scipy 1.16.2__cp314-cp314t-win_arm64.whl

scipy/stats/_survival.py

@@ -0,0 +1,683 @@
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING, Literal
+import warnings
+
+import numpy as np
+from scipy import special, interpolate, stats
+from scipy.stats._censored_data import CensoredData
+from scipy.stats._common import ConfidenceInterval
+
+if TYPE_CHECKING:
+    import numpy.typing as npt
+
+
+__all__ = ['ecdf', 'logrank']
+
+
+@dataclass
+class EmpiricalDistributionFunction:
+    """An empirical distribution function produced by `scipy.stats.ecdf`
+
+    Attributes
+    ----------
+    quantiles : ndarray
+        The unique values of the sample from which the
+        `EmpiricalDistributionFunction` was estimated.
+    probabilities : ndarray
+        The point estimates of the cumulative distribution function (CDF) or
+        its complement, the survival function (SF), corresponding with
+        `quantiles`.
+    """
+    quantiles: np.ndarray
+    probabilities: np.ndarray
+    # Exclude these from __str__
+    _n: np.ndarray = field(repr=False)  # number "at risk"
+    _d: np.ndarray = field(repr=False)  # number of "deaths"
+    _sf: np.ndarray = field(repr=False)  # survival function for var estimate
+    _kind: str = field(repr=False)  # type of function: "cdf" or "sf"
+
+    def __init__(self, q, p, n, d, kind):
+        self.probabilities = p
+        self.quantiles = q
+        self._n = n
+        self._d = d
+        self._sf = p if kind == 'sf' else 1 - p
+        self._kind = kind
+
+        f0 = 1 if kind == 'sf' else 0  # leftmost function value
+        f1 = 1 - f0
+        # fill_value can't handle edge cases at infinity
+        x = np.insert(q, [0, len(q)], [-np.inf, np.inf])
+        y = np.insert(p, [0, len(p)], [f0, f1])
+        # `or` conditions handle the case of empty x, points
+        self._f = interpolate.interp1d(x, y, kind='previous',
+                                       assume_sorted=True)
+
+    def evaluate(self, x):
+        """Evaluate the empirical CDF/SF function at the input.
+
+        Parameters
+        ----------
+        x : ndarray
+            Argument to the CDF/SF
+
+        Returns
+        -------
+        y : ndarray
+            The CDF/SF evaluated at the input
+        """
+        return self._f(x)
+
+    def plot(self, ax=None, **matplotlib_kwargs):
+        """Plot the empirical distribution function
+
+        Available only if ``matplotlib`` is installed.
+
+        Parameters
+        ----------
+        ax : matplotlib.axes.Axes
+            Axes object to draw the plot onto, otherwise uses the current Axes.
+
+        **matplotlib_kwargs : dict, optional
+            Keyword arguments passed directly to `matplotlib.axes.Axes.step`.
+            Unless overridden, ``where='post'``.
+
+        Returns
+        -------
+        lines : list of `matplotlib.lines.Line2D`
+            Objects representing the plotted data
+        """
+        try:
+            import matplotlib  # noqa: F401
+        except ModuleNotFoundError as exc:
+            message = "matplotlib must be installed to use method `plot`."
+            raise ModuleNotFoundError(message) from exc
+
+        if ax is None:
+            import matplotlib.pyplot as plt
+            ax = plt.gca()
+
+        kwargs = {'where': 'post'}
+        kwargs.update(matplotlib_kwargs)
+
+        delta = np.ptp(self.quantiles)*0.05  # how far past sample edge to plot
+        q = self.quantiles
+        q = [q[0] - delta] + list(q) + [q[-1] + delta]
+
+        return ax.step(q, self.evaluate(q), **kwargs)
+
+    def confidence_interval(self, confidence_level=0.95, *, method='linear'):
+        """Compute a confidence interval around the CDF/SF point estimate
+
+        Parameters
+        ----------
+        confidence_level : float, default: 0.95
+            Confidence level for the computed confidence interval
+
+        method : str, {"linear", "log-log"}
+            Method used to compute the confidence interval. Options are
+            "linear" for the conventional Greenwood confidence interval
+            (default)  and "log-log" for the "exponential Greenwood",
+            log-negative-log-transformed confidence interval.
