scipy.stats.chisquare is not working

My issue is about … scipy.stats.chisquare is not working since last update

Reproducing code example:

obs_spec=pd.read_fwf(folder+'obs.txt',header=None)
the_spec=pd.read_fwf(folder+'models/m9.dat',header=None)
sps.chisquare(f_obs=obs_spec[1], f_exp=the_spec[1])

Sample code to reproduce the problem

Error message:

Traceback (most recent call last):
ValueError                                Traceback (most recent call last)
<ipython-input-28-726f4043508e> in <module>
     14 obs_spec,the_spec
     15 
---> 16 a=sps.chisquare(f_obs=obs_spec[1], f_exp=the_spec[1])
     17 a

~/anaconda3/lib/python3.7/site-packages/scipy/stats/stats.py in chisquare(f_obs, f_exp, ddof, axis)
   6851     """
   6852     return power_divergence(f_obs, f_exp=f_exp, ddof=ddof, axis=axis,
-> 6853                             lambda_="pearson")
   6854 
   6855 

~/anaconda3/lib/python3.7/site-packages/scipy/stats/stats.py in power_divergence(f_obs, f_exp, ddof, axis, lambda_)
   6692                    f"of {rtol}, but the percent differences are:\n"
   6693                    f"{relative_diff}")
-> 6694             raise ValueError(msg)
   6695 
   6696     else:

ValueError: For each axis slice, the sum of the observed frequencies must agree with the sum of the expected frequencies to a relative tolerance of 1e-08, but the percent differences are:
0.19829509324291156

  File "<stdin>", line 1, in <module>
  ...

Scipy/Numpy/Python version information:

[mdhaber]

Yup, and that’s why we added the check : ) Thanks!

[mdhaber]

You are welcome to use the old code. This was the relevant code in 87641e3.

from collections import namedtuple
import numpy as np
from scipy import stats, special


