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 # Author: Travis Oliphant, 2002 # # Further updates and enhancements by many SciPy developers. # from __future__ import division, print_function, absolute_import import math import warnings import numpy as np from numpy import (isscalar, r_, log, sum, around, unique, asarray, zeros, arange, sort, amin, amax, any, atleast_1d, sqrt, ceil, floor, array, poly1d, compress, pi, exp, ravel, angle, count_nonzero) from numpy.testing.decorators import setastest from scipy._lib.six import string_types from scipy import optimize from scipy import special from . import statlib from . import stats from .stats import find_repeats from .contingency import chi2_contingency from . import distributions from ._distn_infrastructure import rv_generic __all__ = ['mvsdist', 'bayes_mvs', 'kstat', 'kstatvar', 'probplot', 'ppcc_max', 'ppcc_plot', 'boxcox_llf', 'boxcox', 'boxcox_normmax', 'boxcox_normplot', 'shapiro', 'anderson', 'ansari', 'bartlett', 'levene', 'binom_test', 'fligner', 'mood', 'wilcoxon', 'median_test', 'pdf_fromgamma', 'circmean', 'circvar', 'circstd', 'anderson_ksamp' ] def bayes_mvs(data, alpha=0.90): """ Bayesian confidence intervals for the mean, var, and std. Parameters ---------- data : array_like Input data, if multi-dimensional it is flattened to 1-D by bayes_mvs. Requires 2 or more data points. alpha : float, optional Probability that the returned confidence interval contains the true parameter. Returns ------- mean_cntr, var_cntr, std_cntr : tuple The three results are for the mean, variance and standard deviation, respectively. Each result is a tuple of the form:: (center, (lower, upper)) with center the mean of the conditional pdf of the value given the data, and (lower, upper) a confidence interval, centered on the median, containing the estimate to a probability alpha. Notes ----- Each tuple of mean, variance, and standard deviation estimates represent the (center, (lower, upper)) with center the mean of the conditional pdf of the value given the data and (lower, upper) is a confidence interval centered on the median, containing the estimate to a probability alpha. Converts data to 1-D and assumes all data has the same mean and variance. Uses Jeffrey's prior for variance and std. Equivalent to tuple((x.mean(), x.interval(alpha)) for x in mvsdist(dat)) References ---------- T.E. Oliphant, "A Bayesian perspective on estimating mean, variance, and standard-deviation from data", http://hdl.handle.net/1877/438, 2006. """ res = mvsdist(data) if alpha >= 1 or alpha <= 0: raise ValueError("0 < alpha < 1 is required, but alpha=%s was given." % alpha) return tuple((x.mean(), x.interval(alpha)) for x in res) def mvsdist(data): """ 'Frozen' distributions for mean, variance, and standard deviation of data. Parameters ---------- data : array_like Input array. Converted to 1-D using ravel. Requires 2 or more data-points. Returns ------- mdist : "frozen" distribution object Distribution object representing the mean of the data vdist : "frozen" distribution object Distribution object representing the variance of the data sdist : "frozen" distribution object Distribution object representing the standard deviation of the data Notes ----- The return values from bayes_mvs(data) is equivalent to tuple((x.mean(), x.interval(0.90)) for x in mvsdist(data)). In other words, calling .mean() and .interval(0.90) on the three distribution objects returned from this function will give the same results that are returned from bayes_mvs. Examples -------- >>> from scipy import stats >>> data = [6, 9, 12, 7, 8, 8, 13] >>> mean, var, std = stats.mvsdist(data) We now have frozen distribution objects "mean", "var" and "std" that we can examine: >>> mean.mean() 9.0 >>> mean.interval(0.95) (6.6120585482655692, 11.387941451734431) >>> mean.std() 1.1952286093343936 """ x = ravel(data) n = len(x) if n < 2: raise ValueError("Need at least 2 data-points.") xbar = x.mean() C = x.var() if n > 1000: # gaussian approximations for large n mdist = distributions.norm(loc=xbar, scale=math.sqrt(C / n)) sdist = distributions.norm(loc=math.sqrt(C), scale=math.sqrt(C / (2. * n))) vdist = distributions.norm(loc=C, scale=math.sqrt(2.0 / n) * C) else: nm1 = n - 1 fac = n * C / 2. val = nm1 / 2. mdist = distributions.t(nm1, loc=xbar, scale=math.sqrt(C / nm1)) sdist = distributions.gengamma(val, -2, scale=math.sqrt(fac)) vdist = distributions.invgamma(val, scale=fac) return mdist, vdist, sdist def kstat(data, n=2): """ Return the nth k-statistic (1<=n<=4 so far). The nth k-statistic is the unique symmetric unbiased estimator of the nth cumulant kappa_n. Parameters ---------- data : array_like Input array. n : int, {1, 2, 3, 4}, optional Default is equal to 2. Returns ------- kstat : float The nth k-statistic. See Also -------- kstatvar: Returns an unbiased estimator of the variance of the k-statistic. Notes ----- The cumulants are related to central moments but are specifically defined using a power series expansion of the logarithm of the characteristic function (which is the Fourier transform of the PDF). In particular let phi(t) be the characteristic function, then:: ln phi(t) = > kappa_n (it)^n / n! (sum from n=0 to inf) The first few cumulants (kappa_n) in terms of central moments (mu_n) are:: kappa_1 = mu_1 kappa_2 = mu_2 kappa_3 = mu_3 kappa_4 = mu_4 - 3*mu_2**2 kappa_5 = mu_5 - 10*mu_2 * mu_3 References ---------- http://mathworld.wolfram.com/k-Statistic.html http://mathworld.wolfram.com/Cumulant.html """ if n > 4 or n < 1: raise ValueError("k-statistics only supported for 1<=n<=4") n = int(n) S = zeros(n + 1, 'd') data = ravel(data) N = len(data) for k in range(1, n + 1): S[k] = sum(data**k, axis=0) if n == 1: return S[1] * 1.0/N elif n == 2: return (N*S[2] - S[1]**2.0) / (N*(N - 1.0)) elif n == 3: return (2*S[1]**3 - 3*N*S[1]*S[2] + N*N*S[3]) / (N*(N - 1.0)*(N - 2.0)) elif n == 4: return ((-6*S[1]**4 + 12*N*S[1]**2 * S[2] - 3*N*(N-1.0)*S[2]**2 - 4*N*(N+1)*S[1]*S[3] + N*N*(N+1)*S[4]) / (N*(N-1.0)*(N-2.0)*(N-3.0))) else: raise ValueError("Should not be here.") def kstatvar(data, n=2): """ Returns an unbiased estimator of the variance of the k-statistic. See kstat for more details of the k-statistic. Parameters ---------- data : array_like Input array. n : int, {1, 2}, optional Default is equal to 2. Returns ------- kstatvar : float The nth k-statistic variance. See Also -------- kstat """ data = ravel(data) N = len(data) if n == 1: return kstat(data, n=2) * 1.0/N elif n == 2: k2 = kstat(data, n=2) k4 = kstat(data, n=4) return (2*N*k2**2 + (N-1)*k4) / (N*(N+1)) else: raise ValueError("Only n=1 or n=2 supported.") def _calc_uniform_order_statistic_medians(x): """See Notes section of probplot for details.""" N = len(x) osm_uniform = np.zeros(N, dtype=np.float64) osm_uniform[-1] = 0.5**(1.0 / N) osm_uniform[0] = 1 - osm_uniform[-1] i = np.arange(2, N) osm_uniform[1:-1] = (i - 0.3175) / (N + 0.365) return osm_uniform def _parse_dist_kw(dist, enforce_subclass=True): """Parse dist keyword. Parameters ---------- dist : str or stats.distributions instance. Several functions take dist as a keyword, hence this utility function. enforce_subclass : bool, optional If True (default), dist needs to be a _distn_infrastructure.rv_generic instance. It can sometimes be useful to set this keyword to False, if a function wants to accept objects that just look somewhat like such an instance (for example, they have a ppf method). """ if isinstance(dist, rv_generic): pass elif isinstance(dist, string_types): try: dist = getattr(distributions, dist) except AttributeError: raise ValueError("%s is not a valid distribution name" % dist) elif enforce_subclass: msg = ("dist should be a stats.distributions instance or a string " "with the name of such a distribution.") raise ValueError(msg) return dist def probplot(x, sparams=(), dist='norm', fit=True, plot=None): """ Calculate quantiles for a probability plot, and optionally show the plot. Generates a probability plot of sample data against the quantiles of a specified theoretical distribution (the normal distribution by default). probplot optionally calculates a best-fit line for the data and plots the results using Matplotlib or a given plot function. Parameters ---------- x : array_like