+
+        Returns
+        -------
+        ci : ``ConfidenceInterval``
+            An object with attributes ``low`` and ``high``, instances of
+            `~scipy.stats._result_classes.EmpiricalDistributionFunction` that
+            represent the lower and upper bounds (respectively) of the
+            confidence interval.
+
+        Notes
+        -----
+        Confidence intervals are computed according to the Greenwood formula
+        (``method='linear'``) or the more recent "exponential Greenwood"
+        formula (``method='log-log'``) as described in [1]_. The conventional
+        Greenwood formula can result in lower confidence limits less than 0
+        and upper confidence limits greater than 1; these are clipped to the
+        unit interval. NaNs may be produced by either method; these are
+        features of the formulas.
+
+        References
+        ----------
+        .. [1] Sawyer, Stanley. "The Greenwood and Exponential Greenwood
+               Confidence Intervals in Survival Analysis."
+               https://www.math.wustl.edu/~sawyer/handouts/greenwood.pdf
+
+        """
+        message = ("Confidence interval bounds do not implement a "
+                   "`confidence_interval` method.")
+        if self._n is None:
+            raise NotImplementedError(message)
+
+        methods = {'linear': self._linear_ci,
+                   'log-log': self._loglog_ci}
+
+        message = f"`method` must be one of {set(methods)}."
+        if method.lower() not in methods:
+            raise ValueError(message)
+
+        message = "`confidence_level` must be a scalar between 0 and 1."
+        confidence_level = np.asarray(confidence_level)[()]
+        if confidence_level.shape or not (0 <= confidence_level <= 1):
+            raise ValueError(message)
+
+        method_fun = methods[method.lower()]
+        low, high = method_fun(confidence_level)
+
+        message = ("The confidence interval is undefined at some observations."
+                   " This is a feature of the mathematical formula used, not"
+                   " an error in its implementation.")
+        if np.any(np.isnan(low) | np.isnan(high)):
+            warnings.warn(message, RuntimeWarning, stacklevel=2)
+
+        low, high = np.clip(low, 0, 1), np.clip(high, 0, 1)
+        low = EmpiricalDistributionFunction(self.quantiles, low, None, None,
+                                            self._kind)
+        high = EmpiricalDistributionFunction(self.quantiles, high, None, None,
+                                             self._kind)
+        return ConfidenceInterval(low, high)
+
+    def _linear_ci(self, confidence_level):
+        sf, d, n = self._sf, self._d, self._n
+        # When n == d, Greenwood's formula divides by zero.
+        # When s != 0, this can be ignored: var == inf, and CI is [0, 1]
+        # When s == 0, this results in NaNs. Produce an informative warning.
+        with np.errstate(divide='ignore', invalid='ignore'):
+            var = sf ** 2 * np.cumsum(d / (n * (n - d)))
+
+        se = np.sqrt(var)
+        z = special.ndtri(1 / 2 + confidence_level / 2)
+
+        z_se = z * se
+        low = self.probabilities - z_se
+        high = self.probabilities + z_se
+
+        return low, high
+
+    def _loglog_ci(self, confidence_level):
+        sf, d, n = self._sf, self._d, self._n
+
+        with np.errstate(divide='ignore', invalid='ignore'):
+            var = 1 / np.log(sf) ** 2 * np.cumsum(d / (n * (n - d)))
+
+        se = np.sqrt(var)
+        z = special.ndtri(1 / 2 + confidence_level / 2)
+
+        with np.errstate(divide='ignore'):
+            lnl_points = np.log(-np.log(sf))
+
+        z_se = z * se
+        low = np.exp(-np.exp(lnl_points + z_se))
+        high = np.exp(-np.exp(lnl_points - z_se))
+        if self._kind == "cdf":
+            low, high = 1-high, 1-low
+
+        return low, high
+
+
+@dataclass
+class ECDFResult:
+    """ Result object returned by `scipy.stats.ecdf`
+
+    Attributes
+    ----------
+    cdf : `~scipy.stats._result_classes.EmpiricalDistributionFunction`
+        An object representing the empirical cumulative distribution function.