def chisquare(f_obs, f_exp=None, ddof=0, axis=0):
    """
    Calculate a one-way chi-square test.
    The chi-square test tests the null hypothesis that the categorical data
    has the given frequencies.
    Parameters
    ----------
    f_obs : array_like
        Observed frequencies in each category.
    f_exp : array_like, optional
        Expected frequencies in each category.  By default the categories are
        assumed to be equally likely.
    ddof : int, optional
        "Delta degrees of freedom": adjustment to the degrees of freedom
        for the p-value.  The p-value is computed using a chi-squared
        distribution with ``k - 1 - ddof`` degrees of freedom, where `k`
        is the number of observed frequencies.  The default value of `ddof`
        is 0.
    axis : int or None, optional
        The axis of the broadcast result of `f_obs` and `f_exp` along which to
        apply the test.  If axis is None, all values in `f_obs` are treated
        as a single data set.  Default is 0.
    Returns
    -------
    chisq : float or ndarray
        The chi-squared test statistic.  The value is a float if `axis` is
        None or `f_obs` and `f_exp` are 1-D.
    p : float or ndarray
        The p-value of the test.  The value is a float if `ddof` and the
        return value `chisq` are scalars.
    See Also
    --------
    scipy.stats.power_divergence
    Notes
    -----
    This test is invalid when the observed or expected frequencies in each
    category are too small.  A typical rule is that all of the observed
    and expected frequencies should be at least 5.
    The default degrees of freedom, k-1, are for the case when no parameters
    of the distribution are estimated. If p parameters are estimated by
    efficient maximum likelihood then the correct degrees of freedom are
    k-1-p. If the parameters are estimated in a different way, then the
    dof can be between k-1-p and k-1. However, it is also possible that
    the asymptotic distribution is not chi-square, in which case this test
    is not appropriate.
    References
    ----------
    .. [1] Lowry, Richard.  "Concepts and Applications of Inferential
           Statistics". Chapter 8.
           https://web.archive.org/web/20171022032306/http://vassarstats.net:80/textbook/ch8pt1.html
    .. [2] "Chi-squared test", https://en.wikipedia.org/wiki/Chi-squared_test
    Examples
    --------
    When just `f_obs` is given, it is assumed that the expected frequencies
    are uniform and given by the mean of the observed frequencies.
    >>> from scipy.stats import chisquare
    >>> chisquare([16, 18, 16, 14, 12, 12])
    (2.0, 0.84914503608460956)
    With `f_exp` the expected frequencies can be given.
    >>> chisquare([16, 18, 16, 14, 12, 12], f_exp=[16, 16, 16, 16, 16, 8])
    (3.5, 0.62338762774958223)
    When `f_obs` is 2-D, by default the test is applied to each column.
    >>> obs = np.array([[16, 18, 16, 14, 12, 12], [32, 24, 16, 28, 20, 24]]).T
    >>> obs.shape
    (6, 2)
    >>> chisquare(obs)
    (array([ 2.        ,  6.66666667]), array([ 0.84914504,  0.24663415]))
    By setting ``axis=None``, the test is applied to all data in the array,
    which is equivalent to applying the test to the flattened array.
    >>> chisquare(obs, axis=None)
    (23.31034482758621, 0.015975692534127565)
    >>> chisquare(obs.ravel())
    (23.31034482758621, 0.015975692534127565)
    `ddof` is the change to make to the default degrees of freedom.
    >>> chisquare([16, 18, 16, 14, 12, 12], ddof=1)
    (2.0, 0.73575888234288467)
    The calculation of the p-values is done by broadcasting the
    chi-squared statistic with `ddof`.
    >>> chisquare([16, 18, 16, 14, 12, 12], ddof=[0,1,2])
    (2.0, array([ 0.84914504,  0.73575888,  0.5724067 ]))
    `f_obs` and `f_exp` are also broadcast.  In the following, `f_obs` has
    shape (6,) and `f_exp` has shape (2, 6), so the result of broadcasting
    `f_obs` and `f_exp` has shape (2, 6).  To compute the desired chi-squared
    statistics, we use ``axis=1``:
    >>> chisquare([16, 18, 16, 14, 12, 12],
    ...           f_exp=[[16, 16, 16, 16, 16, 8], [8, 20, 20, 16, 12, 12]],
    ...           axis=1)
    (array([ 3.5 ,  9.25]), array([ 0.62338763,  0.09949846]))
    """
    return power_divergence(f_obs, f_exp=f_exp, ddof=ddof, axis=axis,
                            lambda_="pearson")


# Map from names to lambda_ values used in power_divergence().
_power_div_lambda_names = {
    "pearson": 1,
    "log-likelihood": 0,
    "freeman-tukey": -0.5,
    "mod-log-likelihood": -1,
    "neyman": -2,
    "cressie-read": 2/3,
}


def _count(a, axis=None):
    """
    Count the number of non-masked elements of an array.
    This function behaves like np.ma.count(), but is much faster
    for ndarrays.
    """
    if hasattr(a, 'count'):
        num = a.count(axis=axis)
        if isinstance(num, np.ndarray) and num.ndim == 0:
            # In some cases, the `count` method returns a scalar array (e.g.
            # np.array(3)), but we want a plain integer.
            num = int(num)
    else:
        if axis is None:
            num = a.size
        else:
            num = a.shape[axis]
    return num


Power_divergenceResult = namedtuple('Power_divergenceResult',
                                    ('statistic', 'pvalue'))


