix(cholesky, 'cholesky')
+
+        self._factor = L
+        self._log_pdet = 2*np.log(np.diag(self._factor)).sum(axis=-1)
+        self._rank = L.shape[-1]  # must be full rank for cholesky
+        self._covariance = L @ L.T
+        self._shape = L.shape
+        self._allow_singular = False
+
+    def _whiten(self, x):
+        res = linalg.solve_triangular(self._factor, x.T, lower=True).T
+        return res
+
+    def _colorize(self, x):
+        return x @ self._factor.T
+
+
+class CovViaEigendecomposition(Covariance):
+
+    def __init__(self, eigendecomposition):
+        eigenvalues, eigenvectors = eigendecomposition
+        eigenvalues = self._validate_vector(eigenvalues, 'eigenvalues')
+        eigenvectors = self._validate_matrix(eigenvectors, 'eigenvectors')
+        message = ("The shapes of `eigenvalues` and `eigenvectors` "
+                   "must be compatible.")
+        try:
+            eigenvalues = np.expand_dims(eigenvalues, -2)
+            eigenvectors, eigenvalues = np.broadcast_arrays(eigenvectors,
+                                                            eigenvalues)
+            eigenvalues = eigenvalues[..., 0, :]
+        except ValueError:
+            raise ValueError(message)
+
+        i_zero = eigenvalues <= 0
+        positive_eigenvalues = np.array(eigenvalues, dtype=np.float64)
+
+        positive_eigenvalues[i_zero] = 1  # ones don't affect determinant
+        self._log_pdet = np.sum(np.log(positive_eigenvalues), axis=-1)
+
+        psuedo_reciprocals = 1 / np.sqrt(positive_eigenvalues)
+        psuedo_reciprocals[i_zero] = 0
+
+        self._LP = eigenvectors * psuedo_reciprocals
+        self._LA = eigenvectors * np.sqrt(positive_eigenvalues)
+        self._rank = positive_eigenvalues.shape[-1] - i_zero.sum(axis=-1)
+        self._w = eigenvalues
+        self._v = eigenvectors
+        self._shape = eigenvectors.shape
+        self._null_basis = eigenvectors * i_zero
+        # This is only used for `_support_mask`, not to decide whether
+        # the covariance is singular or not.
+        self._eps = _multivariate._eigvalsh_to_eps(eigenvalues) * 10**3
+        self._allow_singular = True
+
+    def _whiten(self, x):
+        return x @ self._LP
+
+    def _colorize(self, x):
+        return x @ self._LA.T
+
+    @cached_property
+    def _covariance(self):
+        return (self._v * self._w) @ self._v.T
+
+    def _support_mask(self, x):
+        """
+        Check whether x lies in the support of the distribution.
+        """
+        residual = np.linalg.norm(x @ self._null_basis, axis=-1)
+        in_support = residual < self._eps
+        return in_support
+
+class CovViaPSD(Covariance):
+    """
+    Representation of a covariance provided via an instance of _PSD
+    """
+
+    def __init__(self, psd):
+        self._LP = psd.U
+        self._log_pdet = psd.log_pdet
+        self._rank = psd.rank
+        self._covariance = psd._M
+        self._shape = psd._M.shape
+        self._psd = psd
+        self._allow_singular = False  # by default
+
+    def _whiten(self, x):
+        return x @ self._LP
+
+    def _support_mask(self, x):
+        return self._psd._support_mask(x)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_crosstab.py

@@ -0,0 +1,203 @@
+import numpy as np
+from scipy.sparse import coo_matrix
+from scipy._lib._bunch import _make_tuple_bunch
+
+
+CrosstabResult = _make_tuple_bunch(
+    "CrosstabResult", ["elements", "count"]
+)
+
+def crosstab(*args, levels=None, sparse=False):
+    """
+    Return table of counts for each possible unique combination in ``*args``.
+
+    When ``len(args) > 1``, the array computed by this function is
+    often referred to as a *contingency table* [1]_.
+
+    The arguments must be sequences with the same length.  The second return
+    value, `count`, is an integer array with ``len(args)`` dimensions.  If
+    `levels` is None, the shape of `count` is ``(n0, n1, ...)``, where ``nk``
+    is the number of unique elements in ``args[k]``.
+
+    Parameters
+    ----------
+    *args : sequences
+        A sequence of sequences whose unique aligned elements are to be
+        counted.  The sequences in args must all be the same length.
+    levels : sequence, optional
+        If `levels` is given, it must be a sequence that is the same length as
+        `args`.  Each element in `levels` is either a sequence or None.  If it
+        is a sequence, it gives the values in the corresponding sequence in
+        `args` that are to be counted.  If any value in the sequences in `args`
+        does not occur in the corresponding sequence in `levels`, that value
+        is ignored and not counted in the returned array `count`.  The default
+        value of `levels` for ``args[i]`` is ``np.unique(args[i])``
+    sparse : bool, optional
+        If True, return a sparse matrix.  The matrix will be an instance of
+        the `scipy.sparse.coo_matrix` class.  Because SciPy's sparse matrices
+        must be 2-d, only two input sequences are allowed when `sparse` is
+        True.  Default is False.
+
+    Returns
+    -------
+    res : CrosstabResult
+        An object containing the following attributes:
+
+        elements : tuple of numpy.ndarrays.
+            Tuple of length ``len(args)`` containing the arrays of elements
+            that are counted in `count`.  These can be interpreted as the
+            labels of the corresponding dimensions of `count`. If `levels` was
+            given, then if ``levels[i]`` is not None, ``elements[i]`` will
+            hold the values given in ``levels[i]``.
+        count : numpy.ndarray or scipy.sparse.coo_matrix
+            Counts of the unique elements in ``zip(*args)``, stored in an
+            array. Also known as a *contingency table* when ``len(args) > 1``.
+
+    See Also
+    --------
+    numpy.unique
+
+    Notes
+    -----
+    .. versionadded:: 1.7.0
+
+    References
+    ----------
+    .. [1] "Contingency table", http://en.wikipedia.org/wiki/Contingency_table
+
+    Examples
+    --------
+    >>> from scipy.stats.contingency import crosstab
+
+    Given the lists `a` and `x`, create a contingency table that counts the
+    frequencies of the corresponding pairs.
+
+    >>> a = ['A', 'B', 'A', 'A', 'B', 'B', 'A', 'A', 'B', 'B']
+    >>> x = ['X', 'X', 'X', 'Y', 'Z', 'Z', 'Y', 'Y', 'Z', 'Z']
+    >>> res = crosstab(a, x)
+    >>> avals, xvals = res.elements
+    >>> avals
+    array(['A', 'B'], dtype='<U1')
+    >>> xvals
+    array(['X', 'Y', 'Z'], dtype='<U1')
+    >>> res.count
+    array([[2, 3, 0],
+           [1, 0, 4]])
+
+    So `('A', 'X')` occurs twice, `('A', 'Y')` occurs three times, etc.
+
+    Higher dimensional contingency tables can be created.
+
+    >>> p = [0, 0, 0, 0, 1, 1, 1, 0, 0, 1]
+    >>> res = crosstab(a, x, p)
+    >>> res.count
+    array([[[2, 0],
+            [2, 1],
+            [0, 0]],
+           [[1, 0],
+            [0, 0],
+            [1, 3]]])
+    >>> res.count.shape
+    (2, 3, 2)
+
+    The values to be counted can be set by using the `levels` argument.
+    It allows the elements of interest in each input sequence to be
+    given explicitly instead finding the unique elements of the sequence.
+
+    For example, suppose one of the arguments is an array containing the
+    answers to a survey question, with integer values 1 to 4.  Even if the
+    value 1 does not occur in the data, we want an entry for it in the table.
+
+    >>> q1 = [2, 3, 3, 2, 4, 4, 2, 3, 4, 4, 4, 3, 3, 3, 4]  # 1 does not occur.
+    >>> q2 = [4, 4, 2, 2, 2, 4, 1, 1, 2, 2, 4, 2, 2, 2, 4]  # 3 does not occur.
+    >>> options = [1, 2, 3, 4]
+    >>> res = crosstab(q1, q2, levels=(options, options))
+    >>> res.count
+    array([[0, 0, 0, 0],
+           [1, 1, 0, 1],
+           [1, 4, 0, 1],
+           [0, 3, 0, 3]])
+
+    If `levels` is given, but an element of `levels` is None, the unique values
+    of the corresponding argument are used. For example,
+
+    >>> res = crosstab(q1, q2, levels=(None, options))
+    >>> res.elements
+    [array([2, 3, 4]), [1, 2, 3, 4]]
+    >>> res.count
+    array([[1, 1, 0, 1],
+           [1, 4, 0, 1],
+           [0, 3, 0, 3]])
+
+    If we want to ignore the pairs where 4 occurs in ``q2``, we can
+    give just the values [1, 2] to `levels`, and the 4 will be ignored:
+
+    >>> res = crosstab(q1, q2, levels=(None, [1, 2]))
+    >>> res.elements
+    [array([2, 3, 4]), [1, 2]]
+    >>> res.count
+    array([[1, 1],
+           [1, 4],
+           [0, 3]])
+
+    Finally, let's repeat the first example, but return a sparse matrix:
+
+    >>> res = crosstab(a, x, sparse=True)
+    >>> res.count
+    <2x3 sparse matrix of type '<class 'numpy.int64'>'
+            with 4 stored elements in COOrdinate format>
+    >>> res.count.A
+    array([[2, 3, 0],
+           [1, 0, 4]])
+
+    """
+    nargs = len(args)
+    if nargs == 0:
+        raise TypeError("At least one input sequence is required.")
+
+    len0 = len(args[0])
+    if not all(len(a) == len0 for a in args[1:]):
+        raise ValueError("All input sequences must have the same length.")
+
+    if sparse and nargs != 2:
+        raise ValueError("When `sparse` is True, only two input sequences "
+                         "are allowed.")
+
+    if levels is None:
+        # Call np.unique with return_inverse=True on each argument.
+        actual_levels, indices = zip(*[np.unique(a, return_inverse=True)
+                                       for a in args])
+    else:
+        # `levels` is not None...
+        if len(levels) != nargs:
+            raise ValueError('len(levels) must equal the number of input '
+                             'sequences')
+
+        args = [np.asarray(arg) for arg in args]
+        mask = np.zeros((nargs, len0), dtype=np.bool_)
+        inv = np.zeros((nargs, len0), dtype=np.intp)
+        actual_levels = []
+        for k, (levels_list, arg) in enumerate(zip(levels, args)):
+            if levels_list is None:
+                levels_list, inv[k, :] = np.unique(arg, return_inverse=True)
+                mask[k, :] = True
+            else:
+                q = arg == np.asarray(levels_list).reshape(-1, 1)
+                mask[k, :] = np.any(q, axis=0)
+                qnz = q.T.nonzero()
+                inv[k, qnz[0]] = qnz[1]
+            actual_levels.append(levels_list)
+
+        mask_all = mask.all(axis=0)
+        indices = tuple(inv[:, mask_all])
+
+    if sparse:
+        count = coo_matrix((np.ones(len(indices[0]), dtype=int),
+                            (indices[0], indices[1])))
+        count.sum_duplicates()
+    else:
+        shape = [len(u) for u in actual_levels]
+        count = np.zeros(shape, dtype=int)
+        np.add.at(count, indices, 1)
+
+    return CrosstabResult(actual_levels, count)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_distr_params.py

@@ -0,0 +1,281 @@
+"""
+Sane parameters for stats.distributions.
+"""
+import numpy as np
+
+distcont = [
+    ['alpha', (3.5704770516650459,)],
+    ['anglit', ()],
+    ['arcsine', ()],
+    ['argus', (1.0,)],
+    ['beta', (2.3098496451481823, 0.62687954300963677)],
+    ['betaprime', (5, 6)],
+    ['bradford', (0.29891359763170633,)],
+    ['burr', (10.5, 4.3)],
+    ['burr12', (10, 4)],
+    ['cauchy', ()],
+    ['chi', (78,)],
+    ['chi2', (55,)],
+    ['cosine', ()],
+    ['crystalball', (2.0, 3.0)],
+    ['dgamma', (1.1023326088288166,)],
+    ['dweibull', (2.0685080649914673,)],
+    ['erlang', (10,)],
+    ['expon', ()],
+    ['exponnorm', (1.5,)],
+    ['exponpow', (2.697119160358469,)],
+    ['exponweib', (2.8923945291034436, 1.9505288745913174)],
+    ['f', (29, 18)],
+    ['fatiguelife', (29,)],   # correction numargs = 1
+    ['fisk', (3.0857548622253179,)],
+    ['foldcauchy', (4.7164673455831894,)],
+    ['foldnorm', (1.9521253373555869,)],
+    ['gamma', (1.9932305483800778,)],
+    ['gausshyper', (13.763771604130699, 3.1189636648681431,
+                    2.5145980350183019, 5.1811649903971615)],  # veryslow
+    ['genexpon', (9.1325976465418908, 16.231956600590632, 3.2819552690843983)],
+    ['genextreme', (-0.1,)],
+    ['gengamma', (4.4162385429431925, 3.1193091679242761)],
+    ['gengamma', (4.4162385429431925, -3.1193091679242761)],
+    ['genhalflogistic', (0.77274727809929322,)],
+    ['genhyperbolic', (0.5, 1.5, -0.5,)],
+    ['geninvgauss', (2.3, 1.5)],
+    ['genlogistic', (0.41192440799679475,)],
+    ['gennorm', (1.2988442399460265,)],
+    ['halfgennorm', (0.6748054997000371,)],
+    ['genpareto', (0.1,)],   # use case with finite moments
+    ['gibrat', ()],
+    ['gompertz', (0.94743713075105251,)],
+    ['gumbel_l', ()],
+    ['gumbel_r', ()],
+    ['halfcauchy', ()],
+    ['halflogistic', ()],
+    ['halfnorm', ()],
+    ['hypsecant', ()],
+    ['invgamma', (4.0668996136993067,)],
+    ['invgauss', (0.14546264555347513,)],
+    ['invweibull', (10.58,)],
+    ['johnsonsb', (4.3172675099141058, 3.1837781130785063)],
+    ['johnsonsu', (2.554395574161155, 2.2482281679651965)],
+    ['kappa4', (0.0, 0.0)],
+    ['kappa4', (-0.1, 0.1)],
+    ['kappa4', (0.0, 0.1)],
+    ['kappa4', (0.1, 0.0)],
+    ['kappa3', (1.0,)],
+    ['ksone', (1000,)],  # replace 22 by 100 to avoid failing range, ticket 956
+    ['kstwo', (10,)],
+    ['kstwobign', ()],
+    ['laplace', ()],
+    ['laplace_asymmetric', (2,)],
+    ['levy', ()],
+    ['levy_l', ()],
+    ['levy_stable', (1.8, -0.5)],
+    ['loggamma', (0.41411931826052117,)],
+    ['logistic', ()],
+    ['loglaplace', (3.2505926592051435,)],
+    ['lognorm', (0.95368226960575331,)],
+    ['loguniform', (0.01, 1.25)],
+    ['lomax', (1.8771398388773268,)],
+    ['maxwell', ()],
+    ['mielke', (10.4, 4.6)],
+    ['moyal', ()],
+    ['nakagami', (4.9673794866666237,)],
+    ['ncf', (27, 27, 0.41578441799226107)],
+    ['nct', (14, 0.24045031331198066)],
+    ['ncx2', (21, 1.0560465975116415)],
+    ['norm', ()],
+    ['norminvgauss', (1.25, 0.5)],
+    ['pareto', (2.621716532144454,)],
+    ['pearson3', (0.1,)],
+    ['pearson3', (-2,)],
+    ['powerlaw', (1.6591133289905851,)],
+    ['powerlaw', (0.6591133289905851,)],
+    ['powerlognorm', (2.1413923530064087, 0.44639540782048337)],
+    ['powernorm', (4.4453652254590779,)],
+    ['rayleigh', ()],
+    ['rdist', (1.6,)],
+    ['recipinvgauss', (0.63004267809369119,)],
+    ['reciprocal', (0.01, 1.25)],
+    ['rice', (0.7749725210111873,)],
+    ['semicircular', ()],
+    ['skewcauchy', (0.5,)],
+    ['skewnorm', (4.0,)],
+    ['studentized_range', (3.0, 10.0)],
+    ['t', (2.7433514990818093,)],
+    ['trapezoid', (0.2, 0.8)],
+    ['triang', (0.15785029824528218,)],
+    ['truncexpon', (4.6907725456810478,)],
+    ['truncnorm', (-1.0978730080013919, 2.7306754109031979)],
+    ['truncnorm', (0.1, 2.)],
+    ['truncpareto', (1.8, 5.3)],
+    ['truncweibull_min', (2.5, 0.25, 1.75)],
+    ['tukeylambda', (3.1321477856738267,)],
+    ['uniform', ()],
+    ['vonmises', (3.9939042581071398,)],
+    ['vonmises_line', (3.9939042581071398,)],
+    ['wald', ()],
+    ['weibull_max', (2.8687961709100187,)],
+    ['weibull_min', (1.7866166930421596,)],
+    ['wrapcauchy', (0.031071279018614728,)]]
+
+
+distdiscrete = [
+    ['bernoulli',(0.3,)],
+    ['betabinom', (5, 2.3, 0.63)],
+    ['binom', (5, 0.4)],
+    ['boltzmann',(1.4, 19)],
+    ['dlaplace', (0.8,)],  # 0.5
+    ['geom', (0.5,)],
+    ['hypergeom',(30, 12, 6)],
+    ['hypergeom',(21,3,12)],  # numpy.random (3,18,12) numpy ticket:921
+    ['hypergeom',(21,18,11)],  # numpy.random (18,3,11) numpy ticket:921
+    ['nchypergeom_fisher', (140, 80, 60, 0.5)],
+    ['nchypergeom_wallenius', (140, 80, 60, 0.5)],
+    ['logser', (0.6,)],  # re-enabled, numpy ticket:921
+    ['nbinom', (0.4, 0.4)],  # from tickets: 583
+    ['nbinom', (5, 0.5)],
+    ['planck', (0.51,)],   # 4.1
+    ['poisson', (0.6,)],
+    ['randint', (7, 31)],
+    ['skellam', (15, 8)],
+    ['zipf', (6.5,)],
+    ['zipfian', (0.75, 15)],
+    ['zipfian', (1.25, 10)],
+    ['yulesimon', (11.0,)],
+    ['nhypergeom', (20, 7, 1)]
+]
+
+
+invdistdiscrete = [
+    # In each of the following, at least one shape parameter is invalid
+    ['hypergeom', (3, 3, 4)],
+    ['nhypergeom', (5, 2, 8)],
+    ['nchypergeom_fisher', (3, 3, 4, 1)],
+    ['nchypergeom_wallenius', (3, 3, 4, 1)],
+    ['bernoulli', (1.5, )],
+    ['binom', (10, 1.5)],
+    ['betabinom', (10, -0.4, -0.5)],
+    ['boltzmann', (-1, 4)],
+    ['dlaplace', (-0.5, )],
+    ['geom', (1.5, )],
+    ['logser', (1.5, )],
+    ['nbinom', (10, 1.5)],
+    ['planck', (-0.5, )],
+    ['poisson', (-0.5, )],
+    ['randint', (5, 2)],
+    ['skellam', (-5, -2)],
+    ['zipf', (-2, )],
+    ['yulesimon', (-2, )],
+    ['zipfian', (-0.75, 15)]
+]
+
+
+invdistcont = [
+    # In each of the following, at least one shape parameter is invalid
+    ['alpha', (-1, )],
+    ['anglit', ()],
+    ['arcsine', ()],
+    ['argus', (-1, )],
+    ['beta', (-2, 2)],
+    ['betaprime', (-2, 2)],
+    ['bradford', (-1, )],
+    ['burr', (-1, 1)],
+    ['burr12', (-1, 1)],
+    ['cauchy', ()],
+    ['chi', (-1, )],
+    ['chi2', (-1, )],
+    ['cosine', ()],
+    ['crystalball', (-1, 2)],
+    ['dgamma', (-1, )],
+    ['dweibull', (-1, )],
+    ['erlang', (-1, )],
+    ['expon', ()],
+    ['exponnorm', (-1, )],
+    ['exponweib', (1, -1)],
+    ['exponpow', (-1, )],
+    ['f', (10, -10)],
+    ['fatiguelife', (-1, )],
+    ['fisk', (-1, )],
+    ['foldcauchy', (-1, )],
+    ['foldnorm', (-1, )],
+    ['genlogistic', (-1, )],
+    ['gennorm', (-1, )],
+    ['genpareto', (np.inf, )],
+    ['genexpon', (1, 2, -3)],
+    ['genextreme', (np.inf, )],
+    ['genhyperbolic', (0.5, -0.5, -1.5,)],
+    ['gausshyper', (1, 2, 3, -4)],
+    ['gamma', (-1, )],
+    ['gengamma', (-1, 0)],
+    ['genhalflogistic', (-1, )],
+    ['geninvgauss', (1, 0)],
+    ['gibrat', ()],
+    ['gompertz', (-1, )],
+    ['gumbel_r', ()],
+    ['gumbel_l', ()],
+    ['halfcauchy', ()],
+    ['halflogistic', ()],
+    ['halfnorm', ()],
+    ['halfgennorm', (-1, )],
+    ['hypsecant', ()],
+    ['invgamma', (-1, )],
+    ['invgauss', (-1, )],
+    ['invweibull', (-1, )],
+    ['johnsonsb', (1, -2)],
+    ['johnsonsu', (1, -2)],
+    ['kappa4', (np.nan, 0)],
+    ['kappa3', (-1, )],
+    ['ksone', (-1, )],
+    ['kstwo', (-1, )],
+    ['kstwobign', ()],
+    ['laplace', ()],
+    ['laplace_asymmetric', (-1, )],
+    ['levy', ()],
+    ['levy_l', ()],
+    ['levy_stable', (-1, 1)],
+    ['logistic', ()],
+    ['loggamma', (-1, )],
+    ['loglaplace', (-1, )],
+    ['lognorm', (-1, )],
+    ['loguniform', (10, 5)],
+    ['lomax', (-1, )],
+    ['maxwell', ()],
+    ['mielke', (1, -2)],
+    ['moyal', ()],
+    ['nakagami', (-1, )],
+    ['ncx2', (-1, 2)],
+    ['ncf', (10, 20, -1)],
+    ['nct', (-1, 2)],
+    ['norm', ()],
+    ['norminvgauss', (5, -10)],
+    ['pareto', (-1, )],
+    ['pearson3', (np.nan, )],
+    ['powerlaw', (-1, )],
+    ['powerlognorm', (1, -2)],
+    ['powernorm', (-1, )],
+    ['rdist', (-1, )],
+    ['rayleigh', ()],
+    ['rice', (-1, )],
+    ['recipinvgauss', (-1, )],
+    ['semicircular', ()],
+    ['skewnorm', (np.inf, )],
+    ['studentized_range', (-1, 1)],
+    ['t', (-1, )],
+    ['trapezoid', (0, 2)],
+    ['triang', (2, )],
+    ['truncexpon', (-1, )],
+    ['truncnorm', (10, 5)],
+    ['truncpareto', (-1, 5)],
+    ['truncpareto', (1.8, .5)],
+    ['truncweibull_min', (-2.5, 0.25, 1.75)],
+    ['tukeylambda', (np.nan, )],
+    ['uniform', ()],
+    ['vonmises', (-1, )],
+    ['vonmises_line', (-1, )],
+    ['wald', ()],
+    ['weibull_min', (-1, )],
+    ['weibull_max', (-1, )],
+    ['wrapcauchy', (2, )],
+    ['reciprocal', (15, 10)],
+    ['skewcauchy', (2, )]
+]