Sample/response data from which probplot creates the plot. sparams : tuple, optional Distribution-specific shape parameters (shape parameters plus location and scale). dist : str or stats.distributions instance, optional Distribution or distribution function name. The default is 'norm' for a normal probability plot. Objects that look enough like a stats.distributions instance (i.e. they have a ppf method) are also accepted. fit : bool, optional Fit a least-squares regression (best-fit) line to the sample data if True (default). plot : object, optional If given, plots the quantiles and least squares fit. plot is an object that has to have methods "plot" and "text". The matplotlib.pyplot module or a Matplotlib Axes object can be used, or a custom object with the same methods. Default is None, which means that no plot is created. Returns ------- (osm, osr) : tuple of ndarrays Tuple of theoretical quantiles (osm, or order statistic medians) and ordered responses (osr). osr is simply sorted input x. For details on how osm is calculated see the Notes section. (slope, intercept, r) : tuple of floats, optional Tuple containing the result of the least-squares fit, if that is performed by probplot. r is the square root of the coefficient of determination. If fit=False and plot=None, this tuple is not returned. Notes ----- Even if plot is given, the figure is not shown or saved by probplot; plt.show() or plt.savefig('figname.png') should be used after calling probplot. probplot generates a probability plot, which should not be confused with a Q-Q or a P-P plot. Statsmodels has more extensive functionality of this type, see statsmodels.api.ProbPlot. The formula used for the theoretical quantiles (horizontal axis of the probability plot) is Filliben's estimate:: quantiles = dist.ppf(val), for 0.5**(1/n), for i = n val = (i - 0.3175) / (n + 0.365), for i = 2, ..., n-1 1 - 0.5**(1/n), for i = 1 where i indicates the i-th ordered value and n is the total number of values. Examples -------- >>> from scipy import stats >>> import matplotlib.pyplot as plt >>> nsample = 100 >>> np.random.seed(7654321) A t distribution with small degrees of freedom: >>> ax1 = plt.subplot(221) >>> x = stats.t.rvs(3, size=nsample) >>> res = stats.probplot(x, plot=plt) A t distribution with larger degrees of freedom: >>> ax2 = plt.subplot(222) >>> x = stats.t.rvs(25, size=nsample) >>> res = stats.probplot(x, plot=plt) A mixture of two normal distributions with broadcasting: >>> ax3 = plt.subplot(223) >>> x = stats.norm.rvs(loc=[0,5], scale=[1,1.5], ... size=(nsample/2.,2)).ravel() >>> res = stats.probplot(x, plot=plt) A standard normal distribution: >>> ax4 = plt.subplot(224) >>> x = stats.norm.rvs(loc=0, scale=1, size=nsample) >>> res = stats.probplot(x, plot=plt) Produce a new figure with a loggamma distribution, using the dist and sparams keywords: >>> fig = plt.figure() >>> ax = fig.add_subplot(111) >>> x = stats.loggamma.rvs(c=2.5, size=500) >>> stats.probplot(x, dist=stats.loggamma, sparams=(2.5,), plot=ax) >>> ax.set_title("Probplot for loggamma dist with shape parameter 2.5") Show the results with Matplotlib: >>> plt.show() """ x = np.asarray(x) osm_uniform = _calc_uniform_order_statistic_medians(x) dist = _parse_dist_kw(dist, enforce_subclass=False) if sparams is None: sparams = () if isscalar(sparams): sparams = (sparams,) if not isinstance(sparams, tuple): sparams = tuple(sparams) osm = dist.ppf(osm_uniform, *sparams) osr = sort(x) if fit or (plot is not None): # perform a linear fit. slope, intercept, r, prob, sterrest = stats.linregress(osm, osr) if plot is not None: plot.plot(osm, osr, 'bo', osm, slope*osm + intercept, 'r-') try: if hasattr(plot, 'set_title'): # Matplotlib Axes instance or something that looks like it plot.set_title('Probability Plot') plot.set_xlabel('Quantiles') plot.set_ylabel('Ordered Values') else: # matplotlib.pyplot module plot.title('Probability Plot') plot.xlabel('Quantiles') plot.ylabel('Ordered Values') except: # Not an MPL object or something that looks (enough) like it. # Don't crash on adding labels or title pass # Add R^2 value to the plot as text xmin = amin(osm) xmax = amax(osm) ymin = amin(x) ymax = amax(x) posx = xmin + 0.70 * (xmax - xmin) posy = ymin + 0.01 * (ymax - ymin) plot.text(posx, posy, "$R^2=%1.4f$" % r**2) if fit: return (osm, osr), (slope, intercept, r) else: return osm, osr def ppcc_max(x, brack=(0.0, 1.0), dist='tukeylambda'): """Returns the shape parameter that maximizes the probability plot correlation coefficient for the given data to a one-parameter family of distributions. See also ppcc_plot """ dist = _parse_dist_kw(dist) osm_uniform = _calc_uniform_order_statistic_medians(x) osr = sort(x) # this function computes the x-axis values of the probability plot # and computes a linear regression (including the correlation) # and returns 1-r so that a minimization function maximizes the # correlation def tempfunc(shape, mi, yvals, func): xvals = func(mi, shape) r, prob = stats.pearsonr(xvals, yvals) return 1 - r return optimize.brent(tempfunc, brack=brack, args=(osm_uniform, osr, dist.ppf)) def ppcc_plot(x, a, b, dist='tukeylambda', plot=None, N=80): """Returns (shape, ppcc), and optionally plots shape vs. ppcc (probability plot correlation coefficient) as a function of shape parameter for a one-parameter family of distributions from shape value a to b. See also ppcc_max """ svals = r_[a:b:complex(N)] ppcc = svals * 0.0 k = 0 for sval in svals: r1, r2 = probplot(x, sval, dist=dist, fit=1) ppcc[k] = r2[-1] k += 1 if plot is not None: plot.plot(svals, ppcc, 'x') plot.title('(%s) PPCC Plot' % dist) plot.xlabel('Prob Plot Corr. Coef.') plot.ylabel('Shape Values') return svals, ppcc def boxcox_llf(lmb, data): r"""The boxcox log-likelihood function. Parameters ---------- lmb : scalar Parameter for Box-Cox transformation. See boxcox for details. data : array_like Data to calculate Box-Cox log-likelihood for. If data is multi-dimensional, the log-likelihood is calculated along the first axis. Returns ------- llf : float or ndarray Box-Cox log-likelihood of data given lmb. A float for 1-D data, an array otherwise. See Also -------- boxcox, probplot, boxcox_normplot, boxcox_normmax Notes ----- The Box-Cox log-likelihood function is defined here as .. math:: llf = (\lambda - 1) \sum_i(\log(x_i)) - N/2 \log(\sum_i (y_i - \bar{y})^2 / N), where y is the Box-Cox transformed input data x. Examples -------- >>> from scipy import stats >>> import matplotlib.pyplot as plt >>> from mpl_toolkits.axes_grid1.inset_locator import inset_axes >>> np.random.seed(1245) Generate some random variates and calculate Box-Cox log-likelihood values for them for a range of lmbda values: >>> x = stats.loggamma.rvs(5, loc=10, size=1000) >>> lmbdas = np.linspace(-2, 10) >>> llf = np.zeros(lmbdas.shape, dtype=np.float) >>> for ii, lmbda in enumerate(lmbdas): ... llf[ii] = stats.boxcox_llf(lmbda, x) Also find the optimal lmbda value with boxcox: >>> x_most_normal, lmbda_optimal = stats.boxcox(x) Plot the log-likelihood as function of lmbda. Add the optimal lmbda as a horizontal line to check that that's really the optimum: >>> fig = plt.figure() >>> ax = fig.add_subplot(111) >>> ax.plot(lmbdas, llf, 'b.