+    sf : `~scipy.stats._result_classes.EmpiricalDistributionFunction`
+        An object representing the complement of the empirical cumulative
+        distribution function.
+    """
+    cdf: EmpiricalDistributionFunction
+    sf: EmpiricalDistributionFunction
+
+    def __init__(self, q, cdf, sf, n, d):
+        self.cdf = EmpiricalDistributionFunction(q, cdf, n, d, "cdf")
+        self.sf = EmpiricalDistributionFunction(q, sf, n, d, "sf")
+
+
+def _iv_CensoredData(
+    sample: "npt.ArrayLike | CensoredData", param_name: str = "sample"
+) -> CensoredData:
+    """Attempt to convert `sample` to `CensoredData`."""
+    if not isinstance(sample, CensoredData):
+        try:  # takes care of input standardization/validation
+            sample = CensoredData(uncensored=sample)
+        except ValueError as e:
+            message = str(e).replace('uncensored', param_name)
+            raise type(e)(message) from e
+    return sample
+
+
+def ecdf(sample: "npt.ArrayLike | CensoredData") -> ECDFResult:
+    """Empirical cumulative distribution function of a sample.
+
+    The empirical cumulative distribution function (ECDF) is a step function
+    estimate of the CDF of the distribution underlying a sample. This function
+    returns objects representing both the empirical distribution function and
+    its complement, the empirical survival function.
+
+    Parameters
+    ----------
+    sample : 1D array_like or `scipy.stats.CensoredData`
+        Besides array_like, instances of `scipy.stats.CensoredData` containing
+        uncensored and right-censored observations are supported. Currently,
+        other instances of `scipy.stats.CensoredData` will result in a
+        ``NotImplementedError``.
+
+    Returns
+    -------
+    res : `~scipy.stats._result_classes.ECDFResult`
+        An object with the following attributes.
+
+        cdf : `~scipy.stats._result_classes.EmpiricalDistributionFunction`
+            An object representing the empirical cumulative distribution
+            function.
+        sf : `~scipy.stats._result_classes.EmpiricalDistributionFunction`
+            An object representing the empirical survival function.
+
+        The `cdf` and `sf` attributes themselves have the following attributes.
+
+        quantiles : ndarray
+            The unique values in the sample that defines the empirical CDF/SF.
+        probabilities : ndarray
+            The point estimates of the probabilities corresponding with
+            `quantiles`.
+
+        And the following methods:
+
+        evaluate(x) :
+            Evaluate the CDF/SF at the argument.
+
+        plot(ax) :
+            Plot the CDF/SF on the provided axes.
+
+        confidence_interval(confidence_level=0.95) :
+            Compute the confidence interval around the CDF/SF at the values in
+            `quantiles`.
+
+    Notes
+    -----
+    When each observation of the sample is a precise measurement, the ECDF
+    steps up by ``1/len(sample)`` at each of the observations [1]_.
+
+    When observations are lower bounds, upper bounds, or both upper and lower
+    bounds, the data is said to be "censored", and `sample` may be provided as
+    an instance of `scipy.stats.CensoredData`.
+
+    For right-censored data, the ECDF is given by the Kaplan-Meier estimator
+    [2]_; other forms of censoring are not supported at this time.
+
+    Confidence intervals are computed according to the Greenwood formula or the
+    more recent "Exponential Greenwood" formula as described in [4]_.
+
+    References
+    ----------
+    .. [1] Conover, William Jay. Practical nonparametric statistics. Vol. 350.