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_entropy.py

@@ -0,0 +1,399 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Apr  2 09:06:05 2021
+
+@author: matth
+"""
+
+from __future__ import annotations
+import math
+import numpy as np
+from scipy import special
+from typing import Optional, Union
+
+__all__ = ['entropy', 'differential_entropy']
+
+
+def entropy(pk: np.typing.ArrayLike,
+            qk: Optional[np.typing.ArrayLike] = None,
+            base: Optional[float] = None,
+            axis: int = 0
+            ) -> Union[np.number, np.ndarray]:
+    """
+    Calculate the Shannon entropy/relative entropy of given distribution(s).
+
+    If only probabilities `pk` are given, the Shannon entropy is calculated as
+    ``H = -sum(pk * log(pk))``.
+
+    If `qk` is not None, then compute the relative entropy
+    ``D = sum(pk * log(pk / qk))``. This quantity is also known
+    as the Kullback-Leibler divergence.
+
+    This routine will normalize `pk` and `qk` if they don't sum to 1.
+
+    Parameters
+    ----------
+    pk : array_like
+        Defines the (discrete) distribution. Along each axis-slice of ``pk``,
+        element ``i`` is the  (possibly unnormalized) probability of event
+        ``i``.
+    qk : array_like, optional
+        Sequence against which the relative entropy is computed. Should be in
+        the same format as `pk`.
+    base : float, optional
+        The logarithmic base to use, defaults to ``e`` (natural logarithm).
+    axis : int, optional
+        The axis along which the entropy is calculated. Default is 0.
+
+    Returns
+    -------
+    S : {float, array_like}
+        The calculated entropy.
+
+    Notes
+    -----
+    Informally, the Shannon entropy quantifies the expected uncertainty
+    inherent in the possible outcomes of a discrete random variable.
+    For example,
+    if messages consisting of sequences of symbols from a set are to be
+    encoded and transmitted over a noiseless channel, then the Shannon entropy
+    ``H(pk)`` gives a tight lower bound for the average number of units of
+    information needed per symbol if the symbols occur with frequencies
+    governed by the discrete distribution `pk` [1]_. The choice of base
+    determines the choice of units; e.g., ``e`` for nats, ``2`` for bits, etc.
+
+    The relative entropy, ``D(pk|qk)``, quantifies the increase in the average
+    number of units of information needed per symbol if the encoding is
+    optimized for the probability distribution `qk` instead of the true
+    distribution `pk`. Informally, the relative entropy quantifies the expected
+    excess in surprise experienced if one believes the true distribution is
+    `qk` when it is actually `pk`.
+
+    A related quantity, the cross entropy ``CE(pk, qk)``, satisfies the
+    equation ``CE(pk, qk) = H(pk) + D(pk|qk)`` and can also be calculated with
+    the formula ``CE = -sum(pk * log(qk))``. It gives the average
+    number of units of information needed per symbol if an encoding is
+    optimized for the probability distribution `qk` when the true distribution
+    is `pk`. It is not computed directly by `entropy`, but it can be computed
+    using two calls to the function (see Examples).
+
+    See [2]_ for more information.
+
+    References
+    ----------
+    .. [1] Shannon, C.E. (1948), A Mathematical Theory of Communication.
+           Bell System Technical Journal, 27: 379-423.
+           https://doi.org/10.1002/j.1538-7305.1948.tb01338.x
+    .. [2] Thomas M. Cover and Joy A. Thomas. 2006. Elements of Information
+           Theory (Wiley Series in Telecommunications and Signal Processing).
+           Wiley-Interscience, USA.
+
+
+    Examples
+    --------
+    The outcome of a fair coin is the most uncertain:
+
+    >>> import numpy as np
+    >>> from scipy.stats import entropy
+    >>> base = 2  # work in units of bits
+    >>> pk = np.array([1/2, 1/2])  # fair coin
+    >>> H = entropy(pk, base=base)
+    >>> H
+    1.0
+    >>> H == -np.sum(pk * np.log(pk)) / np.log(base)
+    True
+
+    The outcome of a biased coin is less uncertain:
+
+    >>> qk = np.array([9/10, 1/10])  # biased coin
+    >>> entropy(qk, base=base)
+    0.46899559358928117
+
+    The relative entropy between the fair coin and biased coin is calculated
+    as:
+
+    >>> D = entropy(pk, qk, base=base)
+    >>> D
+    0.7369655941662062
+    >>> D == np.sum(pk * np.log(pk/qk)) / np.log(base)
+    True
+
+    The cross entropy can be calculated as the sum of the entropy and
+    relative entropy`:
+
+    >>> CE = entropy(pk, base=base) + entropy(pk, qk, base=base)
+    >>> CE
+    1.736965594166206
+    >>> CE == -np.sum(pk * np.log(qk)) / np.log(base)
+    True
+
+    """
+    if base is not None and base <= 0:
+        raise ValueError("`base` must be a positive number or `None`.")
+
+    pk = np.asarray(pk)
+    pk = 1.0*pk / np.sum(pk, axis=axis, keepdims=True)
+    if qk is None:
+        vec = special.entr(pk)
+    else:
+        qk = np.asarray(qk)
+        pk, qk = np.broadcast_arrays(pk, qk)
+        qk = 1.0*qk / np.sum(qk, axis=axis, keepdims=True)
+        vec = special.rel_entr(pk, qk)
+    S = np.sum(vec, axis=axis)
+    if base is not None:
+        S /= np.log(base)
+    return S
+
+
+def differential_entropy(
+    values: np.typing.ArrayLike,
+    *,
+    window_length: Optional[int] = None,
+    base: Optional[float] = None,
+    axis: int = 0,
+    method: str = "auto",
+) -> Union[np.number, np.ndarray]:
+    r"""Given a sample of a distribution, estimate the differential entropy.
+
+    Several estimation methods are available using the `method` parameter. By
+    default, a method is selected based the size of the sample.
+
+    Parameters
+    ----------
+    values : sequence
+        Sample from a continuous distribution.
+    window_length : int, optional
+        Window length for computing Vasicek estimate. Must be an integer
+        between 1 and half of the sample size. If ``None`` (the default), it
+        uses the heuristic value
+
+        .. math::
+            \left \lfloor \sqrt{n} + 0.5 \right \rfloor
+
+        where :math:`n` is the sample size. This heuristic was originally
+        proposed in [2]_ and has become common in the literature.
+    base : float, optional
+        The logarithmic base to use, defaults to ``e`` (natural logarithm).
+    axis : int, optional
+        The axis along which the differential entropy is calculated.
+        Default is 0.
+    method : {'vasicek', 'van es', 'ebrahimi', 'correa', 'auto'}, optional
+        The method used to estimate the differential entropy from the sample.
+        Default is ``'auto'``.  See Notes for more information.
+
+    Returns
+    -------
+    entropy : float
+        The calculated differential entropy.
+
+    Notes
+    -----
+    This function will converge to the true differential entropy in the limit
+
+    .. math::
+        n \to \infty, \quad m \to \infty, \quad \frac{m}{n} \to 0
+
+    The optimal choice of ``window_length`` for a given sample size depends on
+    the (unknown) distribution. Typically, the smoother the density of the
+    distribution, the larger the optimal value of ``window_length`` [1]_.
+
+    The following options are available for the `method` parameter.
+
+    * ``'vasicek'`` uses the estimator presented in [1]_. This is
+      one of the first and most influential estimators of differential entropy.
+    * ``'van es'`` uses the bias-corrected estimator presented in [3]_, which
+      is not only consistent but, under some conditions, asymptotically normal.
+    * ``'ebrahimi'`` uses an estimator presented in [4]_, which was shown
+      in simulation to have smaller bias and mean squared error than
+      the Vasicek estimator.
+    * ``'correa'`` uses the estimator presented in [5]_ based on local linear
+      regression. In a simulation study, it had consistently smaller mean
+      square error than the Vasiceck estimator, but it is more expensive to
+      compute.
+    * ``'auto'`` selects the method automatically (default). Currently,
+      this selects ``'van es'`` for very small samples (<10), ``'ebrahimi'``
+      for moderate sample sizes (11-1000), and ``'vasicek'`` for larger
+      samples, but this behavior is subject to change in future versions.
+
+    All estimators are implemented as described in [6]_.
+
+    References
+    ----------
+    .. [1] Vasicek, O. (1976). A test for normality based on sample entropy.
+           Journal of the Royal Statistical Society:
+           Series B (Methodological), 38(1), 54-59.
+    .. [2] Crzcgorzewski, P., & Wirczorkowski, R. (1999). Entropy-based
+           goodness-of-fit test for exponentiality. Communications in
+           Statistics-Theory and Methods, 28(5), 1183-1202.
+    .. [3] Van Es, B. (1992). Estimating functionals related to a density by a
+           class of statistics based on spacings. Scandinavian Journal of
+           Statistics, 61-72.
+    .. [4] Ebrahimi, N., Pflughoeft, K., & Soofi, E. S. (1994). Two measures
+           of sample entropy. Statistics & Probability Letters, 20(3), 225-234.
+    .. [5] Correa, J. C. (1995). A new estimator of entropy. Communications
+           in Statistics-Theory and Methods, 24(10), 2439-2449.
+    .. [6] Noughabi, H. A. (2015). Entropy Estimation Using Numerical Methods.
+           Annals of Data Science, 2(2), 231-241.
+           https://link.springer.com/article/10.1007/s40745-015-0045-9
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.stats import differential_entropy, norm
+
+    Entropy of a standard normal distribution:
+
+    >>> rng = np.random.default_rng()
+    >>> values = rng.standard_normal(100)
+    >>> differential_entropy(values)
+    1.3407817436640392
+
+    Compare with the true entropy:
+
+    >>> float(norm.entropy())
+    1.4189385332046727
+
+    For several sample sizes between 5 and 1000, compare the accuracy of
+    the ``'vasicek'``, ``'van es'``, and ``'ebrahimi'`` methods. Specifically,
+    compare the root mean squared error (over 1000 trials) between the estimate
+    and the true differential entropy of the distribution.
+
+    >>> from scipy import stats
+    >>> import matplotlib.pyplot as plt
+    >>>
+    >>>
+    >>> def rmse(res, expected):
+    ...     '''Root mean squared error'''
+    ...     return np.sqrt(np.mean((res - expected)**2))
+    >>>
+    >>>
+    >>> a, b = np.log10(5), np.log10(1000)
+    >>> ns = np.round(np.logspace(a, b, 10)).astype(int)
+    >>> reps = 1000  # number of repetitions for each sample size
+    >>> expected = stats.expon.entropy()
+    >>>
+    >>> method_errors = {'vasicek': [], 'van es': [], 'ebrahimi': []}
+    >>> for method in method_errors:
+    ...     for n in ns:
+    ...        rvs = stats.expon.rvs(size=(reps, n), random_state=rng)
+    ...        res = stats.differential_entropy(rvs, method=method, axis=-1)
+    ...        error = rmse(res, expected)
+    ...        method_errors[method].append(error)
+    >>>
+    >>> for method, errors in method_errors.items():
+    ...     plt.loglog(ns, errors, label=method)
+    >>>
+    >>> plt.legend()
+    >>> plt.xlabel('sample size')
+    >>> plt.ylabel('RMSE (1000 trials)')
+    >>> plt.title('Entropy Estimator Error (Exponential Distribution)')
+
+    """
+    values = np.asarray(values)
+    values = np.moveaxis(values, axis, -1)
+    n = values.shape[-1]  # number of observations
+
+    if window_length is None:
+        window_length = math.floor(math.sqrt(n) + 0.5)
+
+    if not 2 <= 2 * window_length < n:
+        raise ValueError(
+            f"Window length ({window_length}) must be positive and less "
+            f"than half the sample size ({n}).",
+        )
+
+    if base is not None and base <= 0:
+        raise ValueError("`base` must be a positive number or `None`.")
+
+    sorted_data = np.sort(values, axis=-1)
+
+    methods = {"vasicek": _vasicek_entropy,
+               "van es": _van_es_entropy,
+               "correa": _correa_entropy,
+               "ebrahimi": _ebrahimi_entropy,
+               "auto": _vasicek_entropy}
+    method = method.lower()
+    if method not in methods:
+        message = f"`method` must be one of {set(methods)}"
+        raise ValueError(message)
+
+    if method == "auto":
+        if n <= 10:
+            method = 'van es'
+        elif n <= 1000:
+            method = 'ebrahimi'
+        else:
+            method = 'vasicek'
+
+    res = methods[method](sorted_data, window_length)
+
+    if base is not None:
+        res /= np.log(base)
+
+    return res
+
+
+def _pad_along_last_axis(X, m):
+    """Pad the data for computing the rolling window difference."""
+    # scales a  bit better than method in _vasicek_like_entropy
+    shape = np.array(X.shape)
+    shape[-1] = m
+    Xl = np.broadcast_to(X[..., [0]], shape)  # [0] vs 0 to maintain shape
+    Xr = np.broadcast_to(X[..., [-1]], shape)
+    return np.concatenate((Xl, X, Xr), axis=-1)
+
+
+def _vasicek_entropy(X, m):
+    """Compute the Vasicek estimator as described in [6] Eq. 1.3."""
+    n = X.shape[-1]
+    X = _pad_along_last_axis(X, m)
+    differences = X[..., 2 * m:] - X[..., : -2 * m:]
+    logs = np.log(n/(2*m) * differences)
+    return np.mean(logs, axis=-1)
+
+
+def _van_es_entropy(X, m):
+    """Compute the van Es estimator as described in [6]."""
+    # No equation number, but referred to as HVE_mn.
+    # Typo: there should be a log within the summation.
+    n = X.shape[-1]
+    difference = X[..., m:] - X[..., :-m]
+    term1 = 1/(n-m) * np.sum(np.log((n+1)/m * difference), axis=-1)
+    k = np.arange(m, n+1)
+    return term1 + np.sum(1/k) + np.log(m) - np.log(n+1)
+
+
+def _ebrahimi_entropy(X, m):
+    """Compute the Ebrahimi estimator as described in [6]."""
+    # No equation number, but referred to as HE_mn
+    n = X.shape[-1]
+    X = _pad_along_last_axis(X, m)
+
+    differences = X[..., 2 * m:] - X[..., : -2 * m:]
+
+    i = np.arange(1, n+1).astype(float)
+    ci = np.ones_like(i)*2
+    ci[i <= m] = 1 + (i[i <= m] - 1)/m
+    ci[i >= n - m + 1] = 1 + (n - i[i >= n-m+1])/m
+
+    logs = np.log(n * differences / (ci * m))
+    return np.mean(logs, axis=-1)
+
+
+def _correa_entropy(X, m):
+    """Compute the Correa estimator as described in [6]."""
+    # No equation number, but referred to as HC_mn
+    n = X.shape[-1]
+    X = _pad_along_last_axis(X, m)
+
+    i = np.arange(1, n+1)
+    dj = np.arange(-m, m+1)[:, None]
+    j = i + dj
+    j0 = j + m - 1  # 0-indexed version of j
+
+    Xibar = np.mean(X[..., j0], axis=-2, keepdims=True)
+    difference = X[..., j0] - Xibar
+    num = np.sum(difference*dj, axis=-2)  # dj is d-i
+    den = n*np.sum(difference**2, axis=-2)
+    return -np.mean(np.log(num/den), axis=-1)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_generate_pyx.py

@@ -0,0 +1,75 @@
+import pathlib
+import subprocess
+import sys
+import os
+import argparse
+
+
+def isNPY_OLD():
+    '''
+    A new random C API was added in 1.18 and became stable in 1.19.
+    Prefer the new random C API when building with recent numpy.
+    '''
+    import numpy as np
+    ver = tuple(int(num) for num in np.__version__.split('.')[:2])
+    return ver < (1, 19)
+
+
+def make_biasedurn(outdir):
+    '''Substitute True/False values for NPY_OLD Cython build variable.'''
+    biasedurn_base = (pathlib.Path(__file__).parent / '_biasedurn').absolute()
+    with open(biasedurn_base.with_suffix('.pyx.templ'), 'r') as src:
+        contents = src.read()
+
+    outfile = outdir / '_biasedurn.pyx'
+    with open(outfile, 'w') as dest:
+        dest.write(contents.format(NPY_OLD=str(bool(isNPY_OLD()))))
+
+
+def make_unuran(srcdir, outdir):
+    """Substitute True/False values for NPY_OLD Cython build variable."""
+    import re
+    with open(srcdir / "unuran_wrapper.pyx.templ", "r") as src:
+        contents = src.read()
+    with open(outdir / "unuran_wrapper.pyx", "w") as dest:
+        dest.write(re.sub("DEF NPY_OLD = isNPY_OLD",
+                          f"DEF NPY_OLD = {isNPY_OLD()}",
+                          contents))
+
+
+def make_boost(outdir, distutils_build=False):
+    # Call code generator inside _boost directory
+    code_gen = pathlib.Path(__file__).parent / '_boost/include/code_gen.py'
+    if distutils_build:
+        subprocess.run([sys.executable, str(code_gen), '-o', outdir,
+                        '--distutils-build', 'True'], check=True)
+    else:
+        subprocess.run([sys.executable, str(code_gen), '-o', outdir],
+                       check=True)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-o", "--outdir", type=str,
+                        help="Path to the output directory")
+    args = parser.parse_args()
+
+    if not args.outdir:
+        # We're dealing with a distutils build here, write in-place:
+        outdir_abs = pathlib.Path(os.path.abspath(os.path.dirname(__file__)))
+        make_biasedurn(outdir_abs)
+
+        outdir_abs_boost = outdir_abs / '_boost' / 'src'
+        if not os.path.exists(outdir_abs_boost):
+            os.makedirs(outdir_abs_boost)
+        make_boost(outdir_abs_boost, distutils_build=True)
+
+        outdir_abs_unuran = outdir_abs / '_unuran'
+        make_unuran(outdir_abs_unuran, outdir_abs_unuran)
+    else:
+        # Meson build
+        srcdir_abs = pathlib.Path(os.path.abspath(os.path.dirname(__file__)))
+        outdir_abs = pathlib.Path(os.getcwd()) / args.outdir
+        make_biasedurn(outdir_abs)
+        make_boost(outdir_abs)
+        make_unuran(srcdir_abs / '_unuran', outdir_abs)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_kde.py