-') >>> ax.axhline(stats.boxcox_llf(lmbda_optimal, x), color='r') >>> ax.set_xlabel('lmbda parameter') >>> ax.set_ylabel('Box-Cox log-likelihood') Now add some probability plots to show that where the log-likelihood is maximized the data transformed with boxcox looks closest to normal: >>> locs = [3, 10, 4] # 'lower left', 'center', 'lower right' >>> for lmbda, loc in zip([-1, lmbda_optimal, 9], locs): ... xt = stats.boxcox(x, lmbda=lmbda) ... (osm, osr), (slope, intercept, r_sq) = stats.probplot(xt) ... ax_inset = inset_axes(ax, width="20%", height="20%", loc=loc) ... ax_inset.plot(osm, osr, 'c.', osm, slope*osm + intercept, 'k-') ... ax_inset.set_xticklabels([]) ... ax_inset.set_yticklabels([]) ... ax_inset.set_title('$\lambda=%1.2f$' % lmbda) >>> plt.show() """ data = np.asarray(data) N = data.shape[0] if N == 0: return np.nan y = boxcox(data, lmb) y_mean = np.mean(y, axis=0) llf = (lmb - 1) * np.sum(np.log(data), axis=0) llf -= N / 2.0 * np.log(np.sum((y - y_mean)**2. / N, axis=0)) return llf def _boxcox_conf_interval(x, lmax, alpha): # Need to find the lambda for which # f(x,lmbda) >= f(x,lmax) - 0.5*chi^2_alpha;1 fac = 0.5 * distributions.chi2.ppf(1 - alpha, 1) target = boxcox_llf(lmax, x) - fac def rootfunc(lmbda, data, target): return boxcox_llf(lmbda, data) - target # Find positive endpoint of interval in which answer is to be found newlm = lmax + 0.5 N = 0 while (rootfunc(newlm, x, target) > 0.0) and (N < 500): newlm += 0.1 N += 1 if N == 500: raise RuntimeError("Could not find endpoint.") lmplus = optimize.brentq(rootfunc, lmax, newlm, args=(x, target)) # Now find negative interval in the same way newlm = lmax - 0.5 N = 0 while (rootfunc(newlm, x, target) > 0.0) and (N < 500): newlm -= 0.1 N += 1 if N == 500: raise RuntimeError("Could not find endpoint.") lmminus = optimize.brentq(rootfunc, newlm, lmax, args=(x, target)) return lmminus, lmplus def boxcox(x, lmbda=None, alpha=None): r""" Return a positive dataset transformed by a Box-Cox power transformation. Parameters ---------- x : ndarray Input array. Should be 1-dimensional. lmbda : {None, scalar}, optional If lmbda is not None, do the transformation for that value. If lmbda is None, find the lambda that maximizes the log-likelihood function and return it as the second output argument. alpha : {None, float}, optional If alpha is not None, return the 100 * (1-alpha)% confidence interval for lmbda as the third output argument. Must be between 0.0 and 1.0. Returns ------- boxcox : ndarray Box-Cox power transformed array. maxlog : float, optional If the lmbda parameter is None, the second returned argument is the lambda that maximizes the log-likelihood function. (min_ci, max_ci) : tuple of float, optional If lmbda parameter is None and alpha is not None, this returned tuple of floats represents the minimum and maximum confidence limits given alpha. See Also -------- probplot, boxcox_normplot, boxcox_normmax, boxcox_llf Notes ----- The Box-Cox transform is given by:: y = (x**lmbda - 1) / lmbda, for lmbda > 0 log(x), for lmbda = 0 boxcox requires the input data to be positive. Sometimes a Box-Cox transformation provides a shift parameter to achieve this; boxcox does not. Such a shift parameter is equivalent to adding a positive constant to x before calling boxcox. The confidence limits returned when alpha is provided give the interval where: .. math:: llf(\hat{\lambda}) - llf(\lambda) < \frac{1}{2}\chi^2(1 - \alpha, 1), with llf the log-likelihood function and :math:\chi^2 the chi-squared function. References ---------- G.E.P. Box and D.R. Cox, "An Analysis of Transformations", Journal of the Royal Statistical Society B, 26, 211-252 (1964). Examples -------- >>> from scipy import stats >>> import matplotlib.pyplot as plt We generate some random variates from a non-normal distribution and make a probability plot for it, to show it is non-normal in the tails: >>> fig = plt.figure() >>> ax1 = fig.add_subplot(211) >>> x = stats.loggamma.rvs(5, size=500) + 5 >>> stats.probplot(x, dist=stats.norm, plot=ax1) >>> ax1.set_xlabel('') >>> ax1.set_title('Probplot against normal distribution') We now use boxcox to transform the data so it's closest to normal: >>> ax2 = fig.add_subplot(212) >>> xt, _ = stats.boxcox(x) >>> stats.probplot(xt, dist=stats.norm, plot=ax2) >>> ax2.set_title('Probplot after Box-Cox transformation') >>> plt.show() """ x = np.asarray(x) if x.size == 0: return x if any(x <= 0): raise ValueError("Data must be positive.") if lmbda is not None: # single transformation return special.boxcox(x, lmbda) # If lmbda=None, find the lmbda that maximizes the log-likelihood function. lmax = boxcox_normmax(x, method='mle') y = boxcox(x, lmax) if alpha is None: return y, lmax else: # Find confidence interval interval = _boxcox_conf_interval(x, lmax, alpha) return y, lmax, interval def boxcox_normmax(x, brack=(-2.0, 2.0), method='pearsonr'): """Compute optimal Box-Cox transform parameter for input data. Parameters ---------- x : array_like Input array. brack : 2-tuple, optional The starting interval for a downhill bracket search with optimize.brent. Note that this is in most cases not critical; the final result is allowed to be outside this bracket. method : str, optional The method to determine the optimal transform parameter (boxcox lmbda parameter). Options are: 'pearsonr' (default) Maximizes the Pearson correlation coefficient between y = boxcox(x) and the expected values for y if x would be normally-distributed. 'mle' Minimizes the log-likelihood boxcox_llf. This is the method used in boxcox. 'all' Use all optimization methods available, and return all results. Useful to compare different methods. Returns ------- maxlog : float or ndarray The optimal transform parameter found. An array instead of a scalar for method='all'. See Also -------- boxcox, boxcox_llf, boxcox_normplot Examples -------- >>> from scipy import stats >>> import matplotlib.pyplot as plt >>> np.random.seed(1234) # make this example reproducible Generate some data and determine optimal lmbda in various ways: >>> x = stats.loggamma.rvs(5, size=30) + 5 >>> y, lmax_mle = stats.boxcox(x) >>> lmax_pearsonr = stats.boxcox_normmax(x) >>> lmax_mle 7.177... >>> lmax_pearsonr 7.916... >>> stats.boxcox_normmax(x, method='all') array([ 7.91667384, 7.17718692]) >>> fig = plt.figure() >>> ax = fig.add_subplot(111) >>> stats.boxcox_normplot(x, -10, 10, plot=ax) >>> ax.axvline(lmax_mle, color='r') >>> ax.axvline(lmax_pearsonr, color='g', ls='--') >>> plt.show() """ def _pearsonr(x, brack): osm_uniform = _calc_uniform_order_statistic_medians(x) xvals = distributions.norm.ppf(osm_uniform) def _eval_pearsonr(lmbda, xvals, samps): # This function computes the x-axis values of the probability plot # and computes a linear regression (including the correlation) and # returns 1 - r so that a minimization function maximizes the # correlation. y = boxcox(samps, lmbda) yvals = np.sort(y) r, prob = stats.pearsonr(xvals, yvals) return 1 - r return optimize.brent(_eval_pearsonr, brack=brack, args=(xvals, x)) def _mle(x, brack): def _eval_mle(lmb, data): # function to minimize return -boxcox_llf(lmb, data) return optimize.brent(_eval_mle, brack=brack, args=(x,)) def _all(x, brack): maxlog = np.zeros(2, dtype=np.float) maxlog[0] = _pearsonr(x, brack) maxlog[1] = _mle(x, brack) return maxlog methods = {'pearsonr': _pearsonr, 'mle': _mle, 'all': _all} if method not in methods.keys(): raise ValueError("Method %s not recognized." % method) optimfunc = methods[method] return optimfunc(x, brack) def boxcox_normplot(x, la, lb, plot=None, N=80): """Compute parameters for a Box-Cox normality plot, optionally show it. A Box-Cox normality plot shows graphically what the best transformation parameter is to use in boxcox to obtain a distribution that is close to normal. Parameters ---------- x : array_like Input array. la, lb : scalar The lower and upper bounds for the lmbda values to pass to boxcox for Box-Cox transformations. These are also the limits of the horizontal axis of the plot if that is generated. plot : object, optional If given, plots the quantiles and least squares fit. plot is an object that has to have methods "plot" and "text". The matplotlib.pyplot module or a Matplotlib Axes object can be used, or a custom object with the same methods. Default is None, which means that no plot is created. N : int, optional Number of points on the horizontal axis (equally distributed from la to lb). Returns ------- lmbdas : ndarray The lmbda values for which a Box-Cox transform was done. ppcc : ndarray Probability Plot Correlelation Coefficient, as obtained from probplot when fitting the Box-Cox transformed input x against a normal distribution. See Also -------- probplot, boxcox, boxcox_normmax, boxcox_llf, ppcc_max Notes ----- Even if plot is given, the figure is not shown or saved by boxcox_normplot; plt.show() or plt.savefig('figname.png') should be used after calling probplot. Examples -------- >>> from scipy import stats >>> import matplotlib.pyplot as plt Generate some non-normally distributed data, and create a Box-Cox plot: >>> x = stats.loggamma.rvs(5, size=500) + 5 >>> fig = plt.figure() >>> ax = fig.add_subplot(111) >>> stats.boxcox_normplot(x, -20, 20, plot=ax) Determine and plot the optimal lmbda to transform x and plot it in the same plot: >>> _, maxlog = stats.boxcox(x) >>> ax.axvline(maxlog, color='r') >>> plt.show() """ x = np.asarray(x) if x.size == 0: return x if lb <= la: raise ValueError("lb has to be larger than la.") lmbdas = np.linspace(la, lb, num=N) ppcc = lmbdas * 0.0 for i, val in enumerate(lmbdas): # Determine for each lmbda the correlation coefficient of transformed x z = boxcox(x, lmbda=val) _, r2 = probplot(z, dist='norm', fit=True) ppcc[i] = r2[-1] if plot is not None: plot.plot(lmbdas, ppcc, 'x') try: if hasattr(plot, 'set_title'): # Matplotlib Axes instance or something that looks like it plot.set_title('Box-Cox Normality Plot') plot.set_ylabel('Prob Plot Corr. Coef.') plot.set_xlabel('$\lambda$') else: # matplotlib.pyplot module plot.title('Box-Cox Normality Plot') plot.ylabel('Prob Plot Corr. Coef.') plot.xlabel('$\lambda$') except Exception: # Not an MPL object or something that looks (enough) like it. # Don't crash on adding labels or title pass return lmbdas, ppcc def shapiro(x, a=None, reta=False): """ Perform the Shapiro-Wilk test for normality. The Shapiro-Wilk test tests the null hypothesis that the data was drawn from a normal distribution. Parameters ---------- x : array_like Array of sample data. a : array_like, optional Array of internal parameters used in the calculation. If these are not given, they will be computed internally. If x has length n, then a must have length n/2. reta : bool, optional Whether or not to return the internally computed a values. The default is False. Returns ------- W : float The test statistic. p-value : float The p-value for the hypothesis test. a : array_like, optional If reta is True, then these are the internally computed "a" values that may be passed into this function on future calls. See Also -------- anderson : The Anderson-Darling test for normality References ---------- .. [1] http://www.itl.nist.gov/div898/handbook/prc/section2/prc213.htm """ N = len(x) if N < 3: raise ValueError("Data must be at least length 3.") if a is None: a = zeros(N, 'f') init = 0 else: if len(a) != N // 2: raise ValueError("len(a) must equal len(x)/2") init = 1 y = sort(x) a, w, pw, ifault = statlib.swilk(y, a[:N//2], init) if ifault not in [0, 2]: warnings.warn(str(ifault)) if N > 5000: warnings.warn("p-value may not be accurate for N > 5000.") if reta: return w, pw, a else: return w, pw # Values from Stephens, M A, "EDF Statistics for Goodness of Fit and # Some Comparisons", Journal of he American Statistical # Association, Vol. 69, Issue 347, Sept. 1974, pp 730-737 _Avals_norm = array([0.576, 0.656, 0.787, 0.918, 1.092]) _Avals_expon = array([0.922, 1.078, 1.341, 1.606, 1.957]) # From Stephens, M A, "Goodness of Fit for the Extreme Value Distribution", # Biometrika, Vol. 64, Issue 3, Dec. 1977, pp 583-588. _Avals_gumbel = array([0.474, 0.637, 0.757, 0.877, 1.038]) # From Stephens, M A, "Tests of Fit for the Logistic Distribution Based # on the Empirical Distribution Function.", Biometrika, # Vol. 66, Issue 3, Dec. 1979, pp 591-595. _Avals_logistic = array([0.426, 0.563, 0.660, 0.769, 0.906, 1.010]) def anderson(x, dist='norm'): """ Anderson-Darling test for data coming from a particular distribution The Anderson-Darling test is a modification of the Kolmogorov- Smirnov test kstest for the null hypothesis that a sample is drawn from a population that follows a particular distribution. For the Anderson-Darling test, the critical values depend on which distribution is being tested against. This function works for normal, exponential, logistic, or Gumbel (Extreme Value Type I) distributions. Parameters ---------- x : array_like array of sample data dist : {'norm','expon','logistic','gumbel','extreme1'}, optional the type of distribution to test against. The default is 'norm' and 'extreme1' is a synonym for 'gumbel' Returns ------- A2 : float The Anderson-Darling test statistic critical : list The critical values for this distribution sig : list The significance levels for the corresponding critical values in percents. The function returns critical values for a differing set of significance levels depending on the distribution that is being tested against. Notes ----- Critical values provided are for the following significance levels: normal/exponenential 15%, 10%, 5%, 2.5%, 1% logistic 25%, 10%, 5%, 2.5%, 1%, 0.5% Gumbel 25%, 10%, 5%, 2.5%, 1% If A2 is larger than these critical values then for the corresponding significance level, the null hypothesis that the data come from the chosen distribution can be rejected. References ---------- .. [1] http://www.itl.nist.gov/div898/handbook/prc/section2/prc213.htm .. [2] Stephens, M. A. (1974). EDF Statistics for Goodness of Fit and Some Comparisons, Journal of the American Statistical Association, Vol. 69, pp. 730-737. .. [3] Stephens, M. A. (1976). Asymptotic Results for Goodness-of-Fit Statistics with Unknown Parameters, Annals of Statistics, Vol. 4, pp. 357-369. .. [4] Stephens, M. A. (1977). Goodness of Fit for the Extreme Value Distribution, Biometrika, Vol. 64, pp. 583-588. .. [5] Stephens, M. A. (1977). Goodness of Fit with Special Reference to Tests for Exponentiality , Technical Report No. 262, Department of Statistics, Stanford University, Stanford, CA. .. [6] Stephens, M. A. (1979). Tests of Fit for the Logistic Distribution Based on the Empirical Distribution Function, Biometrika, Vol. 66, pp. 591-595. """ if dist not in ['norm', 'expon', 'gumbel', 'extreme1', 'logistic']: raise ValueError("Invalid distribution; dist must be 'norm', " "'expon', 'gumbel', 'extreme1' or 'logistic'.") y = sort(x) xbar = np.mean(x, axis=0) N = len(y) if dist == 'norm': s = np.std(x, ddof=1, axis=0) w = (y - xbar) / s z = distributions.norm.cdf(w) sig = array([15, 10, 5, 2.5, 1]) critical = around(_Avals_norm / (1.0 + 4.0/N - 25.0/N/N), 3) elif dist == 'expon': w = y / xbar z = distributions.expon.cdf(w) sig = array([15, 10, 5, 2.5, 1]) critical = around(_Avals_expon / (1.0 + 0.6/N), 3) elif dist == 'logistic': def rootfunc(ab, xj, N): a, b = ab tmp = (xj - a) / b tmp2 = exp(tmp) val = [sum(1.0/(1+tmp2), axis=0) - 0.5*N, sum(tmp*(1.0-tmp2)/(1+tmp2), axis=0) + N] return array(val) sol0 = array([xbar, np.std(x, ddof=1, axis=0)]) sol = optimize.fsolve(rootfunc, sol0, args=(x, N), xtol=1e-5) w = (y - sol[0]) / sol[1] z = distributions.logistic.cdf(w) sig = array([25, 10, 5, 2.5, 1, 0.5]) critical = around(_Avals_logistic / (1.0 + 0.25/N), 3) else: # (dist == 'gumbel') or (dist == 'extreme1'): xbar, s = distributions.gumbel_l.fit(x) w = (y - xbar) / s z = distributions.gumbel_l.cdf(w) sig = array([25, 10, 5, 2.5, 1]) critical = around(_Avals_gumbel / (1.0 + 0.2/sqrt(N)), 3) i = arange(1, N + 1) A2 = -N - sum((2*i - 1.0) / N * (log(z) + log(1 - z[::-1])), axis=0) return A2, critical, sig def _anderson_ksamp_midrank(samples, Z, Zstar, k, n, N): """ Compute A2akN equation 7 of Scholz and Stephens. Parameters ---------- samples : sequence of 1-D array_like Array of sample arrays. Z : array_like Sorted array of all observations. Zstar : array_like Sorted array of unique observations. k : int Number of samples. n : array_like Number of observations in each sample. N : int Total number of observations. Returns ------- A2aKN : float The A2aKN statistics of Scholz and Stephens 1987. """ A2akN = 0. Z_ssorted_left = Z.searchsorted(Zstar, 'left') if N == Zstar.size: lj = 1. else: lj = Z.searchsorted(Zstar, 'right') - Z_ssorted_left Bj = Z_ssorted_left + lj / 2. for i in arange(0, k): s = np.sort(samples[i]) s_ssorted_right = s.searchsorted(Zstar, side='right') Mij = s_ssorted_right.astype(np.float) fij = s_ssorted_right - s.searchsorted(Zstar, 'left') Mij -= fij / 2. inner = lj / float(N) * (N*Mij - Bj*n[i])**2 / (Bj*(N - Bj) - N*lj/4.) A2akN += inner.sum() / n[i] A2akN *= (N - 1.) / N return A2akN def _anderson_ksamp_right(samples, Z, Zstar, k, n, N): """ Compute A2akN equation 6 of Scholz & Stephens. Parameters ---------- samples : sequence of 1-D array_like Array of sample arrays. Z : array_like Sorted array of all observations. Zstar : array_like Sorted array of unique observations. k : int Number of samples. n : array_like Number of observations in each sample. N : int Total number of observations. Returns ------- A2KN : float The A2KN statistics of Scholz and Stephens 1987. """ A2kN = 0. lj = Z.searchsorted(Zstar[:-1], 'right') - Z.searchsorted(Zstar[:-1], 'left') Bj = lj.cumsum() for i in arange(0, k): s = np.sort(samples[i]) Mij = s.searchsorted(Zstar[:-1], side='right') inner = lj / float(N) * (N * Mij - Bj * n[i])**2 / (Bj * (N - Bj)) A2kN += inner.sum() / n[i] return A2kN def anderson_ksamp(samples, midrank=True): """The Anderson-Darling test for k-samples. The k-sample Anderson-Darling test is a modification of the one-sample Anderson-Darling test. It tests the null hypothesis that k-samples are drawn from the same population without having to specify the distribution function of that population. The critical values depend on the number of samples. Parameters ---------- samples : sequence of 1-D array_like Array of sample data in arrays. midrank : bool, optional Type of Anderson-Darling test which is computed. Default (True) is the midrank test applicable to continuous and discrete populations. If False, the right side empirical distribution is used. Returns ------- A2 : float Normalized k-sample Anderson-Darling test statistic. critical : array The critical values for significance levels 25%, 10%, 5%, 2.5%, 1%. p : float An approximate significance level at which the null hypothesis for the provided samples can be rejected. Raises ------ ValueError If less than 2 samples are provided, a sample is empty, or no distinct observations are in the samples. See Also -------- ks_2samp : 2 sample Kolmogorov-Smirnov test anderson : 1 sample Anderson-Darling test Notes ----- [1]_ Defines three versions of the k-sample Anderson-Darling test: one for continuous distributions and two for discrete distributions, in which ties between samples may occur. The default of this routine is to compute the version based on the midrank empirical distribution function. This test is applicable to continuous and discrete data. If midrank is set to False, the right side empirical distribution is used for a test for discrete data. According to [1]_, the two discrete test statistics differ only slightly if a few collisions due to round-off errors occur in the test not adjusted for ties between samples. .. versionadded:: 0.14.0 References ---------- .. [1] Scholz, F. W and Stephens, M. A. (1987), K-Sample Anderson-Darling Tests, Journal of the American Statistical Association, Vol. 82, pp. 918-924. Examples -------- >>> from scipy import stats >>> np.random.seed(314159) The null hypothesis that the two random samples come from the same distribution can be rejected at the 5% level because the returned test value is greater than the critical value for 5% (1.961) but not at the 2.5% level. The interpolation gives an approximate significance level of 3.1%: >>> stats.anderson_ksamp([np.random.normal(size=50), ... np.random.normal(loc=0.5, size=30)]) (2.4615796189876105, array([ 0.325, 1.226, 1.961, 2.718, 3.752]), 0.03134990135800783) The null hypothesis cannot be rejected for three samples from an identical distribution. The approximate p-value (87%) has to be computed by extrapolation and may not be very accurate: >>> stats.anderson_ksamp([np.random.normal(size=50), ... np.random.normal(size=30), np.random.normal(size=20)]) (-0.73091722665244196, array([ 0.44925884, 1.3052767 , 1.9434184 , 2.57696569, 3.41634856]), 0.8789283903979661) """ k = len(samples) if (k < 2): raise ValueError("anderson_ksamp needs at least two samples") samples = list(map(np.asarray, samples)) Z = np.sort(np.hstack(samples)) N = Z.size Zstar = np.unique(Z) if Zstar.size < 2: raise ValueError("anderson_ksamp needs more than one distinct " "observation") n = np.array([sample.size for sample in samples]) if any(n == 0): raise ValueError("anderson_ksamp encountered sample without " "observations") if midrank: A2kN = _anderson_ksamp_midrank(samples, Z, Zstar, k, n, N) else: A2kN = _anderson_ksamp_right(samples, Z, Zstar, k, n, N) h = (1. / arange(1, N)).sum() H = (1. / n).sum() g = 0 for l in arange(1, N-1): inner = np.array([1. / ((N - l) * m) for m in arange(l+1, N)]) g += inner.sum() a = (4*g - 6) * (k - 1) + (10 - 6*g)*H b = (2*g - 4)*k**2 + 8*h*k + (2*g - 14*h - 4)*H - 8*h + 4*g - 6 c = (6*h + 2*g - 2)*k**2 + (4*h - 4*g + 6)*k + (2*h - 6)*H + 4*h d = (2*h + 6)*k**2 - 4*h*k sigmasq = (a*N**3 + b*N**2 + c*N + d) / ((N - 1.) * (N - 2.) * (N - 3.)) m = k - 1 A2 = (A2kN - m) / math.sqrt(sigmasq) # The b_i values are the interpolation coefficients from Table 2 # of Scholz and Stephens 1987 b0 = np.array([0.675, 1.281, 1.645, 1.96, 2.326]) b1 = np.array([-0.245, 0.25, 0.678, 1.149, 1.822]) b2 = np.array([-0.105, -0.305, -0.362, -0.391, -0.396]) critical = b0 + b1 / math.sqrt(m) + b2 / m pf = np.polyfit(critical, log(np.array([0.25, 0.1, 0.05, 0.025, 0.01])), 2) if A2 < critical.min() or A2 > critical.max(): warnings.warn("approximate p-value will be computed by extrapolation") p = math.exp(np.polyval(pf, A2)) return A2, critical, p def ansari(x, y): """ Perform the Ansari-Bradley test for equal scale parameters The Ansari-Bradley test is a non-parametric test for the equality of the scale parameter of the distributions from which two samples were drawn. Parameters ---------- x, y : array_like arrays of sample data Returns ------- AB : float The Ansari-Bradley test statistic p-value : float The p-value of the hypothesis test See Also -------- fligner : A non-parametric test for the equality of k variances mood : A non-parametric test for the equality of two scale parameters Notes ----- The p-value given is exact when the sample sizes are both less than 55 and there are no ties, otherwise a normal approximation for the p-value is used. References ---------- .. [1] Sprent, Peter and N.C. Smeeton. Applied nonparametric statistical methods. 3rd ed. Chapman and Hall/CRC. 2001. Section 5.8.2. """ x, y = asarray(x), asarray(y) n = len(x) m = len(y) if m < 1: raise ValueError("Not enough other observations.") if n < 1: raise ValueError("Not enough test observations.") N = m + n xy = r_[x, y] # combine rank = stats.rankdata(xy) symrank = amin(array((rank, N - rank + 1)), 0) AB = sum(symrank[:n], axis=0) uxy = unique(xy) repeats = (len(uxy) != len(xy)) exact = ((m < 55) and (n < 55) and not repeats) if repeats and (m < 55 or n < 55): warnings.warn("Ties preclude use of exact statistic.") if exact: astart, a1, ifault = statlib.gscale(n, m) ind = AB - astart total = sum(a1, axis=0) if ind < len(a1)/2.0: cind = int(ceil(ind)) if ind == cind: pval = 2.0 * sum(a1[:cind+1], axis=0) / total else: pval = 2.0 * sum(a1[:cind], axis=0) / total else: find = int(floor(ind)) if ind == floor(ind): pval = 2.0 * sum(a1[find:], axis=0) / total else: pval = 2.0 * sum(a1[find+1:], axis=0) / total return AB, min(1.0, pval) # otherwise compute normal approximation if N % 2: # N odd mnAB = n * (N+1.0)**2 / 4.0 / N varAB = n * m * (N+1.0) * (3+N**2) / (48.0 * N**2) else: mnAB = n * (N+2.0) / 4.0 varAB = m * n * (N+2) * (N-2.0) / 48 / (N-1.0) if repeats: # adjust variance estimates # compute sum(tj * rj**2,axis=0) fac = sum(symrank**2, axis=0) if N % 2: # N odd varAB = m * n * (16*N*fac - (N+1)**4) / (16.0 * N**2 * (N-1)) else: # N even varAB = m * n * (16*fac - N*(N+2)**2) / (16.0 * N * (N-1)) z = (AB - mnAB) / sqrt(varAB) pval = distributions.norm.sf(abs(z)) * 2.0 return AB, pval def bartlett(*args): """ Perform Bartlett's test for equal variances Bartlett's test tests the null hypothesis that all input samples are from populations with equal variances. For samples from significantly non-normal populations, Levene's test levene is more robust. Parameters ---------- sample1, sample2,... : array_like arrays of sample data. May be different lengths. Returns ------- T : float The test statistic. p-value : float The p-value of the test. References ---------- .. [1] http://www.itl.nist.gov/div898/handbook/eda/section3/eda357.htm .. [2] Snedecor, George W. and Cochran, William G. (1989), Statistical Methods, Eighth Edition, Iowa State University Press. """ k = len(args) if k < 2: raise ValueError("Must enter at least two input sample vectors.") Ni = zeros(k) ssq = zeros(k, 'd') for j in range(k): Ni[j] = len(args[j]) ssq[j] = np.var(args[j], ddof=1) Ntot = sum(Ni, axis=0) spsq = sum((Ni - 1)*ssq, axis=0) / (1.0*(Ntot - k)) numer = (Ntot*1.0 - k) * log(spsq) - sum((Ni - 1.0)*log(ssq), axis=0) denom = 1.0 + 