+           John Wiley & Sons, 1999.
+
+    .. [2] Kaplan, Edward L., and Paul Meier. "Nonparametric estimation from
+           incomplete observations." Journal of the American statistical
+           association 53.282 (1958): 457-481.
+
+    .. [3] Goel, Manish Kumar, Pardeep Khanna, and Jugal Kishore.
+           "Understanding survival analysis: Kaplan-Meier estimate."
+           International journal of Ayurveda research 1.4 (2010): 274.
+
+    .. [4] Sawyer, Stanley. "The Greenwood and Exponential Greenwood Confidence
+           Intervals in Survival Analysis."
+           https://www.math.wustl.edu/~sawyer/handouts/greenwood.pdf
+
+    Examples
+    --------
+    **Uncensored Data**
+
+    As in the example from [1]_ page 79, five boys were selected at random from
+    those in a single high school. Their one-mile run times were recorded as
+    follows.
+
+    >>> sample = [6.23, 5.58, 7.06, 6.42, 5.20]  # one-mile run times (minutes)
+
+    The empirical distribution function, which approximates the distribution
+    function of one-mile run times of the population from which the boys were
+    sampled, is calculated as follows.
+
+    >>> from scipy import stats
+    >>> res = stats.ecdf(sample)
+    >>> res.cdf.quantiles
+    array([5.2 , 5.58, 6.23, 6.42, 7.06])
+    >>> res.cdf.probabilities
+    array([0.2, 0.4, 0.6, 0.8, 1. ])
+
+    To plot the result as a step function:
+
+    >>> import matplotlib.pyplot as plt
+    >>> ax = plt.subplot()
+    >>> res.cdf.plot(ax)
+    >>> ax.set_xlabel('One-Mile Run Time (minutes)')
+    >>> ax.set_ylabel('Empirical CDF')
+    >>> plt.show()
+
+    **Right-censored Data**
+
+    As in the example from [1]_ page 91, the lives of ten car fanbelts were
+    tested. Five tests concluded because the fanbelt being tested broke, but
+    the remaining tests concluded for other reasons (e.g. the study ran out of
+    funding, but the fanbelt was still functional). The mileage driven
+    with the fanbelts were recorded as follows.
+
+    >>> broken = [77, 47, 81, 56, 80]  # in thousands of miles driven
+    >>> unbroken = [62, 60, 43, 71, 37]
+
+    Precise survival times of the fanbelts that were still functional at the
+    end of the tests are unknown, but they are known to exceed the values
+    recorded in ``unbroken``. Therefore, these observations are said to be
+    "right-censored", and the data is represented using
+    `scipy.stats.CensoredData`.
+
+    >>> sample = stats.CensoredData(uncensored=broken, right=unbroken)
+
+    The empirical survival function is calculated as follows.
+
+    >>> res = stats.ecdf(sample)
+    >>> res.sf.quantiles
+    array([37., 43., 47., 56., 60., 62., 71., 77., 80., 81.])
+    >>> res.sf.probabilities
+    array([1.   , 1.   , 0.875, 0.75 , 0.75 , 0.75 , 0.75 , 0.5  , 0.25 , 0.   ])
+
+    To plot the result as a step function:
+
+    >>> ax = plt.subplot()
+    >>> res.sf.plot(ax)
+    >>> ax.set_xlabel('Fanbelt Survival Time (thousands of miles)')
+    >>> ax.set_ylabel('Empirical SF')
+    >>> plt.show()
+
+    """
+    sample = _iv_CensoredData(sample)
+
+    if sample.num_censored() == 0:
+        res = _ecdf_uncensored(sample._uncensor())
+    elif sample.num_censored() == sample._right.size:
+        res = _ecdf_right_censored(sample)
+    else:
+        # Support additional censoring options in follow-up PRs
+        message = ("Currently, only uncensored and right-censored data is "
+                   "supported.")