@@ -0,0 +1,725 @@
+#-------------------------------------------------------------------------------
+#
+#  Define classes for (uni/multi)-variate kernel density estimation.
+#
+#  Currently, only Gaussian kernels are implemented.
+#
+#  Written by: Robert Kern
+#
+#  Date: 2004-08-09
+#
+#  Modified: 2005-02-10 by Robert Kern.
+#              Contributed to SciPy
+#            2005-10-07 by Robert Kern.
+#              Some fixes to match the new scipy_core
+#
+#  Copyright 2004-2005 by Enthought, Inc.
+#
+#-------------------------------------------------------------------------------
+
+# Standard library imports.
+import warnings
+
+# SciPy imports.
+from scipy import linalg, special
+from scipy._lib._util import check_random_state
+
+from numpy import (asarray, atleast_2d, reshape, zeros, newaxis, exp, pi,
+                   sqrt, ravel, power, atleast_1d, squeeze, sum, transpose,
+                   ones, cov)
+import numpy as np
+
+# Local imports.
+from . import _mvn
+from ._stats import gaussian_kernel_estimate, gaussian_kernel_estimate_log
+
+
+__all__ = ['gaussian_kde']
+
+
+class gaussian_kde:
+    """Representation of a kernel-density estimate using Gaussian kernels.
+
+    Kernel density estimation is a way to estimate the probability density
+    function (PDF) of a random variable in a non-parametric way.
+    `gaussian_kde` works for both uni-variate and multi-variate data.   It
+    includes automatic bandwidth determination.  The estimation works best for
+    a unimodal distribution; bimodal or multi-modal distributions tend to be
+    oversmoothed.
+
+    Parameters
+    ----------
+    dataset : array_like
+        Datapoints to estimate from. In case of univariate data this is a 1-D
+        array, otherwise a 2-D array with shape (# of dims, # of data).
+    bw_method : str, scalar or callable, optional
+        The method used to calculate the estimator bandwidth.  This can be
+        'scott', 'silverman', a scalar constant or a callable.  If a scalar,
+        this will be used directly as `kde.factor`.  If a callable, it should
+        take a `gaussian_kde` instance as only parameter and return a scalar.
+        If None (default), 'scott' is used.  See Notes for more details.
+    weights : array_like, optional
+        weights of datapoints. This must be the same shape as dataset.
+        If None (default), the samples are assumed to be equally weighted
+
+    Attributes
+    ----------
+    dataset : ndarray
+        The dataset with which `gaussian_kde` was initialized.
+    d : int
+        Number of dimensions.
+    n : int
+        Number of datapoints.
+    neff : int
+        Effective number of datapoints.
+
+        .. versionadded:: 1.2.0
+    factor : float
+        The bandwidth factor, obtained from `kde.covariance_factor`. The square
+        of `kde.factor` multiplies the covariance matrix of the data in the kde
+        estimation.
+    covariance : ndarray
+        The covariance matrix of `dataset`, scaled by the calculated bandwidth
+        (`kde.factor`).
+    inv_cov : ndarray
+        The inverse of `covariance`.
+
+    Methods
+    -------
+    evaluate
+    __call__
+    integrate_gaussian
+    integrate_box_1d
+    integrate_box
+    integrate_kde
+    pdf
+    logpdf
+    resample
+    set_bandwidth
+    covariance_factor
+
+    Notes
+    -----
+    Bandwidth selection strongly influences the estimate obtained from the KDE
+    (much more so than the actual shape of the kernel).  Bandwidth selection
+    can be done by a "rule of thumb", by cross-validation, by "plug-in
+    methods" or by other means; see [3]_, [4]_ for reviews.  `gaussian_kde`
+    uses a rule of thumb, the default is Scott's Rule.
+
+    Scott's Rule [1]_, implemented as `scotts_factor`, is::
+
+        n**(-1./(d+4)),
+
+    with ``n`` the number of data points and ``d`` the number of dimensions.
+    In the case of unequally weighted points, `scotts_factor` becomes::
+
+        neff**(-1./(d+4)),
+
+    with ``neff`` the effective number of datapoints.
+    Silverman's Rule [2]_, implemented as `silverman_factor`, is::
+
+        (n * (d + 2) / 4.)**(-1. / (d + 4)).
+
+    or in the case of unequally weighted points::
+
+        (neff * (d + 2) / 4.)**(-1. / (d + 4)).
+
+    Good general descriptions of kernel density estimation can be found in [1]_
+    and [2]_, the mathematics for this multi-dimensional implementation can be
+    found in [1]_.
+
+    With a set of weighted samples, the effective number of datapoints ``neff``
+    is defined by::
+
+        neff = sum(weights)^2 / sum(weights^2)
+
+    as detailed in [5]_.
+
+    `gaussian_kde` does not currently support data that lies in a
+    lower-dimensional subspace of the space in which it is expressed. For such
+    data, consider performing principle component analysis / dimensionality
+    reduction and using `gaussian_kde` with the transformed data.
+
+    References
+    ----------
+    .. [1] D.W. Scott, "Multivariate Density Estimation: Theory, Practice, and
+           Visualization", John Wiley & Sons, New York, Chicester, 1992.
+    .. [2] B.W. Silverman, "Density Estimation for Statistics and Data
+           Analysis", Vol. 26, Monographs on Statistics and Applied Probability,
+           Chapman and Hall, London, 1986.
+    .. [3] B.A. Turlach, "Bandwidth Selection in Kernel Density Estimation: A
+           Review", CORE and Institut de Statistique, Vol. 19, pp. 1-33, 1993.
+    .. [4] D.M. Bashtannyk and R.J. Hyndman, "Bandwidth selection for kernel
+           conditional density estimation", Computational Statistics & Data
+           Analysis, Vol. 36, pp. 279-298, 2001.
+    .. [5] Gray P. G., 1969, Journal of the Royal Statistical Society.
+           Series A (General), 132, 272
+
+    Examples
+    --------
+    Generate some random two-dimensional data:
+
+    >>> import numpy as np
+    >>> from scipy import stats
+    >>> def measure(n):
+    ...     "Measurement model, return two coupled measurements."
+    ...     m1 = np.random.normal(size=n)
+    ...     m2 = np.random.normal(scale=0.5, size=n)
+    ...     return m1+m2, m1-m2
+
+    >>> m1, m2 = measure(2000)
+    >>> xmin = m1.min()
+    >>> xmax = m1.max()
+    >>> ymin = m2.min()
+    >>> ymax = m2.max()
+
+    Perform a kernel density estimate on the data:
+
+    >>> X, Y = np.mgrid[xmin:xmax:100j, ymin:ymax:100j]
+    >>> positions = np.vstack([X.ravel(), Y.ravel()])
+    >>> values = np.vstack([m1, m2])
+    >>> kernel = stats.gaussian_kde(values)
+    >>> Z = np.reshape(kernel(positions).T, X.shape)
+
+    Plot the results:
+
+    >>> import matplotlib.pyplot as plt
+    >>> fig, ax = plt.subplots()
+    >>> ax.imshow(np.rot90(Z), cmap=plt.cm.gist_earth_r,
+    ...           extent=[xmin, xmax, ymin, ymax])
+    >>> ax.plot(m1, m2, 'k.', markersize=2)
+    >>> ax.set_xlim([xmin, xmax])
+    >>> ax.set_ylim([ymin, ymax])
+    >>> plt.show()
+
+    """
+    def __init__(self, dataset, bw_method=None, weights=None):
+        self.dataset = atleast_2d(asarray(dataset))
+        if not self.dataset.size > 1:
+            raise ValueError("`dataset` input should have multiple elements.")
+
+        self.d, self.n = self.dataset.shape
+
+        if weights is not None:
+            self._weights = atleast_1d(weights).astype(float)
+            self._weights /= sum(self._weights)
+            if self.weights.ndim != 1:
+                raise ValueError("`weights` input should be one-dimensional.")
+            if len(self._weights) != self.n:
+                raise ValueError("`weights` input should be of length n")
+            self._neff = 1/sum(self._weights**2)
+
+        # This can be converted to a warning once gh-10205 is resolved
+        if self.d > self.n:
+            msg = ("Number of dimensions is greater than number of samples. "
+                   "This results in a singular data covariance matrix, which "
+                   "cannot be treated using the algorithms implemented in "
+                   "`gaussian_kde`. Note that `gaussian_kde` interprets each "
+                   "*column* of `dataset` to be a point; consider transposing "
+                   "the input to `dataset`.")
+            raise ValueError(msg)
+
+        try:
+            self.set_bandwidth(bw_method=bw_method)
+        except linalg.LinAlgError as e:
+            msg = ("The data appears to lie in a lower-dimensional subspace "
+                   "of the space in which it is expressed. This has resulted "
+                   "in a singular data covariance matrix, which cannot be "
+                   "treated using the algorithms implemented in "
+                   "`gaussian_kde`. Consider performing principle component "
+                   "analysis / dimensionality reduction and using "
+                   "`gaussian_kde` with the transformed data.")
+            raise linalg.LinAlgError(msg) from e
+
+    def evaluate(self, points):
+        """Evaluate the estimated pdf on a set of points.
+
+        Parameters
+        ----------
+        points : (# of dimensions, # of points)-array
+            Alternatively, a (# of dimensions,) vector can be passed in and
+            treated as a single point.
+
+        Returns
+        -------
+        values : (# of points,)-array
+            The values at each point.
+
+        Raises
+        ------
+        ValueError : if the dimensionality of the input points is different than
+                     the dimensionality of the KDE.
+
+        """
+        points = atleast_2d(asarray(points))
+
+        d, m = points.shape
+        if d != self.d:
+            if d == 1 and m == self.d:
+                # points was passed in as a row vector
+                points = reshape(points, (self.d, 1))
+                m = 1
+            else:
+                msg = "points have dimension %s, dataset has dimension %s" % (d,
+                    self.d)
+                raise ValueError(msg)
+
+        output_dtype, spec = _get_output_dtype(self.covariance, points)
+        result = gaussian_kernel_estimate[spec](
+            self.dataset.T, self.weights[:, None],
+            points.T, self.cho_cov, output_dtype)
+
+        return result[:, 0]
+
+    __call__ = evaluate
+
+    def integrate_gaussian(self, mean, cov):
+        """
+        Multiply estimated density by a multivariate Gaussian and integrate
+        over the whole space.
+
+        Parameters
+        ----------
+        mean : aray_like
+            A 1-D array, specifying the mean of the Gaussian.
+        cov : array_like
+            A 2-D array, specifying the covariance matrix of the Gaussian.
+
+        Returns
+        -------
+        result : scalar
+            The value of the integral.
+
+        Raises
+        ------
+        ValueError
+            If the mean or covariance of the input Gaussian differs from
+            the KDE's dimensionality.
+
+        """
+        mean = atleast_1d(squeeze(mean))
+        cov = atleast_2d(cov)
+
+        if mean.shape != (self.d,):
+            raise ValueError("mean does not have dimension %s" % self.d)
+        if cov.shape != (self.d, self.d):
+            raise ValueError("covariance does not have dimension %s" % self.d)
+
+        # make mean a column vector
+        mean = mean[:, newaxis]
+
+        sum_cov = self.covariance + cov
+
+        # This will raise LinAlgError if the new cov matrix is not s.p.d
+        # cho_factor returns (ndarray, bool) where bool is a flag for whether
+        # or not ndarray is upper or lower triangular
+        sum_cov_chol = linalg.cho_factor(sum_cov)
+
+        diff = self.dataset - mean
+        tdiff = linalg.cho_solve(sum_cov_chol, diff)
+
+        sqrt_det = np.prod(np.diagonal(sum_cov_chol[0]))
+        norm_const = power(2 * pi, sum_cov.shape[0] / 2.0) * sqrt_det
+
+        energies = sum(diff * tdiff, axis=0) / 2.0
+        result = sum(exp(-energies)*self.weights, axis=0) / norm_const
+
+        return result
+
+    def integrate_box_1d(self, low, high):
+        """
+        Computes the integral of a 1D pdf between two bounds.
+
+        Parameters
+        ----------
+        low : scalar
+            Lower bound of integration.
+        high : scalar
+            Upper bound of integration.
+
+        Returns
+        -------
+        value : scalar
+            The result of the integral.
+
+        Raises
+        ------
+        ValueError
+            If the KDE is over more than one dimension.
+
+        """
+        if self.d != 1:
+            raise ValueError("integrate_box_1d() only handles 1D pdfs")
+
+        stdev = ravel(sqrt(self.covariance))[0]
+
+        normalized_low = ravel((low - self.dataset) / stdev)
+        normalized_high = ravel((high - self.dataset) / stdev)
+
+        value = np.sum(self.weights*(
+                        special.ndtr(normalized_high) -
+                        special.ndtr(normalized_low)))
+        return value
+
+    def integrate_box(self, low_bounds, high_bounds, maxpts=None):
+        """Computes the integral of a pdf over a rectangular interval.
+
+        Parameters
+        ----------
+        low_bounds : array_like
+            A 1-D array containing the lower bounds of integration.
+        high_bounds : array_like
+            A 1-D array containing the upper bounds of integration.
+        maxpts : int, optional
+            The maximum number of points to use for integration.
+
+        Returns
+        -------
+        value : scalar
+            The result of the integral.
+
+        """
+        if maxpts is not None:
+            extra_kwds = {'maxpts': maxpts}
+        else:
+            extra_kwds = {}
+
+        value, inform = _mvn.mvnun_weighted(low_bounds, high_bounds,
+                                           self.dataset, self.weights,
+                                           self.covariance, **extra_kwds)
+        if inform:
+            msg = ('An integral in _mvn.mvnun requires more points than %s' %
+                   (self.d * 1000))
+            warnings.warn(msg)
+
+        return value
+
+    def integrate_kde(self, other):
+        """
+        Computes the integral of the product of this  kernel density estimate
+        with another.
+
+        Parameters
+        ----------
+        other : gaussian_kde instance
+            The other kde.
+
+        Returns
+        -------
+        value : scalar
+            The result of the integral.
+
+        Raises
+        ------
+        ValueError
+            If the KDEs have different dimensionality.
+
+        """
+        if other.d != self.d:
+            raise ValueError("KDEs are not the same dimensionality")
+
+        # we want to iterate over the smallest number of points
+        if other.n < self.n:
+            small = other
+            large = self
+        else:
+            small = self
+            large = other
+
+        sum_cov = small.covariance + large.covariance
+        sum_cov_chol = linalg.cho_factor(sum_cov)
+        result = 0.0
+        for i in range(small.n):
+            mean = small.dataset[:, i, newaxis]
+            diff = large.dataset - mean
+            tdiff = linalg.cho_solve(sum_cov_chol, diff)
+
+            energies = sum(diff * tdiff, axis=0) / 2.0
+            result += sum(exp(-energies)*large.weights, axis=0)*small.weights[i]
+
+        sqrt_det = np.prod(np.diagonal(sum_cov_chol[0]))
+        norm_const = power(2 * pi, sum_cov.shape[0] / 2.0) * sqrt_det
+
+        result /= norm_const
+
+        return result
+
+    def resample(self, size=None, seed=None):
+        """Randomly sample a dataset from the estimated pdf.
+
+        Parameters
+        ----------
+        size : int, optional
+            The number of samples to draw.  If not provided, then the size is
+            the same as the effective number of samples in the underlying
+            dataset.
+        seed : {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
+        -------
+        resample : (self.d, `size`) ndarray
+            The sampled dataset.
+
+        """
+        if size is None:
+            size = int(self.neff)
+
+        random_state = check_random_state(seed)
+        norm = transpose(random_state.multivariate_normal(
+            zeros((self.d,), float), self.covariance, size=size
+        ))
+        indices = random_state.choice(self.n, size=size, p=self.weights)
+        means = self.dataset[:, indices]
+
+        return means + norm
+
+    def scotts_factor(self):
+        """Compute Scott's factor.
+
+        Returns
+        -------
+        s : float
+            Scott's factor.
+        """
+        return power(self.neff, -1./(self.d+4))
+
+    def silverman_factor(self):
+        """Compute the Silverman factor.
+
+        Returns
+        -------
+        s : float
+            The silverman factor.
+        """
+        return power(self.neff*(self.d+2.0)/4.0, -1./(self.d+4))
+
+    #  Default method to calculate bandwidth, can be overwritten by subclass
+    covariance_factor = scotts_factor
+    covariance_factor.__doc__ = """Computes the coefficient (`kde.factor`) that
+        multiplies the data covariance matrix to obtain the kernel covariance
+        matrix. The default is `scotts_factor`.  A subclass can overwrite this
+        method to provide a different method, or set it through a call to
+        `kde.set_bandwidth`."""
+
+    def set_bandwidth(self, bw_method=None):
+        """Compute the estimator bandwidth with given method.
+
+        The new bandwidth calculated after a call to `set_bandwidth` is used
+        for subsequent evaluations of the estimated density.
+
+        Parameters
+        ----------
+        bw_method : str, scalar or callable, optional
+            The method used to calculate the estimator bandwidth.  This can be
+            'scott', 'silverman', a scalar constant or a callable.  If a
+            scalar, this will be used directly as `kde.factor`.  If a callable,
+            it should take a `gaussian_kde` instance as only parameter and
+            return a scalar.  If None (default), nothing happens; the current
+            `kde.covariance_factor` method is kept.
+
+        Notes
+        -----
+        .. versionadded:: 0.11
+
+        Examples
+        --------
+        >>> import numpy as np
+        >>> import scipy.stats as stats
+        >>> x1 = np.array([-7, -5, 1, 4, 5.])
+        >>> kde = stats.gaussian_kde(x1)
+        >>> xs = np.linspace(-10, 10, num=50)
+        >>> y1 = kde(xs)
+        >>> kde.set_bandwidth(bw_method='silverman')
+        >>> y2 = kde(xs)
+        >>> kde.set_bandwidth(bw_method=kde.factor / 3.)
+        >>> y3 = kde(xs)
+
+        >>> import matplotlib.pyplot as plt
+        >>> fig, ax = plt.subplots()
+        >>> ax.plot(x1, np.full(x1.shape, 1 / (4. * x1.size)), 'bo',
+        ...         label='Data points (rescaled)')
+        >>> ax.plot(xs, y1, label='Scott (default)')
+        >>> ax.plot(xs, y2, label='Silverman')
+        >>> ax.plot(xs, y3, label='Const (1/3 * Silverman)')
+        >>> ax.legend()
+        >>> plt.show()
+
+        """
+        if bw_method is None:
+            pass
+        elif bw_method == 'scott':
+            self.covariance_factor = self.scotts_factor
+        elif bw_method == 'silverman':
+            self.covariance_factor = self.silverman_factor
+        elif np.isscalar(bw_method) and not isinstance(bw_method, str):
+            self._bw_method = 'use constant'
+            self.covariance_factor = lambda: bw_method
+        elif callable(bw_method):
+            self._bw_method = bw_method
+            self.covariance_factor = lambda: self._bw_method(self)
+        else:
+            msg = "`bw_method` should be 'scott', 'silverman', a scalar " \
+                  "or a callable."
+            raise ValueError(msg)
+
+        self._compute_covariance()
+
+    def _compute_covariance(self):
+        """Computes the covariance matrix for each Gaussian kernel using
+        covariance_factor().
+        """
+        self.factor = self.covariance_factor()
+        # Cache covariance and Cholesky decomp of covariance
+        if not hasattr(self, '_data_cho_cov'):
+            self._data_covariance = atleast_2d(cov(self.dataset, rowvar=1,
+                                               bias=False,
+                                               aweights=self.weights))
+            self._data_cho_cov = linalg.cholesky(self._data_covariance,
+                                                 lower=True)
+
+        self.covariance = self._data_covariance * self.factor**2
+        self.cho_cov = (self._data_cho_cov * self.factor).astype(np.float64)
+        self.log_det = 2*np.log(np.diag(self.cho_cov
+                                        * np.sqrt(2*pi))).sum()
+
+    @property
+    def inv_cov(self):
+        # Re-compute from scratch each time because I'm not sure how this is
+        # used in the wild. (Perhaps users change the `dataset`, since it's
+        # not a private attribute?) `_compute_covariance` used to recalculate
+        # all these, so we'll recalculate everything now that this is a
+        # a property.
+        self.factor = self.covariance_factor()
+        self._data_covariance = atleast_2d(cov(self.dataset, rowvar=1,
+                                           bias=False, aweights=self.weights))
+        return linalg.inv(self._data_covariance) / self.factor**2
+
+    def pdf(self, x):
+        """
+        Evaluate the estimated pdf on a provided set of points.
+
+        Notes
+        -----
+        This is an alias for `gaussian_kde.evaluate`.  See the ``evaluate``
+        docstring for more details.
+
+        """
+        return self.evaluate(x)
+
+    def logpdf(self, x):
+        """
+        Evaluate the log of the estimated pdf on a provided set of points.
+        """
+        points = atleast_2d(x)
+
+        d, m = points.shape
+        if d != self.d:
+            if d == 1 and m == self.d:
+                # points was passed in as a row vector
+                points = reshape(points, (self.d, 1))
+                m = 1
+            else:
+                msg = (f"points have dimension {d}, "
+                       f"dataset has dimension {self.d}")
+                raise ValueError(msg)
+
+        output_dtype, spec = _get_output_dtype(self.covariance, points)
+        result = gaussian_kernel_estimate_log[spec](
+            self.dataset.T, self.weights[:, None],
+            points.T, self.cho_cov, output_dtype)
+
+        return result[:, 0]
+
+    def marginal(self, dimensions):
+        """Return a marginal KDE distribution
+
+        Parameters
+        ----------
+        dimensions : int or 1-d array_like
+            The dimensions of the multivariate distribution corresponding
+            with the marginal variables, that is, the indices of the dimensions
+            that are being retained. The other dimensions are marginalized out.
+
+        Returns
+        -------
+        marginal_kde : gaussian_kde
+            An object representing the marginal distribution.
+
+        Notes
+        -----
+        .. versionadded:: 1.10.0
+
+        """
+
+        dims = np.atleast_1d(dimensions)
+
+        if not np.issubdtype(dims.dtype, np.integer):
+            msg = ("Elements of `dimensions` must be integers - the indices "
+                   "of the marginal variables being retained.")
+            raise ValueError(msg)
+
+        n = len(self.dataset)  # number of dimensions
+        original_dims = dims.copy()
+
+        dims[dims < 0] = n + dims[dims < 0]
+
+        if len(np.unique(dims)) != len(dims):
+            msg = ("All elements of `dimensions` must be unique.")
+            raise ValueError(msg)
+
+        i_invalid = (dims < 0) | (dims >= n)
+        if np.any(i_invalid):
+            msg = (f"Dimensions {original_dims[i_invalid]} are invalid "
+                   f"for a distribution in {n} dimensions.")
+            raise ValueError(msg)
+
+        dataset = self.dataset[dims]
+        weights = self.weights
+
+        return gaussian_kde(dataset, bw_method=self.covariance_factor(),
+                            weights=weights)
+
+    @property
+    def weights(self):
+        try:
+            return self._weights
+        except AttributeError:
+            self._weights = ones(self.n)/self.n
+            return self._weights
+
+    @property
+    def neff(self):
+        try:
+            return self._neff
+        except AttributeError:
+            self._neff = 1/sum(self.weights**2)
+            return self._neff
+
+
+def _get_output_dtype(covariance, points):
+    """
+    Calculates the output dtype and the "spec" (=C type name).
+
+    This was necessary in order to deal with the fused types in the Cython
+    routine `gaussian_kernel_estimate`. See gh-10824 for details.
+    """
+    output_dtype = np.common_type(covariance, points)
+    itemsize = np.dtype(output_dtype).itemsize
+    if itemsize == 4:
+        spec = 'float'
+    elif itemsize == 8:
+        spec = 'double'
+    elif itemsize in (12, 16):
+        spec = 'long double'
+    else:
+        raise ValueError(
+                f"{output_dtype} has unexpected item size: {itemsize}"
+            )
+
+    return output_dtype, spec