1.0/(3*(k - 1)) * ((sum(1.0/(Ni - 1.0), axis=0)) - 1.0/(Ntot - k)) T = numer / denom pval = distributions.chi2.sf(T, k - 1) # 1 - cdf return T, pval def levene(*args, **kwds): """ Perform Levene test for equal variances. The Levene test tests the null hypothesis that all input samples are from populations with equal variances. Levene's test is an alternative to Bartlett's test bartlett in the case where there are significant deviations from normality. Parameters ---------- sample1, sample2, ... : array_like The sample data, possibly with different lengths center : {'mean', 'median', 'trimmed'}, optional Which function of the data to use in the test. The default is 'median'. proportiontocut : float, optional When center is 'trimmed', this gives the proportion of data points to cut from each end. (See scipy.stats.trim_mean.) Default is 0.05. Returns ------- W : float The test statistic. p-value : float The p-value for the test. Notes ----- Three variations of Levene's test are possible. The possibilities and their recommended usages are: * 'median' : Recommended for skewed (non-normal) distributions> * 'mean' : Recommended for symmetric, moderate-tailed distributions. * 'trimmed' : Recommended for heavy-tailed distributions. References ---------- .. [1] http://www.itl.nist.gov/div898/handbook/eda/section3/eda35a.htm .. [2] Levene, H. (1960). In Contributions to Probability and Statistics: Essays in Honor of Harold Hotelling, I. Olkin et al. eds., Stanford University Press, pp. 278-292. .. [3] Brown, M. B. and Forsythe, A. B. (1974), Journal of the American Statistical Association, 69, 364-367 """ # Handle keyword arguments. center = 'median' proportiontocut = 0.05 for kw, value in kwds.items(): if kw not in ['center', 'proportiontocut']: raise TypeError("levene() got an unexpected keyword " "argument '%s'" % kw) if kw == 'center': center = value else: proportiontocut = value k = len(args) if k < 2: raise ValueError("Must enter at least two input sample vectors.") Ni = zeros(k) Yci = zeros(k, 'd') if center not in ['mean', 'median', 'trimmed']: raise ValueError("Keyword argument
must be 'mean', 'median'" + "or 'trimmed'.") if center == 'median': func = lambda x: np.median(x, axis=0) elif center == 'mean': func = lambda x: np.mean(x, axis=0) else: # center == 'trimmed' args = tuple(stats.trimboth(np.sort(arg), proportiontocut) for arg in args) func = lambda x: np.mean(x, axis=0) for j in range(k): Ni[j] = len(args[j]) Yci[j] = func(args[j]) Ntot = sum(Ni, axis=0) # compute Zij's Zij = [None] * k for i in range(k): Zij[i] = abs(asarray(args[i]) - Yci[i]) # compute Zbari Zbari = zeros(k, 'd') Zbar = 0.0 for i in range(k): Zbari[i] = np.mean(Zij[i], axis=0) Zbar += Zbari[i] * Ni[i] Zbar /= Ntot numer = (Ntot - k) * sum(Ni * (Zbari - Zbar)**2, axis=0) # compute denom_variance dvar = 0.0 for i in range(k): dvar += sum((Zij[i] - Zbari[i])**2, axis=0) denom = (k - 1.0) * dvar W = numer / denom pval = distributions.f.sf(W, k-1, Ntot-k) # 1 - cdf return W, pval @setastest(False) def binom_test(x, n=None, p=0.5): """ Perform a test that the probability of success is p. This is an exact, two-sided test of the null hypothesis that the probability of success in a Bernoulli experiment is p. Parameters ---------- x : integer or array_like the number of successes, or if x has length 2, it is the number of successes and the number of failures. n : integer the number of trials. This is ignored if x gives both the number of successes and failures p : float, optional The hypothesized probability of success. 0 <= p <= 1. The default value is p = 0.5 Returns ------- p-value : float The p-value of the hypothesis test References ---------- .. [1] http://en.wikipedia.org/wiki/Binomial_test """ x = atleast_1d(x).astype(np.integer) if len(x) == 2: n = x[1] + x[0] x = x[0] elif len(x) == 1: x = x[0] if n is None or n < x: raise ValueError("n must be >= x") n = np.int_(n) else: raise ValueError("Incorrect length for x.") if (p > 1.0) or (p < 0.0): raise ValueError("p must be in range [0,1]") d = distributions.binom.pmf(x, n, p) rerr = 1 + 1e-7 if x == p * n: # special case as shortcut, would also be handled by else below pval = 1. elif x < p * n: i = np.arange(np.ceil(p * n), n+1) y = np.sum(distributions.binom.pmf(i, n, p) <= d*rerr, axis=0) pval = (distributions.binom.cdf(x, n, p) + distributions.binom.sf(n - y, n, p)) else: i = np.arange(np.floor(p*n) + 1) y = np.sum(distributions.binom.pmf(i, n, p) <= d*rerr, axis=0) pval = (distributions.binom.cdf(y-1, n, p) + distributions.binom.sf(x-1, n, p)) return min(1.0, pval) def _apply_func(x, g, func): # g is list of indices into x # separating x into different groups # func should be applied over the groups g = unique(r_[0, g, len(x)]) output = [] for k in range(len(g) - 1): output.append(func(x[g[k]:g[k+1]])) return asarray(output) def fligner(*args, **kwds): """ Perform Fligner's test for equal variances. Fligner's test tests the null hypothesis that all input samples are from populations with equal variances. Fligner's test is non-parametric in contrast to Bartlett's test bartlett and Levene's test levene. Parameters ---------- sample1, sample2, ... : array_like Arrays of sample data. Need not be the same length. center : {'mean', 'median', 'trimmed'}, optional Keyword argument controlling which function of the data is used in computing the test statistic. The default is 'median'. proportiontocut : float, optional When center is 'trimmed', this gives the proportion of data points to cut from each end. (See scipy.stats.trim_mean.) Default is 0.05. Returns ------- Xsq : float The test statistic. p-value : float The p-value for the hypothesis test. Notes ----- As with Levene's test there are three variants of Fligner's test that differ by the measure of central tendency used in the test. See levene for more information. References ---------- .. [1] http://www.stat.psu.edu/~bgl/center/tr/TR993.ps .. [2] Fligner, M.A. and Killeen, T.J. (1976). Distribution-free two-sample tests for scale. 'Journal of the American Statistical Association.' 71(353), 210-213. """ # Handle keyword arguments. center = 'median' proportiontocut = 0.05 for kw, value in kwds.items(): if kw not in ['center', 'proportiontocut']: raise TypeError("fligner() got an unexpected keyword " "argument '%s'" % kw) if kw == 'center': center = value else: proportiontocut = value k = len(args) if k < 2: raise ValueError("Must enter at least two input sample vectors.") if center not in ['mean', 'median', 'trimmed']: raise ValueError("Keyword argument
must be 'mean', 'median'" + "or 'trimmed'.") if center == 'median': func = lambda x: np.median(x, axis=0) elif center == 'mean': func = lambda x: np.mean(x, axis=0) else: # center == 'trimmed' args = tuple(stats.trimboth(arg, proportiontocut) for arg in args) func = lambda x: np.mean(x, axis=0) Ni = asarray([len(args[j]) for j in range(k)]) Yci = asarray([func(args[j]) for j in range(k)]) Ntot = sum(Ni, axis=0) # compute Zij's Zij = [abs(asarray(args[i]) - Yci[i]) for i in range(k)] allZij = [] g = [0] for i in range(k): allZij.extend(list(Zij[i])) g.append(len(allZij)) ranks = stats.rankdata(allZij) a = distributions.norm.ppf(ranks / (2*(Ntot + 1.0)) + 0.5) # compute Aibar Aibar = _apply_func(a, g, sum) / Ni anbar = np.mean(a, axis=0) varsq = np.var(a, axis=0, ddof=1) Xsq = sum(Ni * (asarray(Aibar) - anbar)**2.0, axis=0) / varsq pval = distributions.chi2.sf(Xsq, k - 1) # 1 - cdf return Xsq, pval def mood(x, y, axis=0): """ Perform Mood's test for equal scale parameters. Mood's two-sample test for scale parameters is a non-parametric test for the null hypothesis that two samples are drawn from the same distribution with the same scale parameter. Parameters ---------- x, y : array_like Arrays of sample data. axis: int, optional The axis along which the samples are tested. x and y can be of different length along axis. If axis is None, x and y are flattened and the test is done on all values in the flattened arrays. Returns ------- z : scalar or ndarray The z-score for the hypothesis test. For 1-D inputs a scalar is returned. p-value : scalar ndarray The p-value for the hypothesis test. See Also -------- fligner : A non-parametric test for the equality of k variances ansari : A non-parametric test