+        raise NotImplementedError(message)
+
+    t, cdf, sf, n, d = res
+    return ECDFResult(t, cdf, sf, n, d)
+
+
+def _ecdf_uncensored(sample):
+    sample = np.sort(sample)
+    x, counts = np.unique(sample, return_counts=True)
+
+    # [1].81 "the fraction of [observations] that are less than or equal to x
+    events = np.cumsum(counts)
+    n = sample.size
+    cdf = events / n
+
+    # [1].89 "the relative frequency of the sample that exceeds x in value"
+    sf = 1 - cdf
+
+    at_risk = np.concatenate(([n], n - events[:-1]))
+    return x, cdf, sf, at_risk, counts
+
+
+def _ecdf_right_censored(sample):
+    # It is conventional to discuss right-censored data in terms of
+    # "survival time", "death", and "loss" (e.g. [2]). We'll use that
+    # terminology here.
+    # This implementation was influenced by the references cited and also
+    # https://www.youtube.com/watch?v=lxoWsVco_iM
+    # https://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator
+    # In retrospect it is probably most easily compared against [3].
+    # Ultimately, the data needs to be sorted, so this implementation is
+    # written to avoid a separate call to `unique` after sorting. In hope of
+    # better performance on large datasets, it also computes survival
+    # probabilities at unique times only rather than at each observation.
+    tod = sample._uncensored  # time of "death"
+    tol = sample._right  # time of "loss"
+    times = np.concatenate((tod, tol))
+    died = np.asarray([1]*tod.size + [0]*tol.size)
+
+    # sort by times
+    i = np.argsort(times)
+    times = times[i]
+    died = died[i]
+    at_risk = np.arange(times.size, 0, -1)
+
+    # logical indices of unique times
+    j = np.diff(times, prepend=-np.inf, append=np.inf) > 0
+    j_l = j[:-1]  # first instances of unique times
+    j_r = j[1:]  # last instances of unique times
+
+    # get number at risk and deaths at each unique time
+    t = times[j_l]  # unique times
+    n = at_risk[j_l]  # number at risk at each unique time
+    cd = np.cumsum(died)[j_r]  # cumulative deaths up to/including unique times
+    d = np.diff(cd, prepend=0)  # deaths at each unique time
+
+    # compute survival function
+    sf = np.cumprod((n - d) / n)
+    cdf = 1 - sf
+    return t, cdf, sf, n, d
+
+
+@dataclass
+class LogRankResult:
+    """Result object returned by `scipy.stats.logrank`.
+
+    Attributes
+    ----------
+    statistic : float ndarray
+        The computed statistic (defined below). Its magnitude is the
+        square root of the magnitude returned by most other logrank test
+        implementations.
+    pvalue : float ndarray
+        The computed p-value of the test.
+    """
+    statistic: np.ndarray
+    pvalue: np.ndarray
+
+
+def logrank(
+    x: "npt.ArrayLike | CensoredData",
+    y: "npt.ArrayLike | CensoredData",
+    alternative: Literal['two-sided', 'less', 'greater'] = "two-sided"
+) -> LogRankResult:
+    r"""Compare the survival distributions of two samples via the logrank test.
+
+    Parameters
+    ----------
+    x, y : array_like or CensoredData
+        Samples to compare based on their empirical survival functions.
+    alternative : {'two-sided', 'less', 'greater'}, optional
+        Defines the alternative hypothesis.
+
+        The null hypothesis is that the survival distributions of the two
+        groups, say *X* and *Y*, are identical.
+
+        The following alternative hypotheses [4]_ are available (default is
+        'two-sided'):
+
+        * 'two-sided': the survival distributions of the two groups are not
+          identical.
+        * 'less': survival of group *X* is favored: the group *X* failure rate
+          function is less than the group *Y* failure rate function at some
+          times.
+        * 'greater': survival of group *Y* is favored: the group *X* failure
+          rate function is greater than the group *Y* failure rate function at
+          some times.