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_ksstats.py

@@ -0,0 +1,596 @@
+# Compute the two-sided one-sample Kolmogorov-Smirnov Prob(Dn <= d) where:
+#    D_n = sup_x{|F_n(x) - F(x)|},
+#    F_n(x) is the empirical CDF for a sample of size n {x_i: i=1,...,n},
+#    F(x) is the CDF of a probability distribution.
+#
+# Exact methods:
+# Prob(D_n >= d) can be computed via a matrix algorithm of Durbin[1]
+#   or a recursion algorithm due to Pomeranz[2].
+# Marsaglia, Tsang & Wang[3] gave a computation-efficient way to perform
+#   the Durbin algorithm.
+#   D_n >= d <==>  D_n+ >= d or D_n- >= d (the one-sided K-S statistics), hence
+#   Prob(D_n >= d) = 2*Prob(D_n+ >= d) - Prob(D_n+ >= d and D_n- >= d).
+#   For d > 0.5, the latter intersection probability is 0.
+#
+# Approximate methods:
+# For d close to 0.5, ignoring that intersection term may still give a
+#   reasonable approximation.
+# Li-Chien[4] and Korolyuk[5] gave an asymptotic formula extending
+# Kolmogorov's initial asymptotic, suitable for large d. (See
+#   scipy.special.kolmogorov for that asymptotic)
+# Pelz-Good[6] used the functional equation for Jacobi theta functions to
+#   transform the Li-Chien/Korolyuk formula produce a computational formula
+#   suitable for small d.
+#
+# Simard and L'Ecuyer[7] provided an algorithm to decide when to use each of
+#   the above approaches and it is that which is used here.
+#
+# Other approaches:
+# Carvalho[8] optimizes Durbin's matrix algorithm for large values of d.
+# Moscovich and Nadler[9] use FFTs to compute the convolutions.
+
+# References:
+# [1] Durbin J (1968).
+#     "The Probability that the Sample Distribution Function Lies Between Two
+#     Parallel Straight Lines."
+#     Annals of Mathematical Statistics, 39, 398-411.
+# [2] Pomeranz J (1974).
+#     "Exact Cumulative Distribution of the Kolmogorov-Smirnov Statistic for
+#     Small Samples (Algorithm 487)."
+#     Communications of the ACM, 17(12), 703-704.
+# [3] Marsaglia G, Tsang WW, Wang J (2003).
+#     "Evaluating Kolmogorov's Distribution."
+#     Journal of Statistical Software, 8(18), 1-4.
+# [4] LI-CHIEN, C. (1956).
+#     "On the exact distribution of the statistics of A. N. Kolmogorov and
+#     their asymptotic expansion."
+#     Acta Matematica Sinica, 6, 55-81.
+# [5] KOROLYUK, V. S. (1960).
+#     "Asymptotic analysis of the distribution of the maximum deviation in
+#     the Bernoulli scheme."
+#     Theor. Probability Appl., 4, 339-366.
+# [6] Pelz W, Good IJ (1976).
+#     "Approximating the Lower Tail-areas of the Kolmogorov-Smirnov One-sample
+#     Statistic."
+#     Journal of the Royal Statistical Society, Series B, 38(2), 152-156.
+#  [7] Simard, R., L'Ecuyer, P. (2011)
+# 	  "Computing the Two-Sided Kolmogorov-Smirnov Distribution",
+# 	  Journal of Statistical Software, Vol 39, 11, 1-18.
+#  [8] Carvalho, Luis (2015)
+#     "An Improved Evaluation of Kolmogorov's Distribution"
+#     Journal of Statistical Software, Code Snippets; Vol 65(3), 1-8.
+#  [9] Amit Moscovich, Boaz Nadler (2017)
+#     "Fast calculation of boundary crossing probabilities for Poisson
+#     processes",
+#     Statistics & Probability Letters, Vol 123, 177-182.
+
+
+import numpy as np
+import scipy.special
+import scipy.special._ufuncs as scu
+from scipy._lib._finite_differences import _derivative
+
+_E128 = 128
+_EP128 = np.ldexp(np.longdouble(1), _E128)
+_EM128 = np.ldexp(np.longdouble(1), -_E128)
+
+_SQRT2PI = np.sqrt(2 * np.pi)
+_LOG_2PI = np.log(2 * np.pi)
+_MIN_LOG = -708
+_SQRT3 = np.sqrt(3)
+_PI_SQUARED = np.pi ** 2
+_PI_FOUR = np.pi ** 4
+_PI_SIX = np.pi ** 6
+
+# [Lifted from _loggamma.pxd.] If B_m are the Bernoulli numbers,
+# then Stirling coeffs are B_{2j}/(2j)/(2j-1) for j=8,...1.
+_STIRLING_COEFFS = [-2.955065359477124183e-2, 6.4102564102564102564e-3,
+                    -1.9175269175269175269e-3, 8.4175084175084175084e-4,
+                    -5.952380952380952381e-4, 7.9365079365079365079e-4,
+                    -2.7777777777777777778e-3, 8.3333333333333333333e-2]
+
+def _log_nfactorial_div_n_pow_n(n):
+    # Computes n! / n**n
+    #    = (n-1)! / n**(n-1)
+    # Uses Stirling's approximation, but removes n*log(n) up-front to
+    # avoid subtractive cancellation.
+    #    = log(n)/2 - n + log(sqrt(2pi)) + sum B_{2j}/(2j)/(2j-1)/n**(2j-1)
+    rn = 1.0/n
+    return np.log(n)/2 - n + _LOG_2PI/2 + rn * np.polyval(_STIRLING_COEFFS, rn/n)
+
+
+def _clip_prob(p):
+    """clips a probability to range 0<=p<=1."""
+    return np.clip(p, 0.0, 1.0)
+
+
+def _select_and_clip_prob(cdfprob, sfprob, cdf=True):
+    """Selects either the CDF or SF, and then clips to range 0<=p<=1."""
+    p = np.where(cdf, cdfprob, sfprob)
+    return _clip_prob(p)
+
+
+def _kolmogn_DMTW(n, d, cdf=True):
+    r"""Computes the Kolmogorov CDF:  Pr(D_n <= d) using the MTW approach to
+    the Durbin matrix algorithm.
+
+    Durbin (1968); Marsaglia, Tsang, Wang (2003). [1], [3].
+    """
+    # Write d = (k-h)/n, where k is positive integer and 0 <= h < 1
+    # Generate initial matrix H of size m*m where m=(2k-1)
+    # Compute k-th row of (n!/n^n) * H^n, scaling intermediate results.
+    # Requires memory O(m^2) and computation O(m^2 log(n)).
+    # Most suitable for small m.
+
+    if d >= 1.0:
+        return _select_and_clip_prob(1.0, 0.0, cdf)
+    nd = n * d
+    if nd <= 0.5:
+        return _select_and_clip_prob(0.0, 1.0, cdf)
+    k = int(np.ceil(nd))
+    h = k - nd
+    m = 2 * k - 1
+
+    H = np.zeros([m, m])
+
+    # Initialize: v is first column (and last row) of H
+    #  v[j] = (1-h^(j+1)/(j+1)!  (except for v[-1])
+    #  w[j] = 1/(j)!
+    # q = k-th row of H (actually i!/n^i*H^i)
+    intm = np.arange(1, m + 1)
+    v = 1.0 - h ** intm
+    w = np.empty(m)
+    fac = 1.0
+    for j in intm:
+        w[j - 1] = fac
+        fac /= j  # This might underflow.  Isn't a problem.
+        v[j - 1] *= fac
+    tt = max(2 * h - 1.0, 0)**m - 2*h**m
+    v[-1] = (1.0 + tt) * fac
+
+    for i in range(1, m):
+        H[i - 1:, i] = w[:m - i + 1]
+    H[:, 0] = v
+    H[-1, :] = np.flip(v, axis=0)
+
+    Hpwr = np.eye(np.shape(H)[0])  # Holds intermediate powers of H
+    nn = n
+    expnt = 0  # Scaling of Hpwr
+    Hexpnt = 0  # Scaling of H
+    while nn > 0:
+        if nn % 2:
+            Hpwr = np.matmul(Hpwr, H)
+            expnt += Hexpnt
+        H = np.matmul(H, H)
+        Hexpnt *= 2
+        # Scale as needed.
+        if np.abs(H[k - 1, k - 1]) > _EP128:
+            H /= _EP128
+            Hexpnt += _E128
+        nn = nn // 2
+
+    p = Hpwr[k - 1, k - 1]
+
+    # Multiply by n!/n^n
+    for i in range(1, n + 1):
+        p = i * p / n
+        if np.abs(p) < _EM128:
+            p *= _EP128
+            expnt -= _E128
+
+    # unscale
+    if expnt != 0:
+        p = np.ldexp(p, expnt)
+
+    return _select_and_clip_prob(p, 1.0-p, cdf)
+
+
+def _pomeranz_compute_j1j2(i, n, ll, ceilf, roundf):
+    """Compute the endpoints of the interval for row i."""
+    if i == 0:
+        j1, j2 = -ll - ceilf - 1, ll + ceilf - 1
+    else:
+        # i + 1 = 2*ip1div2 + ip1mod2
+        ip1div2, ip1mod2 = divmod(i + 1, 2)
+        if ip1mod2 == 0:  # i is odd
+            if ip1div2 == n + 1:
+                j1, j2 = n - ll - ceilf - 1, n + ll + ceilf - 1
+            else:
+                j1, j2 = ip1div2 - 1 - ll - roundf - 1, ip1div2 + ll - 1 + ceilf - 1
+        else:
+            j1, j2 = ip1div2 - 1 - ll - 1, ip1div2 + ll + roundf - 1
+
+    return max(j1 + 2, 0), min(j2, n)
+
+
+def _kolmogn_Pomeranz(n, x, cdf=True):
+    r"""Computes Pr(D_n <= d) using the Pomeranz recursion algorithm.
+
+    Pomeranz (1974) [2]
+    """
+
+    # V is n*(2n+2) matrix.
+    # Each row is convolution of the previous row and probabilities from a
+    #  Poisson distribution.
+    # Desired CDF probability is n! V[n-1, 2n+1]  (final entry in final row).
+    # Only two rows are needed at any given stage:
+    #  - Call them V0 and V1.
+    #  - Swap each iteration
+    # Only a few (contiguous) entries in each row can be non-zero.
+    #  - Keep track of start and end (j1 and j2 below)
+    #  - V0s and V1s track the start in the two rows
+    # Scale intermediate results as needed.
+    # Only a few different Poisson distributions can occur
+    t = n * x
+    ll = int(np.floor(t))
+    f = 1.0 * (t - ll)  # fractional part of t
+    g = min(f, 1.0 - f)
+    ceilf = (1 if f > 0 else 0)
+    roundf = (1 if f > 0.5 else 0)
+    npwrs = 2 * (ll + 1)    # Maximum number of powers needed in convolutions
+    gpower = np.empty(npwrs)  # gpower = (g/n)^m/m!
+    twogpower = np.empty(npwrs)  # twogpower = (2g/n)^m/m!
+    onem2gpower = np.empty(npwrs)  # onem2gpower = ((1-2g)/n)^m/m!
+    # gpower etc are *almost* Poisson probs, just missing normalizing factor.
+
+    gpower[0] = 1.0
+    twogpower[0] = 1.0
+    onem2gpower[0] = 1.0
+    expnt = 0
+    g_over_n, two_g_over_n, one_minus_two_g_over_n = g/n, 2*g/n, (1 - 2*g)/n
+    for m in range(1, npwrs):
+        gpower[m] = gpower[m - 1] * g_over_n / m
+        twogpower[m] = twogpower[m - 1] * two_g_over_n / m
+        onem2gpower[m] = onem2gpower[m - 1] * one_minus_two_g_over_n / m
+
+    V0 = np.zeros([npwrs])
+    V1 = np.zeros([npwrs])
+    V1[0] = 1  # first row
+    V0s, V1s = 0, 0  # start indices of the two rows
+
+    j1, j2 = _pomeranz_compute_j1j2(0, n, ll, ceilf, roundf)
+    for i in range(1, 2 * n + 2):
+        # Preserve j1, V1, V1s, V0s from last iteration
+        k1 = j1
+        V0, V1 = V1, V0
+        V0s, V1s = V1s, V0s
+        V1.fill(0.0)
+        j1, j2 = _pomeranz_compute_j1j2(i, n, ll, ceilf, roundf)
+        if i == 1 or i == 2 * n + 1:
+            pwrs = gpower
+        else:
+            pwrs = (twogpower if i % 2 else onem2gpower)
+        ln2 = j2 - k1 + 1
+        if ln2 > 0:
+            conv = np.convolve(V0[k1 - V0s:k1 - V0s + ln2], pwrs[:ln2])
+            conv_start = j1 - k1  # First index to use from conv
+            conv_len = j2 - j1 + 1  # Number of entries to use from conv
+            V1[:conv_len] = conv[conv_start:conv_start + conv_len]
+            # Scale to avoid underflow.
+            if 0 < np.max(V1) < _EM128:
+                V1 *= _EP128
+                expnt -= _E128
+            V1s = V0s + j1 - k1
+
+    # multiply by n!
+    ans = V1[n - V1s]
+    for m in range(1, n + 1):
+        if np.abs(ans) > _EP128:
+            ans *= _EM128
+            expnt += _E128
+        ans *= m
+
+    # Undo any intermediate scaling
+    if expnt != 0:
+        ans = np.ldexp(ans, expnt)
+    ans = _select_and_clip_prob(ans, 1.0 - ans, cdf)
+    return ans
+
+
+def _kolmogn_PelzGood(n, x, cdf=True):
+    """Computes the Pelz-Good approximation to Prob(Dn <= x) with 0<=x<=1.
+
+    Start with Li-Chien, Korolyuk approximation:
+        Prob(Dn <= x) ~ K0(z) + K1(z)/sqrt(n) + K2(z)/n + K3(z)/n**1.5
+    where z = x*sqrt(n).
+    Transform each K_(z) using Jacobi theta functions into a form suitable
+    for small z.
+    Pelz-Good (1976). [6]
+    """
+    if x <= 0.0:
+        return _select_and_clip_prob(0.0, 1.0, cdf=cdf)
+    if x >= 1.0:
+        return _select_and_clip_prob(1.0, 0.0, cdf=cdf)
+
+    z = np.sqrt(n) * x
+    zsquared, zthree, zfour, zsix = z**2, z**3, z**4, z**6
+
+    qlog = -_PI_SQUARED / 8 / zsquared
+    if qlog < _MIN_LOG:  # z ~ 0.041743441416853426
+        return _select_and_clip_prob(0.0, 1.0, cdf=cdf)
+
+    q = np.exp(qlog)
+
+    # Coefficients of terms in the sums for K1, K2 and K3
+    k1a = -zsquared
+    k1b = _PI_SQUARED / 4
+
+    k2a = 6 * zsix + 2 * zfour
+    k2b = (2 * zfour - 5 * zsquared) * _PI_SQUARED / 4
+    k2c = _PI_FOUR * (1 - 2 * zsquared) / 16
+
+    k3d = _PI_SIX * (5 - 30 * zsquared) / 64
+    k3c = _PI_FOUR * (-60 * zsquared + 212 * zfour) / 16
+    k3b = _PI_SQUARED * (135 * zfour - 96 * zsix) / 4
+    k3a = -30 * zsix - 90 * z**8
+
+    K0to3 = np.zeros(4)
+    # Use a Horner scheme to evaluate sum c_i q^(i^2)
+    # Reduces to a sum over odd integers.
+    maxk = int(np.ceil(16 * z / np.pi))
+    for k in range(maxk, 0, -1):
+        m = 2 * k - 1
+        msquared, mfour, msix = m**2, m**4, m**6
+        qpower = np.power(q, 8 * k)
+        coeffs = np.array([1.0,
+                           k1a + k1b*msquared,
+                           k2a + k2b*msquared + k2c*mfour,
+                           k3a + k3b*msquared + k3c*mfour + k3d*msix])
+        K0to3 *= qpower
+        K0to3 += coeffs
+    K0to3 *= q
+    K0to3 *= _SQRT2PI
+    # z**10 > 0 as z > 0.04
+    K0to3 /= np.array([z, 6 * zfour, 72 * z**7, 6480 * z**10])
+
+    # Now do the other sum over the other terms, all integers k
+    # K_2:  (pi^2 k^2) q^(k^2),
+    # K_3:  (3pi^2 k^2 z^2 - pi^4 k^4)*q^(k^2)
+    # Don't expect much subtractive cancellation so use direct calculation
+    q = np.exp(-_PI_SQUARED / 2 / zsquared)
+    ks = np.arange(maxk, 0, -1)
+    ksquared = ks ** 2
+    sqrt3z = _SQRT3 * z
+    kspi = np.pi * ks
+    qpwers = q ** ksquared
+    k2extra = np.sum(ksquared * qpwers)
+    k2extra *= _PI_SQUARED * _SQRT2PI/(-36 * zthree)
+    K0to3[2] += k2extra
+    k3extra = np.sum((sqrt3z + kspi) * (sqrt3z - kspi) * ksquared * qpwers)
+    k3extra *= _PI_SQUARED * _SQRT2PI/(216 * zsix)
+    K0to3[3] += k3extra
+    powers_of_n = np.power(n * 1.0, np.arange(len(K0to3)) / 2.0)
+    K0to3 /= powers_of_n
+
+    if not cdf:
+        K0to3 *= -1
+        K0to3[0] += 1
+
+    Ksum = sum(K0to3)
+    return Ksum
+
+
+def _kolmogn(n, x, cdf=True):
+    """Computes the CDF(or SF) for the two-sided Kolmogorov-Smirnov statistic.
+
+    x must be of type float, n of type integer.
+
+    Simard & L'Ecuyer (2011) [7].
+    """
+    if np.isnan(n):
+        return n  # Keep the same type of nan
+    if int(n) != n or n <= 0:
+        return np.nan
+    if x >= 1.0:
+        return _select_and_clip_prob(1.0, 0.0, cdf=cdf)
+    if x <= 0.0:
+        return _select_and_clip_prob(0.0, 1.0, cdf=cdf)
+    t = n * x
+    if t <= 1.0:  # Ruben-Gambino: 1/2n <= x <= 1/n
+        if t <= 0.5:
+            return _select_and_clip_prob(0.0, 1.0, cdf=cdf)
+        if n <= 140:
+            prob = np.prod(np.arange(1, n+1) * (1.0/n) * (2*t - 1))
+        else:
+            prob = np.exp(_log_nfactorial_div_n_pow_n(n) + n * np.log(2*t-1))
+        return _select_and_clip_prob(prob, 1.0 - prob, cdf=cdf)
+    if t >= n - 1:  # Ruben-Gambino
+        prob = 2 * (1.0 - x)**n
+        return _select_and_clip_prob(1 - prob, prob, cdf=cdf)
+    if x >= 0.5:  # Exact: 2 * smirnov
+        prob = 2 * scipy.special.smirnov(n, x)
+        return _select_and_clip_prob(1.0 - prob, prob, cdf=cdf)
+
+    nxsquared = t * x
+    if n <= 140:
+        if nxsquared <= 0.754693:
+            prob = _kolmogn_DMTW(n, x, cdf=True)
+            return _select_and_clip_prob(prob, 1.0 - prob, cdf=cdf)
+        if nxsquared <= 4:
+            prob = _kolmogn_Pomeranz(n, x, cdf=True)
+            return _select_and_clip_prob(prob, 1.0 - prob, cdf=cdf)
+        # Now use Miller approximation of 2*smirnov
+        prob = 2 * scipy.special.smirnov(n, x)
+        return _select_and_clip_prob(1.0 - prob, prob, cdf=cdf)
+
+    # Split CDF and SF as they have different cutoffs on nxsquared.
+    if not cdf:
+        if nxsquared >= 370.0:
+            return 0.0
+        if nxsquared >= 2.2:
+            prob = 2 * scipy.special.smirnov(n, x)
+            return _clip_prob(prob)
+        # Fall through and compute the SF as 1.0-CDF
+    if nxsquared >= 18.0:
+        cdfprob = 1.0
+    elif n <= 100000 and n * x**1.5 <= 1.4:
+        cdfprob = _kolmogn_DMTW(n, x, cdf=True)
+    else:
+        cdfprob = _kolmogn_PelzGood(n, x, cdf=True)
+    return _select_and_clip_prob(cdfprob, 1.0 - cdfprob, cdf=cdf)
+
+
+def _kolmogn_p(n, x):
+    """Computes the PDF for the two-sided Kolmogorov-Smirnov statistic.
+
+    x must be of type float, n of type integer.
+    """
+    if np.isnan(n):
+        return n  # Keep the same type of nan
+    if int(n) != n or n <= 0:
+        return np.nan
+    if x >= 1.0 or x <= 0:
+        return 0
+    t = n * x
+    if t <= 1.0:
+        # Ruben-Gambino: n!/n^n * (2t-1)^n -> 2 n!/n^n * n^2 * (2t-1)^(n-1)
+        if t <= 0.5:
+            return 0.0
+        if n <= 140:
+            prd = np.prod(np.arange(1, n) * (1.0 / n) * (2 * t - 1))
+        else:
+            prd = np.exp(_log_nfactorial_div_n_pow_n(n) + (n-1) * np.log(2 * t - 1))
+        return prd * 2 * n**2
+    if t >= n - 1:
+        # Ruben-Gambino : 1-2(1-x)**n -> 2n*(1-x)**(n-1)
+        return 2 * (1.0 - x) ** (n-1) * n
+    if x >= 0.5:
+        return 2 * scipy.stats.ksone.pdf(x, n)
+
+    # Just take a small delta.
+    # Ideally x +/- delta would stay within [i/n, (i+1)/n] for some integer a.
+    # as the CDF is a piecewise degree n polynomial.
+    # It has knots at 1/n, 2/n, ... (n-1)/n
+    # and is not a C-infinity function at the knots
+    delta = x / 2.0**16
+    delta = min(delta, x - 1.0/n)
+    delta = min(delta, 0.5 - x)
+
+    def _kk(_x):
+        return kolmogn(n, _x)
+
+    return _derivative(_kk, x, dx=delta, order=5)
+
+
+def _kolmogni(n, p, q):
+    """Computes the PPF/ISF of kolmogn.
+
+    n of type integer, n>= 1
+    p is the CDF, q the SF, p+q=1
+    """
+    if np.isnan(n):
+        return n  # Keep the same type of nan
+    if int(n) != n or n <= 0:
+        return np.nan
+    if p <= 0:
+        return 1.0/n
+    if q <= 0:
+        return 1.0
+    delta = np.exp((np.log(p) - scipy.special.loggamma(n+1))/n)
+    if delta <= 1.0/n:
+        return (delta + 1.0 / n) / 2
+    x = -np.expm1(np.log(q/2.0)/n)
+    if x >= 1 - 1.0/n:
+        return x
+    x1 = scu._kolmogci(p)/np.sqrt(n)
+    x1 = min(x1, 1.0 - 1.0/n)
+    _f = lambda x: _kolmogn(n, x) - p
+    return scipy.optimize.brentq(_f, 1.0/n, x1, xtol=1e-14)
+
+
+def kolmogn(n, x, cdf=True):
+    """Computes the CDF for the two-sided Kolmogorov-Smirnov distribution.
+
+    The two-sided Kolmogorov-Smirnov distribution has as its CDF Pr(D_n <= x),
+    for a sample of size n drawn from a distribution with CDF F(t), where
+    D_n &= sup_t |F_n(t) - F(t)|, and
+    F_n(t) is the Empirical Cumulative Distribution Function of the sample.
+
+    Parameters
+    ----------
+    n : integer, array_like
+        the number of samples
+    x : float, array_like
+        The K-S statistic, float between 0 and 1
+    cdf : bool, optional
+        whether to compute the CDF(default=true) or the SF.
+
+    Returns
+    -------
+    cdf : ndarray
+        CDF (or SF it cdf is False) at the specified locations.
+
+    The return value has shape the result of numpy broadcasting n and x.
+    """
+    it = np.nditer([n, x, cdf, None],
+                   op_dtypes=[None, np.float64, np.bool_, np.float64])
+    for _n, _x, _cdf, z in it:
+        if np.isnan(_n):
+            z[...] = _n
+            continue
+        if int(_n) != _n:
+            raise ValueError(f'n is not integral: {_n}')
+        z[...] = _kolmogn(int(_n), _x, cdf=_cdf)
+    result = it.operands[-1]
+    return result
+
+
+def kolmognp(n, x):
+    """Computes the PDF for the two-sided Kolmogorov-Smirnov distribution.
+
+    Parameters
+    ----------
+    n : integer, array_like
+        the number of samples
+    x : float, array_like
+        The K-S statistic, float between 0 and 1
+
+    Returns
+    -------
+    pdf : ndarray
+        The PDF at the specified locations
+
+    The return value has shape the result of numpy broadcasting n and x.
+    """
+    it = np.nditer([n, x, None])
+    for _n, _x, z in it:
+        if np.isnan(_n):
+            z[...] = _n
+            continue
+        if int(_n) != _n:
+            raise ValueError(f'n is not integral: {_n}')
+        z[...] = _kolmogn_p(int(_n), _x)
+    result = it.operands[-1]
+    return result
+
+
+def kolmogni(n, q, cdf=True):
+    """Computes the PPF(or ISF) for the two-sided Kolmogorov-Smirnov distribution.
+
+    Parameters
+    ----------
+    n : integer, array_like
+        the number of samples
+    q : float, array_like
+        Probabilities, float between 0 and 1
+    cdf : bool, optional
+        whether to compute the PPF(default=true) or the ISF.
+
+    Returns
+    -------
+    ppf : ndarray
+        PPF (or ISF if cdf is False) at the specified locations
+
+    The return value has shape the result of numpy broadcasting n and x.
+    """
+    it = np.nditer([n, q, cdf, None])
+    for _n, _q, _cdf, z in it:
+        if np.isnan(_n):
+            z[...] = _n
+            continue
+        if int(_n) != _n:
+            raise ValueError(f'n is not integral: {_n}')
+        _pcdf, _psf = (_q, 1-_q) if _cdf else (1-_q, _q)
+        z[...] = _kolmogni(int(_n), _pcdf, _psf)
+    result = it.operands[-1]
+    return result