def power_divergence(f_obs, f_exp=None, ddof=0, axis=0, lambda_=None):
    """
    Cressie-Read power divergence statistic and goodness of fit test.
    This function tests the null hypothesis that the categorical data
    has the given frequencies, using the Cressie-Read power divergence
    statistic.
    Parameters
    ----------
    f_obs : array_like
        Observed frequencies in each category.
    f_exp : array_like, optional
        Expected frequencies in each category.  By default the categories are
        assumed to be equally likely.
    ddof : int, optional
        "Delta degrees of freedom": adjustment to the degrees of freedom
        for the p-value.  The p-value is computed using a chi-squared
        distribution with ``k - 1 - ddof`` degrees of freedom, where `k`
        is the number of observed frequencies.  The default value of `ddof`
        is 0.
    axis : int or None, optional
        The axis of the broadcast result of `f_obs` and `f_exp` along which to
        apply the test.  If axis is None, all values in `f_obs` are treated
        as a single data set.  Default is 0.
    lambda_ : float or str, optional
        The power in the Cressie-Read power divergence statistic.  The default
        is 1.  For convenience, `lambda_` may be assigned one of the following
        strings, in which case the corresponding numerical value is used::
            String              Value   Description
            "pearson"             1     Pearson's chi-squared statistic.
                                        In this case, the function is
                                        equivalent to `stats.chisquare`.
            "log-likelihood"      0     Log-likelihood ratio. Also known as
                                        the G-test [3]_.
            "freeman-tukey"      -1/2   Freeman-Tukey statistic.
            "mod-log-likelihood" -1     Modified log-likelihood ratio.
            "neyman"             -2     Neyman's statistic.
            "cressie-read"        2/3   The power recommended in [5]_.
    Returns
    -------
    statistic : float or ndarray
        The Cressie-Read power divergence test statistic.  The value is
        a float if `axis` is None or if` `f_obs` and `f_exp` are 1-D.
    pvalue : float or ndarray
        The p-value of the test.  The value is a float if `ddof` and the
        return value `stat` are scalars.
    See Also
    --------
    chisquare
    Notes
    -----
    This test is invalid when the observed or expected frequencies in each
    category are too small.  A typical rule is that all of the observed
    and expected frequencies should be at least 5.
    When `lambda_` is less than zero, the formula for the statistic involves
    dividing by `f_obs`, so a warning or error may be generated if any value
    in `f_obs` is 0.
    Similarly, a warning or error may be generated if any value in `f_exp` is
    zero when `lambda_` >= 0.
    The default degrees of freedom, k-1, are for the case when no parameters
    of the distribution are estimated. If p parameters are estimated by
    efficient maximum likelihood then the correct degrees of freedom are
    k-1-p. If the parameters are estimated in a different way, then the
    dof can be between k-1-p and k-1. However, it is also possible that
    the asymptotic distribution is not a chisquare, in which case this
    test is not appropriate.
    This function handles masked arrays.  If an element of `f_obs` or `f_exp`
    is masked, then data at that position is ignored, and does not count
    towards the size of the data set.
    .. versionadded:: 0.13.0
    References
    ----------
    .. [1] Lowry, Richard.  "Concepts and Applications of Inferential
           Statistics". Chapter 8.
           https://web.archive.org/web/20171015035606/http://faculty.vassar.edu/lowry/ch8pt1.html
    .. [2] "Chi-squared test", https://en.wikipedia.org/wiki/Chi-squared_test
    .. [3] "G-test", https://en.wikipedia.org/wiki/G-test
    .. [4] Sokal, R. R. and Rohlf, F. J. "Biometry: the principles and
           practice of statistics in biological research", New York: Freeman
           (1981)
    .. [5] Cressie, N. and Read, T. R. C., "Multinomial Goodness-of-Fit
           Tests", J. Royal Stat. Soc. Series B, Vol. 46, No. 3 (1984),
           pp. 440-464.
    Examples
    --------
    (See `chisquare` for more examples.)
    When just `f_obs` is given, it is assumed that the expected frequencies
    are uniform and given by the mean of the observed frequencies.  Here we
    perform a G-test (i.e. use the log-likelihood ratio statistic):
    >>> from scipy.stats import power_divergence
    >>> power_divergence([16, 18, 16, 14, 12, 12], lambda_='log-likelihood')
    (2.006573162632538, 0.84823476779463769)
    The expected frequencies can be given with the `f_exp` argument:
    >>> power_divergence([16, 18, 16, 14, 12, 12],
    ...                  f_exp=[16, 16, 16, 16, 16, 8],
    ...                  lambda_='log-likelihood')
    (3.3281031458963746, 0.6495419288047497)
    When `f_obs` is 2-D, by default the test is applied to each column.
    >>> obs = np.array([[16, 18, 16, 14, 12, 12], [32, 24, 16, 28, 20, 24]]).T
    >>> obs.shape
    (6, 2)
    >>> power_divergence(obs, lambda_="log-likelihood")
    (array([ 2.00657316,  6.77634498]), array([ 0.84823477,  0.23781225]))
    By setting ``axis=None``, the test is applied to all data in the array,
    which is equivalent to applying the test to the flattened array.
    >>> power_divergence(obs, axis=None)
    (23.31034482758621, 0.015975692534127565)
    >>> power_divergence(obs.ravel())
    (23.31034482758621, 0.015975692534127565)
    `ddof` is the change to make to the default degrees of freedom.
    >>> power_divergence([16, 18, 16, 14, 12, 12], ddof=1)
    (2.0, 0.73575888234288467)
    The calculation of the p-values is done by broadcasting the
    test statistic with `ddof`.
    >>> power_divergence([16, 18, 16, 14, 12, 12], ddof=[0,1,2])
    (2.0, array([ 0.84914504,  0.73575888,  0.5724067 ]))
    `f_obs` and `f_exp` are also broadcast.  In the following, `f_obs` has
    shape (6,) and `f_exp` has shape (2, 6), so the result of broadcasting
    `f_obs` and `f_exp` has shape (2, 6).  To compute the desired chi-squared
    statistics, we must use ``axis=1``:
    >>> power_divergence([16, 18, 16, 14, 12, 12],
    ...                  f_exp=[[16, 16, 16, 16, 16, 8],
    ...                         [8, 20, 20, 16, 12, 12]],
    ...                  axis=1)
    (array([ 3.5 ,  9.25]), array([ 0.62338763,  0.09949846]))
    """
    # Convert the input argument `lambda_` to a numerical value.
    if isinstance(lambda_, str):
        if lambda_ not in _power_div_lambda_names:
            names = repr(list(_power_div_lambda_names.keys()))[1:-1]
            raise ValueError("invalid string for lambda_: {0!r}.  Valid strings "
                             "are {1}".format(lambda_, names))
        lambda_ = _power_div_lambda_names[lambda_]
    elif lambda_ is None:
        lambda_ = 1