for the equality of 2 variances bartlett : A parametric test for equality of k variances in normal samples levene : A parametric test for equality of k variances Notes ----- The data are assumed to be drawn from probability distributions f(x) and f(x/s) / s respectively, for some probability density function f. The null hypothesis is that s == 1. For multi-dimensional arrays, if the inputs are of shapes (n0, n1, n2, n3) and (n0, m1, n2, n3), then if axis=1, the resulting z and p values will have shape (n0, n2, n3). Note that n1 and m1 don't have to be equal, but the other dimensions do. Examples -------- >>> from scipy import stats >>> x2 = np.random.randn(2, 45, 6, 7) >>> x1 = np.random.randn(2, 30, 6, 7) >>> z, p = stats.mood(x1, x2, axis=1) >>> p.shape (2, 6, 7) Find the number of points where the difference in scale is not significant: >>> (p > 0.1).sum() 74 Perform the test with different scales: >>> x1 = np.random.randn(2, 30) >>> x2 = np.random.randn(2, 35) * 10.0 >>> stats.mood(x1, x2, axis=1) (array([-5.84332354, -5.6840814 ]), array([5.11694980e-09, 1.31517628e-08])) """ x = np.asarray(x, dtype=float) y = np.asarray(y, dtype=float) if axis is None: x = x.flatten() y = y.flatten() axis = 0 # Determine shape of the result arrays res_shape = tuple([x.shape[ax] for ax in range(len(x.shape)) if ax != axis]) if not (res_shape == tuple([y.shape[ax] for ax in range(len(y.shape)) if ax != axis])): raise ValueError("Dimensions of x and y on all axes except axis " "should match") n = x.shape[axis] m = y.shape[axis] N = m + n if N < 3: raise ValueError("Not enough observations.") xy = np.concatenate((x, y), axis=axis) if axis != 0: xy = np.rollaxis(xy, axis) xy = xy.reshape(xy.shape[0], -1) # Generalized to the n-dimensional case by adding the axis argument, and # using for loops, since rankdata is not vectorized. For improving # performance consider vectorizing rankdata function. all_ranks = np.zeros_like(xy) for j in range(xy.shape[1]): all_ranks[:, j] = stats.rankdata(xy[:, j]) Ri = all_ranks[:n] M = sum((Ri - (N + 1.0) / 2)**2, axis=0) # Approx stat. mnM = n * (N * N - 1.0) / 12 varM = m * n * (N + 1.0) * (N + 2) * (N - 2) / 180 z = (M - mnM) / sqrt(varM) # sf for right tail, cdf for left tail. Factor 2 for two-sidedness z_pos = z > 0 pval = np.zeros_like(z) pval[z_pos] = 2 * distributions.norm.sf(z[z_pos]) pval[~z_pos] = 2 * distributions.norm.cdf(z[~z_pos]) if res_shape == (): # Return scalars, not 0-D arrays z = z[0] pval = pval[0] else: z.shape = res_shape pval.shape = res_shape return z, pval def wilcoxon(x, y=None, zero_method="wilcox", correction=False): """ Calculate the Wilcoxon signed-rank test. The Wilcoxon signed-rank test tests the null hypothesis that two related paired samples come from the same distribution. In particular, it tests whether the distribution of the differences x - y is symmetric about zero. It is a non-parametric version of the paired T-test. Parameters ---------- x : array_like The first set of measurements. y : array_like, optional The second set of measurements. If y is not given, then the x array is considered to be the differences between the two sets of measurements. zero_method : string, {"pratt", "wilcox", "zsplit"}, optional "pratt": Pratt treatment: includes zero-differences in the ranking process (more conservative) "wilcox": Wilcox treatment: discards all zero-differences "zsplit": Zero rank split: just like Pratt, but spliting the zero rank between positive and negative ones correction : bool, optional If True, apply continuity correction by adjusting the Wilcoxon rank statistic by 0.5 towards the mean value when computing the z-statistic. Default is False. Returns ------- T : float The sum of the ranks of the differences above or below zero, whichever is smaller. p-value : float The two-sided p-value for the test. Notes ----- Because the normal approximation is used for the calculations, the samples used should be large. A typical rule is to require that n > 20. References ---------- .. [1] http://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test """ if zero_method not in ["wilcox", "pratt", "zsplit"]: raise ValueError("Zero method should be either 'wilcox' " "or 'pratt' or 'zsplit'") if y is None: d = x else: x, y = map(asarray, (x, y)) if len(x) != len(y): raise ValueError('Unequal N in wilcoxon. Aborting.') d = x - y if zero_method == "wilcox": # Keep all non-zero differences d = compress(np.not_equal(d, 0), d, axis=-1) count = len(d) if count < 10: warnings.warn("Warning: sample size too small for normal approximation.") r = stats.rankdata(abs(d)) r_plus = sum((d > 0) * r, axis=0) r_minus = sum((d < 0) * r, axis=0) if zero_method == "zsplit": r_zero = sum((d == 0) * r, axis=0) r_plus += r_zero / 2. r_minus += r_zero / 2. T = min(r_plus, r_minus) mn = count * (count + 1.) * 0.25 se = count * (count + 1.) * (2. * count + 1.) if zero_method == "pratt": r = r[d != 0] replist, repnum = find_repeats(r) if repnum.size != 0: # Correction for repeated elements. se -= 0.5 * (repnum * (repnum * repnum - 1)).sum() se = sqrt(se / 24) correction = 0.5 * int(bool(correction)) * np.sign(T - mn) z = (T - mn - correction) / se prob = 2. * distributions.norm.sf(abs(z)) return T, prob @setastest(False) def median_test(*args, **kwds): """ Mood's median test. Test that two or more samples come from populations with the same median. Let n = len(args) be the number of samples. The "grand median" of all the data is computed, and a contingency table is formed by classifying the values in each sample as being above or below the grand median. The contingency table, along with correction and lambda_, are passed to scipy.stats.chi2_contingency to compute the test statistic and p-value. Parameters ---------- sample1, sample2, ... : array_like The set of samples. There must be at least two samples. Each sample must be a one-dimensional sequence containing at least one value. The samples are not required to have the same length. ties : str, optional Determines how values equal to the grand median are classified in the contingency table. The string must be one of:: "below": Values equal to the grand median are counted as "below". "above": Values equal to the grand median are counted as "above". "ignore": Values equal to the grand median are not counted. The default is "below". correction : bool, optional If True, *and* there are just two samples, apply Yates' correction for continuity when computing the test statistic associated with the contingency table. Default is True. lambda_ : float or str, optional. By default, the statistic computed in this test is Pearson's chi-squared statistic. lambda_ allows a statistic from the Cressie-Read power divergence family to be used instead. See power_divergence for details. Default is 1 (Pearson's chi-squared statistic). Returns ------- stat : float The test statistic. The statistic that is returned is determined by lambda_. The default is Pearson's chi-squared statistic. p : float The p-value of the test. m : float The grand median. table : ndarray The contingency table. The shape of the table is (2, n), where n is the number of samples. The first row holds the counts of the values above the grand median, and the second row holds the counts of the values below the grand median. The table allows further analysis with, for example, scipy.stats.chi2_contingency, or with scipy.stats.fisher_exact if there are two samples, without having to recompute the table. See Also -------- kruskal : Compute the Kruskal-Wallis H-test for independent samples. mannwhitneyu : Computes the Mann-Whitney rank test on samples x and y. Notes ----- .. versionadded:: 0.15.0 References ---------- .. [1] Mood, A. M., Introduction to the Theory of Statistics. McGraw-Hill (1950), pp. 394-399. .. [2] Zar, J. H., Biostatistical Analysis, 5th ed. Prentice Hall (2010). See Sections 8.12 and 10.15. Examples -------- A biologist runs an experiment in which there are three groups of plants. Group 1 has 16 plants, group 2 has 15 plants, and group 3 has 17 plants. Each plant produces a number of seeds. The seed counts for each group are:: Group 1: 10 14 14 18 20 22 24 25 31 31 32 39 43 43 48 49 Group 2: 28 30 31 33 34 35 36 40 44 55 57 61 91 92 99 Group 3: 0 3 9 22 23 25 25 33 34 34 40 45 46 