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_mannwhitneyu.py

@@ -0,0 +1,493 @@
+import numpy as np
+from collections import namedtuple
+from scipy import special
+from scipy import stats
+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):
+        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'''
+        # We could use the fact that the distribution is symmetric to avoid
+        # summing more than m*n/2 terms, but it might not be worth the
+        # overhead. Let's leave that to an improvement.
+        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'''
+        # 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
+        k = m*n - k
+        # 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
+        return self.cdf(k, m, n)
+
+    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 _tie_term(ranks):
+    """Tie correction term"""
+    # element i of t is the number of elements sharing rank i
+    _, t = np.unique(ranks, return_counts=True, axis=-1)
+    return (t**3 - t).sum(axis=-1)
+
+
+def _get_mwu_z(U, n1, n2, ranks, axis=0, continuity=True):
+    '''Standardized MWU statistic'''
+    # Follows mannwhitneyu [2]
+    mu = n1 * n2 / 2
+    n = n1 + n2
+
+    # Tie correction according to [2]
+    tie_term = np.apply_along_axis(_tie_term, -1, ranks)
+    s = np.sqrt(n1*n2/12 * ((n + 1) - tie_term/(n*(n-1))))
+
+    # equivalent to using scipy.stats.tiecorrect
+    # T = np.apply_along_axis(stats.tiecorrect, -1, ranks)
+    # s = np.sqrt(T * n1 * n2 * (n1+n2+1) / 12.0)
+
+    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.')
+
+    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 _tie_check(xy):
+    """Find any ties in data"""
+    _, t = np.unique(xy, return_counts=True, axis=-1)
+    return np.any(t != 1)
+
+
+def _mwu_choose_method(n1, n2, xy, method):
+    """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 np.apply_along_axis(_tie_check, -1, xy).any():
+        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*.
+
+        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'}, 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 8 and there are no ties; chooses ``'asymptotic'``
+          otherwise.
+
+    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.
+
+    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]
+
+    if method == "auto":
+        method = _mwu_choose_method(n1, n2, xy, method)
+
+    # Follows [2]
+    ranks = stats.rankdata(xy, axis=-1)  # 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 == "exact":
+        p = _mwu_state.sf(U.astype(int), n1, n2)
+    elif method == "asymptotic":
+        z = _get_mwu_z(U, n1, n2, ranks, continuity=use_continuity)
+        p = stats.norm.sf(z)
+    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)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_mstats_extras.py

@@ -0,0 +1,500 @@
+"""
+Additional statistics functions with support for masked arrays.
+
+"""
+
+# Original author (2007): Pierre GF Gerard-Marchant
+
+
+__all__ = ['compare_medians_ms',
+           'hdquantiles', 'hdmedian', 'hdquantiles_sd',
+           'idealfourths',
+           'median_cihs','mjci','mquantiles_cimj',
+           'rsh',
+           'trimmed_mean_ci',]
+
+
+import numpy as np
+from numpy import float_, int_, ndarray
+
+import numpy.ma as ma
+from numpy.ma import MaskedArray
+
+from . import _mstats_basic as mstats
+
+from scipy.stats.distributions import norm, beta, t, binom
+
+
+def hdquantiles(data, prob=list([.25,.5,.75]), axis=None, var=False,):
+    """
+    Computes quantile estimates with the Harrell-Davis method.
+
+    The quantile estimates are calculated as a weighted linear combination
+    of order statistics.
+
+    Parameters
+    ----------
+    data : array_like
+        Data array.
+    prob : sequence, optional
+        Sequence of quantiles to compute.
+    axis : int or None, optional
+        Axis along which to compute the quantiles. If None, use a flattened
+        array.
+    var : bool, optional
+        Whether to return the variance of the estimate.
+
+    Returns
+    -------
+    hdquantiles : MaskedArray
+        A (p,) array of quantiles (if `var` is False), or a (2,p) array of
+        quantiles and variances (if `var` is True), where ``p`` is the
+        number of quantiles.
+
+    See Also
+    --------
+    hdquantiles_sd
+
+    """
+    def _hd_1D(data,prob,var):
+        "Computes the HD quantiles for a 1D array. Returns nan for invalid data."
+        xsorted = np.squeeze(np.sort(data.compressed().view(ndarray)))
+        # Don't use length here, in case we have a numpy scalar
+        n = xsorted.size
+
+        hd = np.empty((2,len(prob)), float_)
+        if n < 2:
+            hd.flat = np.nan
+            if var:
+                return hd
+            return hd[0]
+
+        v = np.arange(n+1) / float(n)
+        betacdf = beta.cdf
+        for (i,p) in enumerate(prob):
+            _w = betacdf(v, (n+1)*p, (n+1)*(1-p))
+            w = _w[1:] - _w[:-1]
+            hd_mean = np.dot(w, xsorted)
+            hd[0,i] = hd_mean
+            #
+            hd[1,i] = np.dot(w, (xsorted-hd_mean)**2)
+            #
+        hd[0, prob == 0] = xsorted[0]
+        hd[0, prob == 1] = xsorted[-1]
+        if var:
+            hd[1, prob == 0] = hd[1, prob == 1] = np.nan
+            return hd
+        return hd[0]
+    # Initialization & checks
+    data = ma.array(data, copy=False, dtype=float_)
+    p = np.array(prob, copy=False, ndmin=1)
+    # Computes quantiles along axis (or globally)
+    if (axis is None) or (data.ndim == 1):
+        result = _hd_1D(data, p, var)
+    else:
+        if data.ndim > 2:
+            raise ValueError("Array 'data' must be at most two dimensional, "
+                             "but got data.ndim = %d" % data.ndim)
+        result = ma.apply_along_axis(_hd_1D, axis, data, p, var)
+
+    return ma.fix_invalid(result, copy=False)
+
+
+def hdmedian(data, axis=-1, var=False):
+    """
+    Returns the Harrell-Davis estimate of the median along the given axis.
+
+    Parameters
+    ----------
+    data : ndarray
+        Data array.
+    axis : int, optional
+        Axis along which to compute the quantiles. If None, use a flattened
+        array.
+    var : bool, optional
+        Whether to return the variance of the estimate.
+
+    Returns
+    -------
+    hdmedian : MaskedArray
+        The median values.  If ``var=True``, the variance is returned inside
+        the masked array.  E.g. for a 1-D array the shape change from (1,) to
+        (2,).
+
+    """
+    result = hdquantiles(data,[0.5], axis=axis, var=var)
+    return result.squeeze()
+
+
+def hdquantiles_sd(data, prob=list([.25,.5,.75]), axis=None):
+    """
+    The standard error of the Harrell-Davis quantile estimates by jackknife.
+
+    Parameters
+    ----------
+    data : array_like
+        Data array.
+    prob : sequence, optional
+        Sequence of quantiles to compute.
+    axis : int, optional
+        Axis along which to compute the quantiles. If None, use a flattened
+        array.
+
+    Returns
+    -------
+    hdquantiles_sd : MaskedArray
+        Standard error of the Harrell-Davis quantile estimates.
+
+    See Also
+    --------
+    hdquantiles
+
+    """
+    def _hdsd_1D(data, prob):
+        "Computes the std error for 1D arrays."
+        xsorted = np.sort(data.compressed())
+        n = len(xsorted)
+
+        hdsd = np.empty(len(prob), float_)
+        if n < 2:
+            hdsd.flat = np.nan
+
+        vv = np.arange(n) / float(n-1)
+        betacdf = beta.cdf
+
+        for (i,p) in enumerate(prob):
+            _w = betacdf(vv, n*p, n*(1-p))
+            w = _w[1:] - _w[:-1]
+            # cumulative sum of weights and data points if
+            # ith point is left out for jackknife
+            mx_ = np.zeros_like(xsorted)
+            mx_[1:] = np.cumsum(w * xsorted[:-1])
+            # similar but from the right
+            mx_[:-1] += np.cumsum(w[::-1] * xsorted[:0:-1])[::-1]
+            hdsd[i] = np.sqrt(mx_.var() * (n - 1))
+        return hdsd
+
+    # Initialization & checks
+    data = ma.array(data, copy=False, dtype=float_)
+    p = np.array(prob, copy=False, ndmin=1)
+    # Computes quantiles along axis (or globally)
+    if (axis is None):
+        result = _hdsd_1D(data, p)
+    else:
+        if data.ndim > 2:
+            raise ValueError("Array 'data' must be at most two dimensional, "
+                             "but got data.ndim = %d" % data.ndim)
+        result = ma.apply_along_axis(_hdsd_1D, axis, data, p)
+
+    return ma.fix_invalid(result, copy=False).ravel()
+
+
+def trimmed_mean_ci(data, limits=(0.2,0.2), inclusive=(True,True),
+                    alpha=0.05, axis=None):
+    """
+    Selected confidence interval of the trimmed mean along the given axis.
+
+    Parameters
+    ----------
+    data : array_like
+        Input data.
+    limits : {None, tuple}, optional
+        None or a two item tuple.
+        Tuple of the percentages to cut on each side of the array, with respect
+        to the number of unmasked data, as floats between 0. and 1. If ``n``
+        is the number of unmasked data before trimming, then
+        (``n * limits[0]``)th smallest data and (``n * limits[1]``)th
+        largest data are masked.  The total number of unmasked data after
+        trimming is ``n * (1. - sum(limits))``.
+        The value of one limit can be set to None to indicate an open interval.
+
+        Defaults to (0.2, 0.2).
+    inclusive : (2,) tuple of boolean, optional
+        If relative==False, tuple indicating whether values exactly equal to
+        the absolute limits are allowed.
+        If relative==True, tuple indicating whether the number of data being
+        masked on each side should be rounded (True) or truncated (False).
+
+        Defaults to (True, True).
+    alpha : float, optional
+        Confidence level of the intervals.
+
+        Defaults to 0.05.
+    axis : int, optional
+        Axis along which to cut. If None, uses a flattened version of `data`.
+
+        Defaults to None.
+
+    Returns
+    -------
+    trimmed_mean_ci : (2,) ndarray
+        The lower and upper confidence intervals of the trimmed data.
+
+    """
+    data = ma.array(data, copy=False)
+    trimmed = mstats.trimr(data, limits=limits, inclusive=inclusive, axis=axis)
+    tmean = trimmed.mean(axis)
+    tstde = mstats.trimmed_stde(data,limits=limits,inclusive=inclusive,axis=axis)
+    df = trimmed.count(axis) - 1
+    tppf = t.ppf(1-alpha/2.,df)
+    return np.array((tmean - tppf*tstde, tmean+tppf*tstde))
+
+
+def mjci(data, prob=[0.25,0.5,0.75], axis=None):
+    """
+    Returns the Maritz-Jarrett estimators of the standard error of selected
+    experimental quantiles of the data.
+
+    Parameters
+    ----------
+    data : ndarray
+        Data array.
+    prob : sequence, optional
+        Sequence of quantiles to compute.
+    axis : int or None, optional
+        Axis along which to compute the quantiles. If None, use a flattened
+        array.
+
+    """
+    def _mjci_1D(data, p):
+        data = np.sort(data.compressed())
+        n = data.size
+        prob = (np.array(p) * n + 0.5).astype(int_)
+        betacdf = beta.cdf
+
+        mj = np.empty(len(prob), float_)
+        x = np.arange(1,n+1, dtype=float_) / n
+        y = x - 1./n
+        for (i,m) in enumerate(prob):
+            W = betacdf(x,m-1,n-m) - betacdf(y,m-1,n-m)
+            C1 = np.dot(W,data)
+            C2 = np.dot(W,data**2)
+            mj[i] = np.sqrt(C2 - C1**2)
+        return mj
+
+    data = ma.array(data, copy=False)
+    if data.ndim > 2:
+        raise ValueError("Array 'data' must be at most two dimensional, "
+                         "but got data.ndim = %d" % data.ndim)
+
+    p = np.array(prob, copy=False, ndmin=1)
+    # Computes quantiles along axis (or globally)
+    if (axis is None):
+        return _mjci_1D(data, p)
+    else:
+        return ma.apply_along_axis(_mjci_1D, axis, data, p)
+
+
+def mquantiles_cimj(data, prob=[0.25,0.50,0.75], alpha=0.05, axis=None):
+    """
+    Computes the alpha confidence interval for the selected quantiles of the
+    data, with Maritz-Jarrett estimators.
+
+    Parameters
+    ----------
+    data : ndarray
+        Data array.
+    prob : sequence, optional
+        Sequence of quantiles to compute.
+    alpha : float, optional
+        Confidence level of the intervals.
+    axis : int or None, optional
+        Axis along which to compute the quantiles.
+        If None, use a flattened array.
+
+    Returns
+    -------
+    ci_lower : ndarray
+        The lower boundaries of the confidence interval.  Of the same length as
+        `prob`.
+    ci_upper : ndarray
+        The upper boundaries of the confidence interval.  Of the same length as
+        `prob`.
+
+    """
+    alpha = min(alpha, 1 - alpha)
+    z = norm.ppf(1 - alpha/2.)
+    xq = mstats.mquantiles(data, prob, alphap=0, betap=0, axis=axis)
+    smj = mjci(data, prob, axis=axis)
+    return (xq - z * smj, xq + z * smj)
+
+
+def median_cihs(data, alpha=0.05, axis=None):
+    """
+    Computes the alpha-level confidence interval for the median of the data.
+
+    Uses the Hettmasperger-Sheather method.
+
+    Parameters
+    ----------
+    data : array_like
+        Input data. Masked values are discarded. The input should be 1D only,
+        or `axis` should be set to None.
+    alpha : float, optional
+        Confidence level of the intervals.
+    axis : int or None, optional
+        Axis along which to compute the quantiles. If None, use a flattened
+        array.
+
+    Returns
+    -------
+    median_cihs
+        Alpha level confidence interval.
+
+    """
+    def _cihs_1D(data, alpha):
+        data = np.sort(data.compressed())
+        n = len(data)
+        alpha = min(alpha, 1-alpha)
+        k = int(binom._ppf(alpha/2., n, 0.5))
+        gk = binom.cdf(n-k,n,0.5) - binom.cdf(k-1,n,0.5)
+        if gk < 1-alpha:
+            k -= 1
+            gk = binom.cdf(n-k,n,0.5) - binom.cdf(k-1,n,0.5)
+        gkk = binom.cdf(n-k-1,n,0.5) - binom.cdf(k,n,0.5)
+        I = (gk - 1 + alpha)/(gk - gkk)
+        lambd = (n-k) * I / float(k + (n-2*k)*I)
+        lims = (lambd*data[k] + (1-lambd)*data[k-1],
+                lambd*data[n-k-1] + (1-lambd)*data[n-k])
+        return lims
+    data = ma.array(data, copy=False)
+    # Computes quantiles along axis (or globally)
+    if (axis is None):
+        result = _cihs_1D(data, alpha)
+    else:
+        if data.ndim > 2:
+            raise ValueError("Array 'data' must be at most two dimensional, "
+                             "but got data.ndim = %d" % data.ndim)
+        result = ma.apply_along_axis(_cihs_1D, axis, data, alpha)
+
+    return result
+
+
+def compare_medians_ms(group_1, group_2, axis=None):
+    """
+    Compares the medians from two independent groups along the given axis.
+
+    The comparison is performed using the McKean-Schrader estimate of the
+    standard error of the medians.
+
+    Parameters
+    ----------
+    group_1 : array_like
+        First dataset.  Has to be of size >=7.
+    group_2 : array_like
+        Second dataset.  Has to be of size >=7.
+    axis : int, optional
+        Axis along which the medians are estimated. If None, the arrays are
+        flattened.  If `axis` is not None, then `group_1` and `group_2`
+        should have the same shape.
+
+    Returns
+    -------
+    compare_medians_ms : {float, ndarray}
+        If `axis` is None, then returns a float, otherwise returns a 1-D
+        ndarray of floats with a length equal to the length of `group_1`
+        along `axis`.
+
+    Examples
+    --------
+
+    >>> from scipy import stats
+    >>> a = [1, 2, 3, 4, 5, 6, 7]
+    >>> b = [8, 9, 10, 11, 12, 13, 14]
+    >>> stats.mstats.compare_medians_ms(a, b, axis=None)
+    1.0693225866553746e-05
+
+    The function is vectorized to compute along a given axis.
+
+    >>> import numpy as np
+    >>> rng = np.random.default_rng()
+    >>> x = rng.random(size=(3, 7))
+    >>> y = rng.random(size=(3, 8))
+    >>> stats.mstats.compare_medians_ms(x, y, axis=1)
+    array([0.36908985, 0.36092538, 0.2765313 ])
+
+    References
+    ----------
+    .. [1] McKean, Joseph W., and Ronald M. Schrader. "A comparison of methods
+       for studentizing the sample median." Communications in
+       Statistics-Simulation and Computation 13.6 (1984): 751-773.
+
+    """
+    (med_1, med_2) = (ma.median(group_1,axis=axis), ma.median(group_2,axis=axis))
+    (std_1, std_2) = (mstats.stde_median(group_1, axis=axis),
+                      mstats.stde_median(group_2, axis=axis))
+    W = np.abs(med_1 - med_2) / ma.sqrt(std_1**2 + std_2**2)
+    return 1 - norm.cdf(W)
+
+
+def idealfourths(data, axis=None):
+    """
+    Returns an estimate of the lower and upper quartiles.
+
+    Uses the ideal fourths algorithm.
+
+    Parameters
+    ----------
+    data : array_like
+        Input array.
+    axis : int, optional
+        Axis along which the quartiles are estimated. If None, the arrays are
+        flattened.
+
+    Returns
+    -------
+    idealfourths : {list of floats, masked array}
+        Returns the two internal values that divide `data` into four parts
+        using the ideal fourths algorithm either along the flattened array
+        (if `axis` is None) or along `axis` of `data`.
+
+    """
+    def _idf(data):
+        x = data.compressed()
+        n = len(x)
+        if n < 3:
+            return [np.nan,np.nan]
+        (j,h) = divmod(n/4. + 5/12.,1)
+        j = int(j)
+        qlo = (1-h)*x[j-1] + h*x[j]
+        k = n - j
+        qup = (1-h)*x[k] + h*x[k-1]
+        return [qlo, qup]
+    data = ma.sort(data, axis=axis).view(MaskedArray)
+    if (axis is None):
+        return _idf(data)
+    else:
+        return ma.apply_along_axis(_idf, axis, data)
+
+
+def rsh(data, points=None):
+    """
+    Evaluates Rosenblatt's shifted histogram estimators for each data point.
+
+    Rosenblatt's estimator is a centered finite-difference approximation to the
+    derivative of the empirical cumulative distribution function.
+
+    Parameters
+    ----------
+    data : sequence
+        Input data, should be 1-D. Masked values are ignored.
+    points : sequence or None, optional
+        Sequence of points where to evaluate Rosenblatt shifted histogram.
+        If None, use the data.
+
+    """
+    data = ma.array(data, copy=False)
+    if points is None:
+        points = data
+    else:
+        points = np.array(points, copy=False, ndmin=1)
+
+    if data.ndim != 1:
+        raise AttributeError("The input array should be 1D only !")
+
+    n = data.count()
+    r = idealfourths(data, axis=None)
+    h = 1.2 * (r[-1]-r[0]) / n**(1./5)
+    nhi = (data[:,None] <= points[None,:] + h).sum(0)
+    nlo = (data[:,None] < points[None,:] - h).sum(0)
+    return (nhi-nlo) / (2.*n*h)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_odds_ratio.py