    f_obs = np.asanyarray(f_obs)

    if f_exp is not None:
        f_exp = np.asanyarray(f_exp)
    else:
        # Ignore 'invalid' errors so the edge case of a data set with length 0
        # is handled without spurious warnings.
        with np.errstate(invalid='ignore'):
            f_exp = f_obs.mean(axis=axis, keepdims=True)

    # `terms` is the array of terms that are summed along `axis` to create
    # the test statistic.  We use some specialized code for a few special
    # cases of lambda_.
    if lambda_ == 1:
        # Pearson's chi-squared statistic
        terms = (f_obs.astype(np.float64) - f_exp)**2 / f_exp
    elif lambda_ == 0:
        # Log-likelihood ratio (i.e. G-test)
        terms = 2.0 * special.xlogy(f_obs, f_obs / f_exp)
    elif lambda_ == -1:
        # Modified log-likelihood ratio
        terms = 2.0 * special.xlogy(f_exp, f_exp / f_obs)
    else:
        # General Cressie-Read power divergence.
        terms = f_obs * ((f_obs / f_exp)**lambda_ - 1)
        terms /= 0.5 * lambda_ * (lambda_ + 1)

    stat = terms.sum(axis=axis)

    num_obs = _count(terms, axis=axis)
    ddof = np.asarray(ddof)
    p = stats.distributions.chi2.sf(stat, num_obs - 1 - ddof)

    return Power_divergenceResult(stat, p)