+
+    Returns
+    -------
+    res : `~scipy.stats._result_classes.LogRankResult`
+        An object containing attributes:
+
+        statistic : float ndarray
+            The computed statistic (defined below). Its magnitude is the
+            square root of the magnitude returned by most other logrank test
+            implementations.
+        pvalue : float ndarray
+            The computed p-value of the test.
+
+    See Also
+    --------
+    scipy.stats.ecdf
+
+    Notes
+    -----
+    The logrank test [1]_ compares the observed number of events to
+    the expected number of events under the null hypothesis that the two
+    samples were drawn from the same distribution. The statistic is
+
+    .. math::
+
+        Z_i = \frac{\sum_{j=1}^J(O_{i,j}-E_{i,j})}{\sqrt{\sum_{j=1}^J V_{i,j}}}
+        \rightarrow \mathcal{N}(0,1)
+
+    where
+
+    .. math::
+
+        E_{i,j} = O_j \frac{N_{i,j}}{N_j},
+        \qquad
+        V_{i,j} = E_{i,j} \left(\frac{N_j-O_j}{N_j}\right)
+        \left(\frac{N_j-N_{i,j}}{N_j-1}\right),
+
+    :math:`i` denotes the group (i.e. it may assume values :math:`x` or
+    :math:`y`, or it may be omitted to refer to the combined sample)
+    :math:`j` denotes the time (at which an event occurred),
+    :math:`N` is the number of subjects at risk just before an event occurred,
+    and :math:`O` is the observed number of events at that time.
+
+    The ``statistic`` :math:`Z_x` returned by `logrank` is the (signed) square
+    root of the statistic returned by many other implementations. Under the
+    null hypothesis, :math:`Z_x**2` is asymptotically distributed according to
+    the chi-squared distribution with one degree of freedom. Consequently,
+    :math:`Z_x` is asymptotically distributed according to the standard normal
+    distribution. The advantage of using :math:`Z_x` is that the sign
+    information (i.e. whether the observed number of events tends to be less
+    than or greater than the number expected under the null hypothesis) is
+    preserved, allowing `scipy.stats.logrank` to offer one-sided alternative
+    hypotheses.
+
+    References
+    ----------
+    .. [1] Mantel N. "Evaluation of survival data and two new rank order
+           statistics arising in its consideration."
+           Cancer Chemotherapy Reports, 50(3):163-170, PMID: 5910392, 1966
+    .. [2] Bland, Altman, "The logrank test", BMJ, 328:1073,
+           :doi:`10.1136/bmj.328.7447.1073`, 2004
+    .. [3] "Logrank test", Wikipedia,
+           https://en.wikipedia.org/wiki/Logrank_test
+    .. [4] Brown, Mark. "On the choice of variance for the log rank test."
+           Biometrika 71.1 (1984): 65-74.
+    .. [5] Klein, John P., and Melvin L. Moeschberger. Survival analysis:
+           techniques for censored and truncated data. Vol. 1230. New York:
+           Springer, 2003.
+
+    Examples
+    --------
+    Reference [2]_ compared the survival times of patients with two different
+    types of recurrent malignant gliomas. The samples below record the time
+    (number of weeks) for which each patient participated in the study. The
+    `scipy.stats.CensoredData` class is used because the data is
+    right-censored: the uncensored observations correspond with observed deaths
+    whereas the censored observations correspond with the patient leaving the
+    study for another reason.
+
+    >>> from scipy import stats
+    >>> x = stats.CensoredData(
+    ...     uncensored=[6, 13, 21, 30, 37, 38, 49, 50,
+    ...                 63, 79, 86, 98, 202, 219],
+    ...     right=[31, 47, 80, 82, 82, 149]
+    ... )
+    >>> y = stats.CensoredData(
+    ...     uncensored=[10, 10, 12, 13, 14, 15, 16, 17, 18, 20, 24, 24,
+    ...                 25, 28,30, 33, 35, 37, 40, 40, 46, 48, 76, 81,
+    ...                 82, 91, 112, 181],
+    ...     right=[34, 40, 70]
+    ... )
+
+    We can calculate and visualize the empirical survival functions
+    of both groups as follows.