@@ -0,0 +1,465 @@
+
+import numpy as np
+
+from scipy.special import ndtri
+from scipy.optimize import brentq
+from ._discrete_distns import nchypergeom_fisher
+from ._common import ConfidenceInterval
+
+
+def _sample_odds_ratio(table):
+    """
+    Given a table [[a, b], [c, d]], compute a*d/(b*c).
+
+    Return nan if the numerator and denominator are 0.
+    Return inf if just the denominator is 0.
+    """
+    # table must be a 2x2 numpy array.
+    if table[1, 0] > 0 and table[0, 1] > 0:
+        oddsratio = table[0, 0] * table[1, 1] / (table[1, 0] * table[0, 1])
+    elif table[0, 0] == 0 or table[1, 1] == 0:
+        oddsratio = np.nan
+    else:
+        oddsratio = np.inf
+    return oddsratio
+
+
+def _solve(func):
+    """
+    Solve func(nc) = 0.  func must be an increasing function.
+    """
+    # We could just as well call the variable `x` instead of `nc`, but we
+    # always call this function with functions for which nc (the noncentrality
+    # parameter) is the variable for which we are solving.
+    nc = 1.0
+    value = func(nc)
+    if value == 0:
+        return nc
+
+    # Multiplicative factor by which to increase or decrease nc when
+    # searching for a bracketing interval.
+    factor = 2.0
+    # Find a bracketing interval.
+    if value > 0:
+        nc /= factor
+        while func(nc) > 0:
+            nc /= factor
+        lo = nc
+        hi = factor*nc
+    else:
+        nc *= factor
+        while func(nc) < 0:
+            nc *= factor
+        lo = nc/factor
+        hi = nc
+
+    # lo and hi bracket the solution for nc.
+    nc = brentq(func, lo, hi, xtol=1e-13)
+    return nc
+
+
+def _nc_hypergeom_mean_inverse(x, M, n, N):
+    """
+    For the given noncentral hypergeometric parameters x, M, n,and N
+    (table[0,0], total, row 0 sum and column 0 sum, resp., of a 2x2
+    contingency table), find the noncentrality parameter of Fisher's
+    noncentral hypergeometric distribution whose mean is x.
+    """
+    nc = _solve(lambda nc: nchypergeom_fisher.mean(M, n, N, nc) - x)
+    return nc
+
+
+def _hypergeom_params_from_table(table):
+    # The notation M, n and N is consistent with stats.hypergeom and
+    # stats.nchypergeom_fisher.
+    x = table[0, 0]
+    M = table.sum()
+    n = table[0].sum()
+    N = table[:, 0].sum()
+    return x, M, n, N
+
+
+def _ci_upper(table, alpha):
+    """
+    Compute the upper end of the confidence interval.
+    """
+    if _sample_odds_ratio(table) == np.inf:
+        return np.inf
+
+    x, M, n, N = _hypergeom_params_from_table(table)
+
+    # nchypergeom_fisher.cdf is a decreasing function of nc, so we negate
+    # it in the lambda expression.
+    nc = _solve(lambda nc: -nchypergeom_fisher.cdf(x, M, n, N, nc) + alpha)
+    return nc
+
+
+def _ci_lower(table, alpha):
+    """
+    Compute the lower end of the confidence interval.
+    """
+    if _sample_odds_ratio(table) == 0:
+        return 0
+
+    x, M, n, N = _hypergeom_params_from_table(table)
+
+    nc = _solve(lambda nc: nchypergeom_fisher.sf(x - 1, M, n, N, nc) - alpha)
+    return nc
+
+
+def _conditional_oddsratio(table):
+    """
+    Conditional MLE of the odds ratio for the 2x2 contingency table.
+    """
+    x, M, n, N = _hypergeom_params_from_table(table)
+    # Get the bounds of the support.  The support of the noncentral
+    # hypergeometric distribution with parameters M, n, and N is the same
+    # for all values of the noncentrality parameter, so we can use 1 here.
+    lo, hi = nchypergeom_fisher.support(M, n, N, 1)
+
+    # Check if x is at one of the extremes of the support.  If so, we know
+    # the odds ratio is either 0 or inf.
+    if x == lo:
+        # x is at the low end of the support.
+        return 0
+    if x == hi:
+        # x is at the high end of the support.
+        return np.inf
+
+    nc = _nc_hypergeom_mean_inverse(x, M, n, N)
+    return nc
+
+
+def _conditional_oddsratio_ci(table, confidence_level=0.95,
+                              alternative='two-sided'):
+    """
+    Conditional exact confidence interval for the odds ratio.
+    """
+    if alternative == 'two-sided':
+        alpha = 0.5*(1 - confidence_level)
+        lower = _ci_lower(table, alpha)
+        upper = _ci_upper(table, alpha)
+    elif alternative == 'less':
+        lower = 0.0
+        upper = _ci_upper(table, 1 - confidence_level)
+    else:
+        # alternative == 'greater'
+        lower = _ci_lower(table, 1 - confidence_level)
+        upper = np.inf
+
+    return lower, upper
+
+
+def _sample_odds_ratio_ci(table, confidence_level=0.95,
+                          alternative='two-sided'):
+    oddsratio = _sample_odds_ratio(table)
+    log_or = np.log(oddsratio)
+    se = np.sqrt((1/table).sum())
+    if alternative == 'less':
+        z = ndtri(confidence_level)
+        loglow = -np.inf
+        loghigh = log_or + z*se
+    elif alternative == 'greater':
+        z = ndtri(confidence_level)
+        loglow = log_or - z*se
+        loghigh = np.inf
+    else:
+        # alternative is 'two-sided'
+        z = ndtri(0.5*confidence_level + 0.5)
+        loglow = log_or - z*se
+        loghigh = log_or + z*se
+
+    return np.exp(loglow), np.exp(loghigh)
+
+
+class OddsRatioResult:
+    """
+    Result of `scipy.stats.contingency.odds_ratio`.  See the
+    docstring for `odds_ratio` for more details.
+
+    Attributes
+    ----------
+    statistic : float
+        The computed odds ratio.
+
+        * If `kind` is ``'sample'``, this is sample (or unconditional)
+          estimate, given by
+          ``table[0, 0]*table[1, 1]/(table[0, 1]*table[1, 0])``.
+        * If `kind` is ``'conditional'``, this is the conditional
+          maximum likelihood estimate for the odds ratio. It is
+          the noncentrality parameter of Fisher's noncentral
+          hypergeometric distribution with the same hypergeometric
+          parameters as `table` and whose mean is ``table[0, 0]``.
+
+    Methods
+    -------
+    confidence_interval :
+        Confidence interval for the odds ratio.
+    """
+
+    def __init__(self, _table, _kind, statistic):
+        # for now, no need to make _table and _kind public, since this sort of
+        # information is returned in very few `scipy.stats` results
+        self._table = _table
+        self._kind = _kind
+        self.statistic = statistic
+
+    def __repr__(self):
+        return f"OddsRatioResult(statistic={self.statistic})"
+
+    def confidence_interval(self, confidence_level=0.95,
+                            alternative='two-sided'):
+        """
+        Confidence interval for the odds ratio.
+
+        Parameters
+        ----------
+        confidence_level: float
+            Desired confidence level for the confidence interval.
+            The value must be given as a fraction between 0 and 1.
+            Default is 0.95 (meaning 95%).
+
+        alternative : {'two-sided', 'less', 'greater'}, optional
+            The alternative hypothesis of the hypothesis test to which the
+            confidence interval corresponds. That is, suppose the null
+            hypothesis is that the true odds ratio equals ``OR`` and the
+            confidence interval is ``(low, high)``. Then the following options
+            for `alternative` are available (default is 'two-sided'):
+
+            * 'two-sided': the true odds ratio is not equal to ``OR``. There
+              is evidence against the null hypothesis at the chosen
+              `confidence_level` if ``high < OR`` or ``low > OR``.
+            * 'less': the true odds ratio is less than ``OR``. The ``low`` end
+              of the confidence interval is 0, and there is evidence against
+              the null hypothesis at  the chosen `confidence_level` if
+              ``high < OR``.
+            * 'greater': the true odds ratio is greater than ``OR``.  The
+              ``high`` end of the confidence interval is ``np.inf``, and there
+              is evidence against the null hypothesis at the chosen
+              `confidence_level` if ``low > OR``.
+
+        Returns
+        -------
+        ci : ``ConfidenceInterval`` instance
+            The confidence interval, represented as an object with
+            attributes ``low`` and ``high``.
+
+        Notes
+        -----
+        When `kind` is ``'conditional'``, the limits of the confidence
+        interval are the conditional "exact confidence limits" as described
+        by Fisher [1]_. The conditional odds ratio and confidence interval are
+        also discussed in Section 4.1.2 of the text by Sahai and Khurshid [2]_.
+
+        When `kind` is ``'sample'``, the confidence interval is computed
+        under the assumption that the logarithm of the odds ratio is normally
+        distributed with standard error given by::
+
+            se = sqrt(1/a + 1/b + 1/c + 1/d)
+
+        where ``a``, ``b``, ``c`` and ``d`` are the elements of the
+        contingency table.  (See, for example, [2]_, section 3.1.3.2,
+        or [3]_, section 2.3.3).
+
+        References
+        ----------
+        .. [1] R. A. Fisher (1935), The logic of inductive inference,
+               Journal of the Royal Statistical Society, Vol. 98, No. 1,
+               pp. 39-82.
+        .. [2] H. Sahai and A. Khurshid (1996), Statistics in Epidemiology:
+               Methods, Techniques, and Applications, CRC Press LLC, Boca
+               Raton, Florida.
+        .. [3] Alan Agresti, An Introduction to Categorical Data Analyis
+               (second edition), Wiley, Hoboken, NJ, USA (2007).
+        """
+        if alternative not in ['two-sided', 'less', 'greater']:
+            raise ValueError("`alternative` must be 'two-sided', 'less' or "
+                             "'greater'.")
+
+        if confidence_level < 0 or confidence_level > 1:
+            raise ValueError('confidence_level must be between 0 and 1')
+
+        if self._kind == 'conditional':
+            ci = self._conditional_odds_ratio_ci(confidence_level, alternative)
+        else:
+            ci = self._sample_odds_ratio_ci(confidence_level, alternative)
+        return ci
+
+    def _conditional_odds_ratio_ci(self, confidence_level=0.95,
+                                   alternative='two-sided'):
+        """
+        Confidence interval for the conditional odds ratio.
+        """
+
+        table = self._table
+        if 0 in table.sum(axis=0) or 0 in table.sum(axis=1):
+            # If both values in a row or column are zero, the p-value is 1,
+            # the odds ratio is NaN and the confidence interval is (0, inf).
+            ci = (0, np.inf)
+        else:
+            ci = _conditional_oddsratio_ci(table,
+                                           confidence_level=confidence_level,
+                                           alternative=alternative)
+        return ConfidenceInterval(low=ci[0], high=ci[1])
+
+    def _sample_odds_ratio_ci(self, confidence_level=0.95,
+                              alternative='two-sided'):
+        """
+        Confidence interval for the sample odds ratio.
+        """
+        if confidence_level < 0 or confidence_level > 1:
+            raise ValueError('confidence_level must be between 0 and 1')
+
+        table = self._table
+        if 0 in table.sum(axis=0) or 0 in table.sum(axis=1):
+            # If both values in a row or column are zero, the p-value is 1,
+            # the odds ratio is NaN and the confidence interval is (0, inf).
+            ci = (0, np.inf)
+        else:
+            ci = _sample_odds_ratio_ci(table,
+                                       confidence_level=confidence_level,
+                                       alternative=alternative)
+        return ConfidenceInterval(low=ci[0], high=ci[1])
+
+
+def odds_ratio(table, *, kind='conditional'):
+    r"""
+    Compute the odds ratio for a 2x2 contingency table.
+
+    Parameters
+    ----------
+    table : array_like of ints
+        A 2x2 contingency table.  Elements must be non-negative integers.
+    kind : str, optional
+        Which kind of odds ratio to compute, either the sample
+        odds ratio (``kind='sample'``) or the conditional odds ratio
+        (``kind='conditional'``).  Default is ``'conditional'``.
+
+    Returns
+    -------
+    result : `~scipy.stats._result_classes.OddsRatioResult` instance
+        The returned object has two computed attributes:
+
+        statistic : float
+            * If `kind` is ``'sample'``, this is sample (or unconditional)
+              estimate, given by
+              ``table[0, 0]*table[1, 1]/(table[0, 1]*table[1, 0])``.
+            * If `kind` is ``'conditional'``, this is the conditional
+              maximum likelihood estimate for the odds ratio. It is
+              the noncentrality parameter of Fisher's noncentral
+              hypergeometric distribution with the same hypergeometric
+              parameters as `table` and whose mean is ``table[0, 0]``.
+
+        The object has the method `confidence_interval` that computes
+        the confidence interval of the odds ratio.
+
+    See Also
+    --------
+    scipy.stats.fisher_exact
+    relative_risk
+
+    Notes
+    -----
+    The conditional odds ratio was discussed by Fisher (see "Example 1"
+    of [1]_).  Texts that cover the odds ratio include [2]_ and [3]_.
+
+    .. versionadded:: 1.10.0
+
+    References
+    ----------
+    .. [1] R. A. Fisher (1935), The logic of inductive inference,
+           Journal of the Royal Statistical Society, Vol. 98, No. 1,
+           pp. 39-82.
+    .. [2] Breslow NE, Day NE (1980). Statistical methods in cancer research.
+           Volume I - The analysis of case-control studies. IARC Sci Publ.
+           (32):5-338. PMID: 7216345. (See section 4.2.)
+    .. [3] H. Sahai and A. Khurshid (1996), Statistics in Epidemiology:
+           Methods, Techniques, and Applications, CRC Press LLC, Boca
+           Raton, Florida.
+
+    Examples
+    --------
+    In epidemiology, individuals are classified as "exposed" or
+    "unexposed" to some factor or treatment. If the occurrence of some
+    illness is under study, those who have the illness are often
+    classifed as "cases", and those without it are "noncases".  The
+    counts of the occurrences of these classes gives a contingency
+    table::
+
+                    exposed    unexposed
+        cases          a           b
+        noncases       c           d
+
+    The sample odds ratio may be written ``(a/c) / (b/d)``.  ``a/c`` can
+    be interpreted as the odds of a case occurring in the exposed group,
+    and ``b/d`` as the odds of a case occurring in the unexposed group.
+    The sample odds ratio is the ratio of these odds.  If the odds ratio
+    is greater than 1, it suggests that there is a positive association
+    between being exposed and being a case.
+
+    Interchanging the rows or columns of the contingency table inverts
+    the odds ratio, so it is import to understand the meaning of labels
+    given to the rows and columns of the table when interpreting the
+    odds ratio.
+
+    Consider a hypothetical example where it is hypothesized that
+    exposure to a certain chemical is assocated with increased occurrence
+    of a certain disease.  Suppose we have the following table for a
+    collection of 410 people::
+
+                  exposed   unexposed
+        cases         7         15
+        noncases     58        472
+
+    The question we ask is "Is exposure to the chemical associated with
+    increased risk of the disease?"
+
+    Compute the odds ratio:
+
+    >>> from scipy.stats.contingency import odds_ratio
+    >>> res = odds_ratio([[7, 15], [58, 472]])
+    >>> res.statistic
+    3.7836687705553493
+
+    For this sample, the odds of getting the disease for those who have
+    been exposed to the chemical are almost 3.8 times that of those who
+    have not been exposed.
+
+    We can compute the 95% confidence interval for the odds ratio:
+
+    >>> res.confidence_interval(confidence_level=0.95)
+    ConfidenceInterval(low=1.2514829132266785, high=10.363493716701269)
+
+    The 95% confidence interval for the conditional odds ratio is
+    approximately (1.25, 10.4).
+    """
+    if kind not in ['conditional', 'sample']:
+        raise ValueError("`kind` must be 'conditional' or 'sample'.")
+
+    c = np.asarray(table)
+
+    if c.shape != (2, 2):
+        raise ValueError(f"Invalid shape {c.shape}. The input `table` must be "
+                         "of shape (2, 2).")
+
+    if not np.issubdtype(c.dtype, np.integer):
+        raise ValueError("`table` must be an array of integers, but got "
+                         f"type {c.dtype}")
+    c = c.astype(np.int64)
+
+    if np.any(c < 0):
+        raise ValueError("All values in `table` must be nonnegative.")
+
+    if 0 in c.sum(axis=0) or 0 in c.sum(axis=1):
+        # If both values in a row or column are zero, the p-value is NaN and
+        # the odds ratio is NaN.
+        result = OddsRatioResult(_table=c, _kind=kind, statistic=np.nan)
+        return result
+
+    if kind == 'sample':
+        oddsratio = _sample_odds_ratio(c)
+    else:  # kind is 'conditional'
+        oddsratio = _conditional_oddsratio(c)
+
+    result = OddsRatioResult(_table=c, _kind=kind, statistic=oddsratio)
+    return result