48 62 67 84 The following code applies Mood's median test to these samples. >>> g1 = [10, 14, 14, 18, 20, 22, 24, 25, 31, 31, 32, 39, 43, 43, 48, 49] >>> g2 = [28, 30, 31, 33, 34, 35, 36, 40, 44, 55, 57, 61, 91, 92, 99] >>> g3 = [0, 3, 9, 22, 23, 25, 25, 33, 34, 34, 40, 45, 46, 48, 62, 67, 84] >>> stat, p, med, tbl = median_test(g1, g2, g3) The median is >>> med 34.0 and the contingency table is >>> tbl array([[ 5, 10, 7], [11, 5, 10]]) p is too large to conclude that the medians are not the same: >>> p 0.12609082774093244 The "G-test" can be performed by passing lambda_="log-likelihood" to median_test. >>> g, p, med, tbl = median_test(g1, g2, g3, lambda_="log-likelihood") >>> p 0.12224779737117837 The median occurs several times in the data, so we'll get a different result if, for example, ties="above" is used: >>> stat, p, med, tbl = median_test(g1, g2, g3, ties="above") >>> p 0.063873276069553273 >>> tbl array([[ 5, 11, 9], [11, 4, 8]]) This example demonstrates that if the data set is not large and there are values equal to the median, the p-value can be sensitive to the choice of ties. """ ties = kwds.pop('ties', 'below') correction = kwds.pop('correction', True) lambda_ = kwds.pop('lambda_', None) if len(kwds) > 0: bad_kwd = kwds.keys()[0] raise TypeError("median_test() got an unexpected keyword " "argument %r" % bad_kwd) if len(args) < 2: raise ValueError('median_test requires two or more samples.') ties_options = ['below', 'above', 'ignore'] if ties not in ties_options: raise ValueError("invalid 'ties' option '%s'; 'ties' must be one " "of: %s" % (ties, str(ties_options)[1:-1])) data = [np.asarray(arg) for arg in args] # Validate the sizes and shapes of the arguments. for k, d in enumerate(data): if d.size == 0: raise ValueError("Sample %d is empty. All samples must " "contain at least one value." % (k + 1)) if d.ndim != 1: raise ValueError("Sample %d has %d dimensions. All " "samples must be one-dimensional sequences." % (k + 1, d.ndim)) grand_median = np.median(np.concatenate(data)) # Create the contingency table. table = np.zeros((2, len(data)), dtype=np.int64) for k, sample in enumerate(data): nabove = count_nonzero(sample > grand_median) nbelow = count_nonzero(sample < grand_median) nequal = sample.size - (nabove + nbelow) table[0, k] += nabove table[1, k] += nbelow if ties == "below": table[1, k] += nequal elif ties == "above": table[0, k] += nequal # Check that no row or column of the table is all zero. # Such a table can not be given to chi2_contingency, because it would have # a zero in the table of expected frequencies. rowsums = table.sum(axis=1) if rowsums[0] == 0: raise ValueError("All values are below the grand median (%r)." % grand_median) if rowsums[1] == 0: raise ValueError("All values are above the grand median (%r)." % grand_median) if ties == "ignore": # We already checked that each sample has at least one value, but it # is possible that all those values equal the grand median. If ties # is "ignore", that would result in a column of zeros in table. We # check for that case here. zero_cols = np.where((table == 0).all(axis=0))[0] if len(zero_cols) > 0: msg = ("All values in sample %d are equal to the grand " "median (%r), so they are ignored, resulting in an " "empty sample." % (zero_cols[0] + 1, grand_median)) raise ValueError(msg) stat, p, dof, expected = chi2_contingency(table, lambda_=lambda_, correction=correction) return stat, p, grand_median, table def _hermnorm(N): # return the negatively normalized hermite polynomials up to order N-1 # (inclusive) # using the recursive relationship # p_n+1 = p_n(x)' - x*p_n(x) # and p_0(x) = 1 plist = [None] * N plist[0] = poly1d(1) for n in range(1, N): plist[n] = plist[n-1].deriv() - poly1d([1, 0]) * plist[n-1] return plist # Note: when removing pdf_fromgamma, also remove the _hermnorm support function @np.deprecate(message="scipy.stats.pdf_fromgamma is deprecated in scipy 0.16.0 " "in favour of statsmodels.distributions.ExpandedNormal.") def pdf_fromgamma(g1, g2, g3=0.0, g4=None): if g4 is None: g4 = 3 * g2**2 sigsq = 1.0 / g2 sig = sqrt(sigsq) mu = g1 * sig**3.0 p12 = _hermnorm(13) for k in range(13): p12[k] /= sig**k # Add all of the terms to polynomial totp = (p12[0] - g1/6.0*p12[3] + g2/24.0*p12[4] + g1**2/72.0 * p12[6] - g3/120.0*p12[5] - g1*g2/144.0*p12[7] - g1**3.0/1296.0*p12[9] + g4/720*p12[6] + (g2**2/1152.0 + g1*g3/720)*p12[8] + g1**2 * g2/1728.0*p12[10] + g1**4.0 / 31104.0*p12[12]) # Final normalization totp = totp / sqrt(2*pi) / sig def thefunc(x): xn = (x - mu) / sig return totp(xn) * exp(-xn**2 / 2.) return thefunc def _circfuncs_common(samples, high, low): samples = np.asarray(samples) if samples.size == 0: return np.nan, np.nan ang = (samples - low)*2*pi / (high - low) return samples, ang def circmean(samples, high=2*pi, low=0, axis=None): """ Compute the circular mean for samples in a range. Parameters ---------- samples : array_like Input array. high : float or int, optional High boundary for circular mean range. Default is 2*pi. low : float or int, optional Low boundary for circular mean range. Default is 0. axis : int, optional Axis along which means are computed. The default is to compute the mean of the flattened array. Returns ------- circmean : float Circular mean. """ samples, ang = _circfuncs_common(samples, high, low) res = angle(np.mean(exp(1j * ang), axis=axis)) mask = res < 0 if mask.ndim > 0: res[mask] += 2*pi elif mask: res += 2*pi return res*(high - low)/2.0/pi + low def circvar(samples, high=2*pi, low=0, axis=None): """ Compute the circular variance for samples assumed to be in a range Parameters ---------- samples : array_like Input array. low : float or int, optional Low boundary for circular variance range. Default is 0. high : float or int, optional High boundary for circular variance range. Default is 2*pi. axis : int, optional Axis along which variances are computed. The default is to compute the variance of the flattened array. Returns ------- circvar : float Circular variance. Notes ----- This uses a definition of circular variance that in the limit of small angles returns a number close to the 'linear' variance. """ samples, ang = _circfuncs_common(samples, high, low) res = np.mean(exp(1j * ang), axis=axis) R = abs(res) return ((high - low)/2.0/pi)**2 * 2 * log(1/R) def circstd(samples, high=2*pi, low=0, axis=None): """ Compute the circular standard deviation for samples assumed to be in the range [low to high]. Parameters ---------- samples : array_like Input array. low : float or int, optional Low boundary for circular standard deviation range. Default is 0. high : float or int, optional High boundary for circular standard deviation range. Default is 2*pi. axis : int, optional Axis along which standard deviations are computed. The default is to compute the standard deviation of the flattened array. Returns ------- circstd : float Circular standard deviation. Notes ----- This uses a definition of circular standard deviation that in the limit of small angles returns a number close to the 'linear' standard deviation. """ samples, ang = _circfuncs_common(samples, high, low) res = np.mean(exp(1j * ang), axis=axis) R = abs(res) return ((high - low)/2.0/pi) * sqrt(-2*log(R)) # Tests to include (from R) -- some of these already in stats. ######## # X Ansari-Bradley # X Bartlett (and Levene) # X Binomial # Y Pearson's Chi-squared (stats.chisquare) # Y Association Between Paired samples (stats.pearsonr, stats.spearmanr) # stats.kendalltau) -- these need work though # Fisher's exact test # X Fligner-Killeen Test # Y Friedman Rank Sum (stats.friedmanchisquare?) # Y Kruskal-Wallis # Y Kolmogorov-Smirnov # Cochran-Mantel-Haenszel Chi-Squared for Count # McNemar's Chi-squared for Count # X Mood Two-Sample # X Test For Equal Means in One-Way Layout (see stats.ttest also) # Pairwise Comparisons of proportions # Pairwise t tests # Tabulate p values for pairwise comparisons # Pairwise Wilcoxon rank sum tests # Power calculations two sample test of prop. # Power calculations for one and two sample t tests # Equal or Given Proportions # Trend in Proportions # Quade Test # Y Student's T Test # Y F Test to compare two variances # XY Wilcoxon Rank Sum and Signed Rank Tests
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