+
+    >>> import numpy as np
+    >>> import matplotlib.pyplot as plt
+    >>> ax = plt.subplot()
+    >>> ecdf_x = stats.ecdf(x)
+    >>> ecdf_x.sf.plot(ax, label='Astrocytoma')
+    >>> ecdf_y = stats.ecdf(y)
+    >>> ecdf_y.sf.plot(ax, label='Glioblastoma')
+    >>> ax.set_xlabel('Time to death (weeks)')
+    >>> ax.set_ylabel('Empirical SF')
+    >>> plt.legend()
+    >>> plt.show()
+
+    Visual inspection of the empirical survival functions suggests that the
+    survival times tend to be different between the two groups. To formally
+    assess whether the difference is significant at the 1% level, we use the
+    logrank test.
+
+    >>> res = stats.logrank(x=x, y=y)
+    >>> res.statistic
+    -2.73799
+    >>> res.pvalue
+    0.00618
+
+    The p-value is less than 1%, so we can consider the data to be evidence
+    against the null hypothesis in favor of the alternative that there is a
+    difference between the two survival functions.
+
+    """
+    # Input validation. `alternative` IV handled in `_get_pvalue` below.
+    x = _iv_CensoredData(sample=x, param_name='x')
+    y = _iv_CensoredData(sample=y, param_name='y')
+
+    # Combined sample. (Under H0, the two groups are identical.)
+    xy = CensoredData(
+        uncensored=np.concatenate((x._uncensored, y._uncensored)),
+        right=np.concatenate((x._right, y._right))
+    )
+
+    # Extract data from the combined sample
+    res = ecdf(xy)
+    idx = res.sf._d.astype(bool)  # indices of observed events
+    times_xy = res.sf.quantiles[idx]  # unique times of observed events
+    at_risk_xy = res.sf._n[idx]  # combined number of subjects at risk
+    deaths_xy = res.sf._d[idx]  # combined number of events
+
+    # Get the number at risk within each sample.
+    # First compute the number at risk in group X at each of the `times_xy`.
+    # Could use `interpolate_1d`, but this is more compact.
+    res_x = ecdf(x)
+    i = np.searchsorted(res_x.sf.quantiles, times_xy)
+    at_risk_x = np.append(res_x.sf._n, 0)[i]  # 0 at risk after last time
+    # Subtract from the combined number at risk to get number at risk in Y
+    at_risk_y = at_risk_xy - at_risk_x
+
+    # Compute the variance.
+    num = at_risk_x * at_risk_y * deaths_xy * (at_risk_xy - deaths_xy)
+    den = at_risk_xy**2 * (at_risk_xy - 1)
+    # Note: when `at_risk_xy == 1`, we would have `at_risk_xy - 1 == 0` in the
+    # numerator and denominator. Simplifying the fraction symbolically, we
+    # would always find the overall quotient to be zero, so don't compute it.
+    i = at_risk_xy > 1
+    sum_var = np.sum(num[i]/den[i])
+
+    # Get the observed and expected number of deaths in group X
+    n_died_x = x._uncensored.size
+    sum_exp_deaths_x = np.sum(at_risk_x * (deaths_xy/at_risk_xy))
+
+    # Compute the statistic. This is the square root of that in references.
+    statistic = (n_died_x - sum_exp_deaths_x)/np.sqrt(sum_var)
+
+    # Equivalent to chi2(df=1).sf(statistic**2) when alternative='two-sided'
+    norm = stats._stats_py._SimpleNormal()
+    pvalue = stats._stats_py._get_pvalue(statistic, norm, alternative, xp=np)
+
+    return LogRankResult(statistic=statistic[()], pvalue=pvalue[()])