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_page_trend_test.py

@@ -0,0 +1,476 @@
+from itertools import permutations
+import numpy as np
+import math
+from ._continuous_distns import norm
+import scipy.stats
+from dataclasses import make_dataclass
+
+
+PageTrendTestResult = make_dataclass("PageTrendTestResult",
+                                     ("statistic", "pvalue", "method"))
+
+
+def page_trend_test(data, ranked=False, predicted_ranks=None, method='auto'):
+    r"""
+    Perform Page's Test, a measure of trend in observations between treatments.
+
+    Page's Test (also known as Page's :math:`L` test) is useful when:
+
+    * there are :math:`n \geq 3` treatments,
+    * :math:`m \geq 2` subjects are observed for each treatment, and
+    * the observations are hypothesized to have a particular order.
+
+    Specifically, the test considers the null hypothesis that
+
+    .. math::
+
+        m_1 = m_2 = m_3 \cdots = m_n,
+
+    where :math:`m_j` is the mean of the observed quantity under treatment
+    :math:`j`, against the alternative hypothesis that
+
+    .. math::
+
+        m_1 \leq m_2 \leq m_3 \leq \cdots \leq m_n,
+
+    where at least one inequality is strict.
+
+    As noted by [4]_, Page's :math:`L` test has greater statistical power than
+    the Friedman test against the alternative that there is a difference in
+    trend, as Friedman's test only considers a difference in the means of the
+    observations without considering their order. Whereas Spearman :math:`\rho`
+    considers the correlation between the ranked observations of two variables
+    (e.g. the airspeed velocity of a swallow vs. the weight of the coconut it
+    carries), Page's :math:`L` is concerned with a trend in an observation
+    (e.g. the airspeed velocity of a swallow) across several distinct
+    treatments (e.g. carrying each of five coconuts of different weight) even
+    as the observation is repeated with multiple subjects (e.g. one European
+    swallow and one African swallow).
+
+    Parameters
+    ----------
+    data : array-like
+        A :math:`m \times n` array; the element in row :math:`i` and
+        column :math:`j` is the observation corresponding with subject
+        :math:`i` and treatment :math:`j`. By default, the columns are
+        assumed to be arranged in order of increasing predicted mean.
+
+    ranked : boolean, optional
+        By default, `data` is assumed to be observations rather than ranks;
+        it will be ranked with `scipy.stats.rankdata` along ``axis=1``. If
+        `data` is provided in the form of ranks, pass argument ``True``.
+
+    predicted_ranks : array-like, optional
+        The predicted ranks of the column means. If not specified,
+        the columns are assumed to be arranged in order of increasing
+        predicted mean, so the default `predicted_ranks` are
+        :math:`[1, 2, \dots, n-1, n]`.
+
+    method : {'auto', 'asymptotic', 'exact'}, optional
+        Selects the method used to calculate the *p*-value. The following
+        options are available.
+
+        * 'auto': selects between 'exact' and 'asymptotic' to
+          achieve reasonably accurate results in reasonable time (default)
+        * 'asymptotic': compares the standardized test statistic against
+          the normal distribution
+        * 'exact': computes the exact *p*-value by comparing the observed
+          :math:`L` statistic against those realized by all possible
+          permutations of ranks (under the null hypothesis that each
+          permutation is equally likely)
+
+    Returns
+    -------
+    res : PageTrendTestResult
+        An object containing attributes:
+
+        statistic : float
+            Page's :math:`L` test statistic.
+        pvalue : float
+            The associated *p*-value
+        method : {'asymptotic', 'exact'}
+            The method used to compute the *p*-value
+
+    See Also
+    --------
+    rankdata, friedmanchisquare, spearmanr
+
+    Notes
+    -----
+    As noted in [1]_, "the :math:`n` 'treatments' could just as well represent
+    :math:`n` objects or events or performances or persons or trials ranked."
+    Similarly, the :math:`m` 'subjects' could equally stand for :math:`m`
+    "groupings by ability or some other control variable, or judges doing
+    the ranking, or random replications of some other sort."
+
+    The procedure for calculating the :math:`L` statistic, adapted from
+    [1]_, is:
+
+    1. "Predetermine with careful logic the appropriate hypotheses
+       concerning the predicted ording of the experimental results.
+       If no reasonable basis for ordering any treatments is known, the
+       :math:`L` test is not appropriate."
+    2. "As in other experiments, determine at what level of confidence
+       you will reject the null hypothesis that there is no agreement of
+       experimental results with the monotonic hypothesis."
+    3. "Cast the experimental material into a two-way table of :math:`n`
+       columns (treatments, objects ranked, conditions) and :math:`m`
+       rows (subjects, replication groups, levels of control variables)."
+    4. "When experimental observations are recorded, rank them across each
+       row", e.g. ``ranks = scipy.stats.rankdata(data, axis=1)``.
+    5. "Add the ranks in each column", e.g.
+       ``colsums = np.sum(ranks, axis=0)``.
+    6. "Multiply each sum of ranks by the predicted rank for that same
+       column", e.g. ``products = predicted_ranks * colsums``.
+    7. "Sum all such products", e.g. ``L = products.sum()``.
+
+    [1]_ continues by suggesting use of the standardized statistic
+
+    .. math::
+
+        \chi_L^2 = \frac{\left[12L-3mn(n+1)^2\right]^2}{mn^2(n^2-1)(n+1)}
+
+    "which is distributed approximately as chi-square with 1 degree of
+    freedom. The ordinary use of :math:`\chi^2` tables would be
+    equivalent to a two-sided test of agreement. If a one-sided test
+    is desired, *as will almost always be the case*, the probability
+    discovered in the chi-square table should be *halved*."
+
+    However, this standardized statistic does not distinguish between the
+    observed values being well correlated with the predicted ranks and being
+    _anti_-correlated with the predicted ranks. Instead, we follow [2]_
+    and calculate the standardized statistic
+
+    .. math::
+
+        \Lambda = \frac{L - E_0}{\sqrt{V_0}},
+
+    where :math:`E_0 = \frac{1}{4} mn(n+1)^2` and
+    :math:`V_0 = \frac{1}{144} mn^2(n+1)(n^2-1)`, "which is asymptotically
+    normal under the null hypothesis".
+
+    The *p*-value for ``method='exact'`` is generated by comparing the observed
+    value of :math:`L` against the :math:`L` values generated for all
+    :math:`(n!)^m` possible permutations of ranks. The calculation is performed
+    using the recursive method of [5].
+
+    The *p*-values are not adjusted for the possibility of ties. When
+    ties are present, the reported  ``'exact'`` *p*-values may be somewhat
+    larger (i.e. more conservative) than the true *p*-value [2]_. The
+    ``'asymptotic'``` *p*-values, however, tend to be smaller (i.e. less
+    conservative) than the ``'exact'`` *p*-values.
+
+    References
+    ----------
+    .. [1] Ellis Batten Page, "Ordered hypotheses for multiple treatments:
+       a significant test for linear ranks", *Journal of the American
+       Statistical Association* 58(301), p. 216--230, 1963.
+
+    .. [2] Markus Neuhauser, *Nonparametric Statistical Test: A computational
+       approach*, CRC Press, p. 150--152, 2012.
+
+    .. [3] Statext LLC, "Page's L Trend Test - Easy Statistics", *Statext -
+       Statistics Study*, https://www.statext.com/practice/PageTrendTest03.php,
+       Accessed July 12, 2020.
+
+    .. [4] "Page's Trend Test", *Wikipedia*, WikimediaFoundation,
+       https://en.wikipedia.org/wiki/Page%27s_trend_test,
+       Accessed July 12, 2020.
+
+    .. [5] Robert E. Odeh, "The exact distribution of Page's L-statistic in
+       the two-way layout", *Communications in Statistics - Simulation and
+       Computation*,  6(1), p. 49--61, 1977.
+
+    Examples
+    --------
+    We use the example from [3]_: 10 students are asked to rate three
+    teaching methods - tutorial, lecture, and seminar - on a scale of 1-5,
+    with 1 being the lowest and 5 being the highest. We have decided that
+    a confidence level of 99% is required to reject the null hypothesis in
+    favor of our alternative: that the seminar will have the highest ratings
+    and the tutorial will have the lowest. Initially, the data have been
+    tabulated with each row representing an individual student's ratings of
+    the three methods in the following order: tutorial, lecture, seminar.
+
+    >>> table = [[3, 4, 3],
+    ...          [2, 2, 4],
+    ...          [3, 3, 5],
+    ...          [1, 3, 2],
+    ...          [2, 3, 2],
+    ...          [2, 4, 5],
+    ...          [1, 2, 4],
+    ...          [3, 4, 4],
+    ...          [2, 4, 5],
+    ...          [1, 3, 4]]
+
+    Because the tutorial is hypothesized to have the lowest ratings, the
+    column corresponding with tutorial rankings should be first; the seminar
+    is hypothesized to have the highest ratings, so its column should be last.
+    Since the columns are already arranged in this order of increasing
+    predicted mean, we can pass the table directly into `page_trend_test`.
+
+    >>> from scipy.stats import page_trend_test
+    >>> res = page_trend_test(table)
+    >>> res
+    PageTrendTestResult(statistic=133.5, pvalue=0.0018191161948127822,
+                        method='exact')
+
+    This *p*-value indicates that there is a 0.1819% chance that
+    the :math:`L` statistic would reach such an extreme value under the null
+    hypothesis. Because 0.1819% is less than 1%, we have evidence to reject
+    the null hypothesis in favor of our alternative at a 99% confidence level.
+
+    The value of the :math:`L` statistic is 133.5. To check this manually,
+    we rank the data such that high scores correspond with high ranks, settling
+    ties with an average rank:
+
+    >>> from scipy.stats import rankdata
+    >>> ranks = rankdata(table, axis=1)
+    >>> ranks
+    array([[1.5, 3. , 1.5],
+           [1.5, 1.5, 3. ],
+           [1.5, 1.5, 3. ],
+           [1. , 3. , 2. ],
+           [1.5, 3. , 1.5],
+           [1. , 2. , 3. ],
+           [1. , 2. , 3. ],
+           [1. , 2.5, 2.5],
+           [1. , 2. , 3. ],
+           [1. , 2. , 3. ]])
+
+    We add the ranks within each column, multiply the sums by the
+    predicted ranks, and sum the products.
+
+    >>> import numpy as np
+    >>> m, n = ranks.shape
+    >>> predicted_ranks = np.arange(1, n+1)
+    >>> L = (predicted_ranks * np.sum(ranks, axis=0)).sum()
+    >>> res.statistic == L
+    True
+
+    As presented in [3]_, the asymptotic approximation of the *p*-value is the
+    survival function of the normal distribution evaluated at the standardized
+    test statistic:
+
+    >>> from scipy.stats import norm
+    >>> E0 = (m*n*(n+1)**2)/4
+    >>> V0 = (m*n**2*(n+1)*(n**2-1))/144
+    >>> Lambda = (L-E0)/np.sqrt(V0)
+    >>> p = norm.sf(Lambda)
+    >>> p
+    0.0012693433690751756
+
+    This does not precisely match the *p*-value reported by `page_trend_test`
+    above. The asymptotic distribution is not very accurate, nor conservative,
+    for :math:`m \leq 12` and :math:`n \leq 8`, so `page_trend_test` chose to
+    use ``method='exact'`` based on the dimensions of the table and the
+    recommendations in Page's original paper [1]_. To override
+    `page_trend_test`'s choice, provide the `method` argument.
+
+    >>> res = page_trend_test(table, method="asymptotic")
+    >>> res
+    PageTrendTestResult(statistic=133.5, pvalue=0.0012693433690751756,
+                        method='asymptotic')
+
+    If the data are already ranked, we can pass in the ``ranks`` instead of
+    the ``table`` to save computation time.
+
+    >>> res = page_trend_test(ranks,             # ranks of data
+    ...                       ranked=True,       # data is already ranked
+    ...                       )
+    >>> res
+    PageTrendTestResult(statistic=133.5, pvalue=0.0018191161948127822,
+                        method='exact')
+
+    Suppose the raw data had been tabulated in an order different from the
+    order of predicted means, say lecture, seminar, tutorial.
+
+    >>> table = np.asarray(table)[:, [1, 2, 0]]
+
+    Since the arrangement of this table is not consistent with the assumed
+    ordering, we can either rearrange the table or provide the
+    `predicted_ranks`. Remembering that the lecture is predicted
+    to have the middle rank, the seminar the highest, and tutorial the lowest,
+    we pass:
+
+    >>> res = page_trend_test(table,             # data as originally tabulated
+    ...                       predicted_ranks=[2, 3, 1],  # our predicted order
+    ...                       )
+    >>> res
+    PageTrendTestResult(statistic=133.5, pvalue=0.0018191161948127822,
+                        method='exact')
+
+    """
+
+    # Possible values of the method parameter and the corresponding function
+    # used to evaluate the p value
+    methods = {"asymptotic": _l_p_asymptotic,
+               "exact": _l_p_exact,
+               "auto": None}
+    if method not in methods:
+        raise ValueError(f"`method` must be in {set(methods)}")
+
+    ranks = np.array(data, copy=False)
+    if ranks.ndim != 2:  # TODO: relax this to accept 3d arrays?
+        raise ValueError("`data` must be a 2d array.")
+
+    m, n = ranks.shape
+    if m < 2 or n < 3:
+        raise ValueError("Page's L is only appropriate for data with two "
+                         "or more rows and three or more columns.")
+
+    if np.any(np.isnan(data)):
+        raise ValueError("`data` contains NaNs, which cannot be ranked "
+                         "meaningfully")
+
+    # ensure NumPy array and rank the data if it's not already ranked
+    if ranked:
+        # Only a basic check on whether data is ranked. Checking that the data
+        # is properly ranked could take as much time as ranking it.
+        if not (ranks.min() >= 1 and ranks.max() <= ranks.shape[1]):
+            raise ValueError("`data` is not properly ranked. Rank the data or "
+                             "pass `ranked=False`.")
+    else:
+        ranks = scipy.stats.rankdata(data, axis=-1)
+
+    # generate predicted ranks if not provided, ensure valid NumPy array
+    if predicted_ranks is None:
+        predicted_ranks = np.arange(1, n+1)
+    else:
+        predicted_ranks = np.array(predicted_ranks, copy=False)
+        if (predicted_ranks.ndim < 1 or
+                (set(predicted_ranks) != set(range(1, n+1)) or
+                 len(predicted_ranks) != n)):
+            raise ValueError(f"`predicted_ranks` must include each integer "
+                             f"from 1 to {n} (the number of columns in "
+                             f"`data`) exactly once.")
+
+    if type(ranked) is not bool:
+        raise TypeError("`ranked` must be boolean.")
+
+    # Calculate the L statistic
+    L = _l_vectorized(ranks, predicted_ranks)
+
+    # Calculate the p-value
+    if method == "auto":
+        method = _choose_method(ranks)
+    p_fun = methods[method]  # get the function corresponding with the method
+    p = p_fun(L, m, n)
+
+    page_result = PageTrendTestResult(statistic=L, pvalue=p, method=method)
+    return page_result
+
+
+def _choose_method(ranks):
+    '''Choose method for computing p-value automatically'''
+    m, n = ranks.shape
+    if n > 8 or (m > 12 and n > 3) or m > 20:  # as in [1], [4]
+        method = "asymptotic"
+    else:
+        method = "exact"
+    return method
+
+
+def _l_vectorized(ranks, predicted_ranks):
+    '''Calculate's Page's L statistic for each page of a 3d array'''
+    colsums = ranks.sum(axis=-2, keepdims=True)
+    products = predicted_ranks * colsums
+    Ls = products.sum(axis=-1)
+    Ls = Ls[0] if Ls.size == 1 else Ls.ravel()
+    return Ls
+
+
+def _l_p_asymptotic(L, m, n):
+    '''Calculate the p-value of Page's L from the asymptotic distribution'''
+    # Using [1] as a reference, the asymptotic p-value would be calculated as:
+    # chi_L = (12*L - 3*m*n*(n+1)**2)**2/(m*n**2*(n**2-1)*(n+1))
+    # p = chi2.sf(chi_L, df=1, loc=0, scale=1)/2
+    # but this is insentive to the direction of the hypothesized ranking
+
+    # See [2] page 151
+    E0 = (m*n*(n+1)**2)/4
+    V0 = (m*n**2*(n+1)*(n**2-1))/144
+    Lambda = (L-E0)/np.sqrt(V0)
+    # This is a one-sided "greater" test - calculate the probability that the
+    # L statistic under H0 would be greater than the observed L statistic
+    p = norm.sf(Lambda)
+    return p
+
+
+def _l_p_exact(L, m, n):
+    '''Calculate the p-value of Page's L exactly'''
+    # [1] uses m, n; [5] uses n, k.
+    # Switch convention here because exact calculation code references [5].
+    L, n, k = int(L), int(m), int(n)
+    _pagel_state.set_k(k)
+    return _pagel_state.sf(L, n)
+
+
+class _PageL:
+    '''Maintains state between `page_trend_test` executions'''
+
+    def __init__(self):
+        '''Lightweight initialization'''
+        self.all_pmfs = {}
+
+    def set_k(self, k):
+        '''Calculate lower and upper limits of L for single row'''
+        self.k = k
+        # See [5] top of page 52
+        self.a, self.b = (k*(k+1)*(k+2))//6, (k*(k+1)*(2*k+1))//6
+
+    def sf(self, l, n):
+        '''Survival function of Page's L statistic'''
+        ps = [self.pmf(l, n) for l in range(l, n*self.b + 1)]
+        return np.sum(ps)
+
+    def p_l_k_1(self):
+        '''Relative frequency of each L value over all possible single rows'''
+
+        # See [5] Equation (6)
+        ranks = range(1, self.k+1)
+        # generate all possible rows of length k
+        rank_perms = np.array(list(permutations(ranks)))
+        # compute Page's L for all possible rows
+        Ls = (ranks*rank_perms).sum(axis=1)
+        # count occurences of each L value
+        counts = np.histogram(Ls, np.arange(self.a-0.5, self.b+1.5))[0]
+        # factorial(k) is number of possible permutations
+        return counts/math.factorial(self.k)
+
+    def pmf(self, l, n):
+        '''Recursive function to evaluate p(l, k, n); see [5] Equation 1'''
+
+        if n not in self.all_pmfs:
+            self.all_pmfs[n] = {}
+        if self.k not in self.all_pmfs[n]:
+            self.all_pmfs[n][self.k] = {}
+
+        # Cache results to avoid repeating calculation. Initially this was
+        # written with lru_cache, but this seems faster? Also, we could add
+        # an option to save this for future lookup.
+        if l in self.all_pmfs[n][self.k]:
+            return self.all_pmfs[n][self.k][l]
+
+        if n == 1:
+            ps = self.p_l_k_1()  # [5] Equation 6
+            ls = range(self.a, self.b+1)
+            # not fast, but we'll only be here once
+            self.all_pmfs[n][self.k] = {l: p for l, p in zip(ls, ps)}
+            return self.all_pmfs[n][self.k][l]
+
+        p = 0
+        low = max(l-(n-1)*self.b, self.a)  # [5] Equation 2
+        high = min(l-(n-1)*self.a, self.b)
+
+        # [5] Equation 1
+        for t in range(low, high+1):
+            p1 = self.pmf(l-t, n-1)
+            p2 = self.pmf(t, 1)
+            p += p1*p2
+        self.all_pmfs[n][self.k][l] = p
+        return p
+
+
+# Maintain state for faster repeat calls to page_trend_test w/ method='exact'
+_pagel_state = _PageL()

