scipy 1.16.1__cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl

scipy/stats/_page_trend_test.py

@@ -0,0 +1,486 @@
+from dataclasses import dataclass
+from itertools import permutations
+import math
+import threading
+
+import numpy as np
+
+from ._continuous_distns import norm
+import scipy.stats
+
+
+@dataclass
+class PageTrendTestResult:
+    statistic: float
+    pvalue: float
+    method: str
+
+
+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 ordering 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')
+
+    """
+    if not hasattr(_pagel_state, 'state'):
+        _pagel_state.state = _PageL()
+
+    # 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.asarray(data)
+    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.asarray(predicted_ranks)
+        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 not isinstance(ranked, 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 insensitive 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.state.set_k(k)
+    return _pagel_state.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 occurrences 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() is calculated once per thread and stored as an attribute on
+# this thread-local variable inside page_trend_test().
+_pagel_state = threading.local()