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_qmc_cy.pyi

@@ -0,0 +1,54 @@
+import numpy as np
+from scipy._lib._util import DecimalNumber, IntNumber
+
+
+def _cy_wrapper_centered_discrepancy(
+        sample: np.ndarray, 
+        iterative: bool, 
+        workers: IntNumber,
+) -> float: ...
+
+
+def _cy_wrapper_wrap_around_discrepancy(
+        sample: np.ndarray,
+        iterative: bool, 
+        workers: IntNumber,
+) -> float: ...
+
+
+def _cy_wrapper_mixture_discrepancy(
+        sample: np.ndarray,
+        iterative: bool, 
+        workers: IntNumber,
+) -> float: ...
+
+
+def _cy_wrapper_l2_star_discrepancy(
+        sample: np.ndarray,
+        iterative: bool,
+        workers: IntNumber,
+) -> float: ...
+
+
+def _cy_wrapper_update_discrepancy(
+        x_new_view: np.ndarray,
+        sample_view: np.ndarray,
+        initial_disc: DecimalNumber,
+) -> float: ...
+
+
+def _cy_van_der_corput(
+        n: IntNumber,
+        base: IntNumber,
+        start_index: IntNumber,
+        workers: IntNumber,
+) -> np.ndarray: ...
+
+
+def _cy_van_der_corput_scrambled(
+        n: IntNumber,
+        base: IntNumber,
+        start_index: IntNumber,
+        permutations: np.ndarray,
+        workers: IntNumber,
+) -> np.ndarray: ...

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_rcont/__init__.py

@@ -0,0 +1,5 @@
+# -*- coding: utf-8 -*-
+#
+from .rcont import rvs_rcont1, rvs_rcont2
+
+__all__ = ["rvs_rcont1", "rvs_rcont2"]

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_relative_risk.py

@@ -0,0 +1,264 @@
+
+import operator
+from dataclasses import dataclass
+import numpy as np
+from scipy.special import ndtri
+from ._common import ConfidenceInterval
+
+
+def _validate_int(n, bound, name):
+    msg = f'{name} must be an integer not less than {bound}, but got {n!r}'
+    try:
+        n = operator.index(n)
+    except TypeError:
+        raise TypeError(msg) from None
+    if n < bound:
+        raise ValueError(msg)
+    return n
+
+
+@dataclass
+class RelativeRiskResult:
+    """
+    Result of `scipy.stats.contingency.relative_risk`.
+
+    Attributes
+    ----------
+    relative_risk : float
+        This is::
+
+            (exposed_cases/exposed_total) / (control_cases/control_total)
+
+    exposed_cases : int
+        The number of "cases" (i.e. occurrence of disease or other event
+        of interest) among the sample of "exposed" individuals.
+    exposed_total : int
+        The total number of "exposed" individuals in the sample.
+    control_cases : int
+        The number of "cases" among the sample of "control" or non-exposed
+        individuals.
+    control_total : int
+        The total number of "control" individuals in the sample.
+
+    Methods
+    -------
+    confidence_interval :
+        Compute the confidence interval for the relative risk estimate.
+    """
+
+    relative_risk: float
+    exposed_cases: int
+    exposed_total: int
+    control_cases: int
+    control_total: int
+
+    def confidence_interval(self, confidence_level=0.95):
+        """
+        Compute the confidence interval for the relative risk.
+
+        The confidence interval is computed using the Katz method
+        (i.e. "Method C" of [1]_; see also [2]_, section 3.1.2).
+
+        Parameters
+        ----------
+        confidence_level : float, optional
+            The confidence level to use for the confidence interval.
+            Default is 0.95.
+
+        Returns
+        -------
+        ci : ConfidenceInterval instance
+            The return value is an object with attributes ``low`` and
+            ``high`` that hold the confidence interval.
+
+        References
+        ----------
+        .. [1] D. Katz, J. Baptista, S. P. Azen and M. C. Pike, "Obtaining
+               confidence intervals for the risk ratio in cohort studies",
+               Biometrics, 34, 469-474 (1978).
+        .. [2] Hardeo Sahai and Anwer Khurshid, Statistics in Epidemiology,
+               CRC Press LLC, Boca Raton, FL, USA (1996).
+
+
+        Examples
+        --------
+        >>> from scipy.stats.contingency import relative_risk
+        >>> result = relative_risk(exposed_cases=10, exposed_total=75,
+        ...                        control_cases=12, control_total=225)
+        >>> result.relative_risk
+        2.5
+        >>> result.confidence_interval()
+        ConfidenceInterval(low=1.1261564003469628, high=5.549850800541033)
+        """
+        if not 0 <= confidence_level <= 1:
+            raise ValueError('confidence_level must be in the interval '
+                             '[0, 1].')
+
+        # Handle edge cases where either exposed_cases or control_cases
+        # is zero.  We follow the convention of the R function riskratio
+        # from the epitools library.
+        if self.exposed_cases == 0 and self.control_cases == 0:
+            # relative risk is nan.
+            return ConfidenceInterval(low=np.nan, high=np.nan)
+        elif self.exposed_cases == 0:
+            # relative risk is 0.
+            return ConfidenceInterval(low=0.0, high=np.nan)
+        elif self.control_cases == 0:
+            # relative risk is inf
+            return ConfidenceInterval(low=np.nan, high=np.inf)
+
+        alpha = 1 - confidence_level
+        z = ndtri(1 - alpha/2)
+        rr = self.relative_risk
+
+        # Estimate of the variance of log(rr) is
+        # var(log(rr)) = 1/exposed_cases - 1/exposed_total +
+        #                1/control_cases - 1/control_total
+        # and the standard error is the square root of that.
+        se = np.sqrt(1/self.exposed_cases - 1/self.exposed_total +
+                     1/self.control_cases - 1/self.control_total)
+        delta = z*se
+        katz_lo = rr*np.exp(-delta)
+        katz_hi = rr*np.exp(delta)
+        return ConfidenceInterval(low=katz_lo, high=katz_hi)
+
+
+def relative_risk(exposed_cases, exposed_total, control_cases, control_total):
+    """
+    Compute the relative risk (also known as the risk ratio).
+
+    This function computes the relative risk associated with a 2x2
+    contingency table ([1]_, section 2.2.3; [2]_, section 3.1.2). Instead
+    of accepting a table as an argument, the individual numbers that are
+    used to compute the relative risk are given as separate parameters.
+    This is to avoid the ambiguity of which row or column of the contingency
+    table corresponds to the "exposed" cases and which corresponds to the
+    "control" cases.  Unlike, say, the odds ratio, the relative risk is not
+    invariant under an interchange of the rows or columns.
+
+    Parameters
+    ----------
+    exposed_cases : nonnegative int
+        The number of "cases" (i.e. occurrence of disease or other event
+        of interest) among the sample of "exposed" individuals.
+    exposed_total : positive int
+        The total number of "exposed" individuals in the sample.
+    control_cases : nonnegative int
+        The number of "cases" among the sample of "control" or non-exposed
+        individuals.
+    control_total : positive int
+        The total number of "control" individuals in the sample.
+
+    Returns
+    -------
+    result : instance of `~scipy.stats._result_classes.RelativeRiskResult`
+        The object has the float attribute ``relative_risk``, which is::
+
+            rr = (exposed_cases/exposed_total) / (control_cases/control_total)
+
+        The object also has the method ``confidence_interval`` to compute
+        the confidence interval of the relative risk for a given confidence
+        level.
+
+    See Also
+    --------
+    odds_ratio
+
+    Notes
+    -----
+    The R package epitools has the function `riskratio`, which accepts
+    a table with the following layout::
+
+                        disease=0   disease=1
+        exposed=0 (ref)    n00         n01
+        exposed=1          n10         n11
+
+    With a 2x2 table in the above format, the estimate of the CI is
+    computed by `riskratio` when the argument method="wald" is given,
+    or with the function `riskratio.wald`.
+
+    For example, in a test of the incidence of lung cancer among a
+    sample of smokers and nonsmokers, the "exposed" category would
+    correspond to "is a smoker" and the "disease" category would
+    correspond to "has or had lung cancer".
+
+    To pass the same data to ``relative_risk``, use::
+
+        relative_risk(n11, n10 + n11, n01, n00 + n01)
+
+    .. versionadded:: 1.7.0
+
+    References
+    ----------
+    .. [1] Alan Agresti, An Introduction to Categorical Data Analysis
+           (second edition), Wiley, Hoboken, NJ, USA (2007).
+    .. [2] Hardeo Sahai and Anwer Khurshid, Statistics in Epidemiology,
+           CRC Press LLC, Boca Raton, FL, USA (1996).
+
+    Examples
+    --------
+    >>> from scipy.stats.contingency import relative_risk
+
+    This example is from Example 3.1 of [2]_.  The results of a heart
+    disease study are summarized in the following table::
+
+                 High CAT   Low CAT    Total
+                 --------   -------    -----
+        CHD         27         44        71
+        No CHD      95        443       538
+
+        Total      122        487       609
+
+    CHD is coronary heart disease, and CAT refers to the level of
+    circulating catecholamine.  CAT is the "exposure" variable, and
+    high CAT is the "exposed" category. So the data from the table
+    to be passed to ``relative_risk`` is::
+
+        exposed_cases = 27
+        exposed_total = 122
+        control_cases = 44
+        control_total = 487
+
+    >>> result = relative_risk(27, 122, 44, 487)
+    >>> result.relative_risk
+    2.4495156482861398
+
+    Find the confidence interval for the relative risk.
+
+    >>> result.confidence_interval(confidence_level=0.95)
+    ConfidenceInterval(low=1.5836990926700116, high=3.7886786315466354)
+
+    The interval does not contain 1, so the data supports the statement
+    that high CAT is associated with greater risk of CHD.
+    """
+    # Relative risk is a trivial calculation.  The nontrivial part is in the
+    # `confidence_interval` method of the RelativeRiskResult class.
+
+    exposed_cases = _validate_int(exposed_cases, 0, "exposed_cases")
+    exposed_total = _validate_int(exposed_total, 1, "exposed_total")
+    control_cases = _validate_int(control_cases, 0, "control_cases")
+    control_total = _validate_int(control_total, 1, "control_total")
+
+    if exposed_cases > exposed_total:
+        raise ValueError('exposed_cases must not exceed exposed_total.')
+    if control_cases > control_total:
+        raise ValueError('control_cases must not exceed control_total.')
+
+    if exposed_cases == 0 and control_cases == 0:
+        # relative risk is 0/0.
+        rr = np.nan
+    elif exposed_cases == 0:
+        # relative risk is 0/nonzero
+        rr = 0.0
+    elif control_cases == 0:
+        # relative risk is nonzero/0.
+        rr = np.inf
+    else:
+        p1 = exposed_cases / exposed_total
+        p2 = control_cases / control_total
+        rr = p1 / p2
+    return RelativeRiskResult(relative_risk=rr,
+                              exposed_cases=exposed_cases,
+                              exposed_total=exposed_total,
+                              control_cases=control_cases,
+                              control_total=control_total)

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_result_classes.py

@@ -0,0 +1,34 @@
+# This module exists only to allow Sphinx to generate docs
+# for the result objects returned by some functions in stats
+# _without_ adding them to the main stats documentation page.
+
+"""
+Result classes
+--------------
+
+.. currentmodule:: scipy.stats._result_classes
+
+.. autosummary::
+   :toctree: generated/
+
+   RelativeRiskResult
+   BinomTestResult
+   TukeyHSDResult
+   PearsonRResult
+   FitResult
+   OddsRatioResult
+   TtestResult
+
+"""
+
+__all__ = ['BinomTestResult', 'RelativeRiskResult', 'TukeyHSDResult',
+           'PearsonRResult', 'FitResult', 'OddsRatioResult',
+           'TtestResult']
+
+
+from ._binomtest import BinomTestResult
+from ._odds_ratio import OddsRatioResult
+from ._relative_risk import RelativeRiskResult
+from ._hypotests import TukeyHSDResult
+from ._stats_py import PearsonRResult, TtestResult
+from ._fit import FitResult

.CondaPkg/env/lib/python3.11/site-packages/scipy/stats/_rvs_sampling.py

@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+import numpy as np
+from scipy._lib._util import check_random_state
+
+
+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.
+
+    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
+    -----
+    Given a univariate probability density function `pdf` and a constant `c`,
+    define the set ``A = {(u, v) : 0 < u <= sqrt(pdf(v/u + c))}``.
+    If `(U, V)` is a random vector uniformly distributed over `A`,
+    then `V/U + c` follows a distribution according to `pdf`.
+
+    The above result (see [1]_, [2]_) can be used to sample random variables
+    using only the pdf, i.e. no inversion of the cdf is required. Typical
+    choices of `c` are zero or the mode of `pdf`. The set `A` is a subset of
+    the rectangle ``R = [0, umax] x [vmin, vmax]`` where
+
+    - ``umax = sup sqrt(pdf(x))``
+    - ``vmin = inf (x - c) sqrt(pdf(x))``
+    - ``vmax = sup (x - c) sqrt(pdf(x))``
+
+    In particular, these values are finite if `pdf` is bounded and
+    ``x**2 * pdf(x)`` is bounded (i.e. subquadratic tails).
+    One can generate `(U, V)` uniformly on `R` and return
+    `V/U + c` if `(U, V)` are also in `A` which can be directly
+    verified.
+
+    The algorithm is not changed if one replaces `pdf` by k * `pdf` for any
+    constant k > 0. Thus, it is often convenient to work with a function
+    that is proportional to the probability density function by dropping
+    unneccessary normalization factors.
+
+    Intuitively, the method works well if `A` fills up most of the
+    enclosing rectangle such that the probability is high that `(U, V)`
+    lies in `A` whenever it lies in `R` as the number of required
+    iterations becomes too large otherwise. To be more precise, note that
+    the expected number of iterations to draw `(U, V)` uniformly
+    distributed on `R` such that `(U, V)` is also in `A` is given by
+    the ratio ``area(R) / area(A) = 2 * umax * (vmax - vmin) / area(pdf)``,
+    where `area(pdf)` is the integral of `pdf` (which is equal to one if the
+    probability density function is used but can take on other values if a
+    function proportional to the density is used). The equality holds since
+    the area of `A` is equal to 0.5 * area(pdf) (Theorem 7.1 in [1]_).
+    If the sampling fails to generate a single random variate after 50000
+    iterations (i.e. not a single draw is in `A`), an exception is raised.
+
+    If the bounding rectangle is not correctly specified (i.e. if it does not
+    contain `A`), the algorithm samples from a distribution different from
+    the one given by `pdf`. It is therefore recommended to perform a
+    test such as `~scipy.stats.kstest` as a check.
+
+    References
+    ----------
+    .. [1] L. Devroye, "Non-Uniform Random Variate Generation",
+       Springer-Verlag, 1986.
+
+    .. [2] W. Hoermann and J. Leydold, "Generating generalized inverse Gaussian
+       random variates", Statistics and Computing, 24(4), p. 547--557, 2014.
+
+    .. [3] A.J. Kinderman and J.F. Monahan, "Computer Generation of Random
+       Variables Using the Ratio of Uniform Deviates",
+       ACM Transactions on Mathematical Software, 3(3), p. 257--260, 1977.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy import stats
+    >>> rng = np.random.default_rng()
+
+    Simulate normally distributed random variables. It is easy to compute the
+    bounding rectangle explicitly in that case. For simplicity, we drop the
+    normalization factor of the density.
+
+    >>> f = lambda x: np.exp(-x**2 / 2)
+    >>> v_bound = np.sqrt(f(np.sqrt(2))) * np.sqrt(2)
+    >>> umax, vmin, vmax = np.sqrt(f(0)), -v_bound, v_bound
+    >>> rvs = stats.rvs_ratio_uniforms(f, umax, vmin, vmax, size=2500,
+    ...                                random_state=rng)
+
+    The K-S test confirms that the random variates are indeed normally
+    distributed (normality is not rejected at 5% significance level):
+
+    >>> stats.kstest(rvs, 'norm')[1]
+    0.250634764150542
+
+    The exponential distribution provides another example where the bounding
+    rectangle can be determined explicitly.
+
+    >>> rvs = stats.rvs_ratio_uniforms(lambda x: np.exp(-x), umax=1,
+    ...                                vmin=0, vmax=2*np.exp(-1), size=1000,
+    ...                                random_state=rng)
+    >>> stats.kstest(rvs, 'expon')[1]
+    0.21121052054580314
+
+    """
+    if vmin >= vmax:
+        raise ValueError("vmin must be smaller than vmax.")
+
+    if umax <= 0:
+        raise ValueError("umax must be positive.")
+
+    size1d = tuple(np.atleast_1d(size))
+    N = np.prod(size1d)  # number of rvs needed, reshape upon return
+
+    # start sampling using ratio of uniforms method
+    rng = check_random_state(random_state)
+    x = np.zeros(N)
+    simulated, i = 0, 1
+
+    # loop until N rvs have been generated: expected runtime is finite.
+    # to avoid infinite loop, raise exception if not a single rv has been
+    # generated after 50000 tries. even if the expected numer of iterations
+    # is 1000, the probability of this event is (1-1/1000)**50000
+    # which is of order 10e-22
+    while simulated < N:
+        k = N - simulated
+        # simulate uniform rvs on [0, umax] and [vmin, vmax]
+        u1 = umax * rng.uniform(size=k)
+        v1 = rng.uniform(vmin, vmax, size=k)
+        # apply rejection method
+        rvs = v1 / u1 + c
+        accept = (u1**2 <= pdf(rvs))
+        num_accept = np.sum(accept)
+        if num_accept > 0:
+            x[simulated:(simulated + num_accept)] = rvs[accept]
+            simulated += num_accept
+
+        if (simulated == 0) and (i*N >= 50000):
+            msg = ("Not a single random variate could be generated in {} "
+                   "attempts. The ratio of uniforms method does not appear "
+                   "to work for the provided parameters. Please check the "
+                   "pdf and the bounds.".format(i*N))
+            raise RuntimeError(msg)
+        i += 1
+
+    return np.reshape(x, size1d)