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author | Devtools Arcadia <arcadia-devtools@yandex-team.ru> | 2022-02-07 18:08:42 +0300 |
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committer | Devtools Arcadia <arcadia-devtools@mous.vla.yp-c.yandex.net> | 2022-02-07 18:08:42 +0300 |
commit | 1110808a9d39d4b808aef724c861a2e1a38d2a69 (patch) | |
tree | e26c9fed0de5d9873cce7e00bc214573dc2195b7 /contrib/tools/python3/src/Lib/statistics.py | |
download | ydb-1110808a9d39d4b808aef724c861a2e1a38d2a69.tar.gz |
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diff --git a/contrib/tools/python3/src/Lib/statistics.py b/contrib/tools/python3/src/Lib/statistics.py new file mode 100644 index 0000000000..463ac9e92c --- /dev/null +++ b/contrib/tools/python3/src/Lib/statistics.py @@ -0,0 +1,1120 @@ +""" +Basic statistics module. + +This module provides functions for calculating statistics of data, including +averages, variance, and standard deviation. + +Calculating averages +-------------------- + +================== ================================================== +Function Description +================== ================================================== +mean Arithmetic mean (average) of data. +fmean Fast, floating point arithmetic mean. +geometric_mean Geometric mean of data. +harmonic_mean Harmonic mean of data. +median Median (middle value) of data. +median_low Low median of data. +median_high High median of data. +median_grouped Median, or 50th percentile, of grouped data. +mode Mode (most common value) of data. +multimode List of modes (most common values of data). +quantiles Divide data into intervals with equal probability. +================== ================================================== + +Calculate the arithmetic mean ("the average") of data: + +>>> mean([-1.0, 2.5, 3.25, 5.75]) +2.625 + + +Calculate the standard median of discrete data: + +>>> median([2, 3, 4, 5]) +3.5 + + +Calculate the median, or 50th percentile, of data grouped into class intervals +centred on the data values provided. E.g. if your data points are rounded to +the nearest whole number: + +>>> median_grouped([2, 2, 3, 3, 3, 4]) #doctest: +ELLIPSIS +2.8333333333... + +This should be interpreted in this way: you have two data points in the class +interval 1.5-2.5, three data points in the class interval 2.5-3.5, and one in +the class interval 3.5-4.5. The median of these data points is 2.8333... + + +Calculating variability or spread +--------------------------------- + +================== ============================================= +Function Description +================== ============================================= +pvariance Population variance of data. +variance Sample variance of data. +pstdev Population standard deviation of data. +stdev Sample standard deviation of data. +================== ============================================= + +Calculate the standard deviation of sample data: + +>>> stdev([2.5, 3.25, 5.5, 11.25, 11.75]) #doctest: +ELLIPSIS +4.38961843444... + +If you have previously calculated the mean, you can pass it as the optional +second argument to the four "spread" functions to avoid recalculating it: + +>>> data = [1, 2, 2, 4, 4, 4, 5, 6] +>>> mu = mean(data) +>>> pvariance(data, mu) +2.5 + + +Exceptions +---------- + +A single exception is defined: StatisticsError is a subclass of ValueError. + +""" + +__all__ = [ + 'NormalDist', + 'StatisticsError', + 'fmean', + 'geometric_mean', + 'harmonic_mean', + 'mean', + 'median', + 'median_grouped', + 'median_high', + 'median_low', + 'mode', + 'multimode', + 'pstdev', + 'pvariance', + 'quantiles', + 'stdev', + 'variance', +] + +import math +import numbers +import random + +from fractions import Fraction +from decimal import Decimal +from itertools import groupby +from bisect import bisect_left, bisect_right +from math import hypot, sqrt, fabs, exp, erf, tau, log, fsum +from operator import itemgetter +from collections import Counter + +# === Exceptions === + +class StatisticsError(ValueError): + pass + + +# === Private utilities === + +def _sum(data, start=0): + """_sum(data [, start]) -> (type, sum, count) + + Return a high-precision sum of the given numeric data as a fraction, + together with the type to be converted to and the count of items. + + If optional argument ``start`` is given, it is added to the total. + If ``data`` is empty, ``start`` (defaulting to 0) is returned. + + + Examples + -------- + + >>> _sum([3, 2.25, 4.5, -0.5, 1.0], 0.75) + (<class 'float'>, Fraction(11, 1), 5) + + Some sources of round-off error will be avoided: + + # Built-in sum returns zero. + >>> _sum([1e50, 1, -1e50] * 1000) + (<class 'float'>, Fraction(1000, 1), 3000) + + Fractions and Decimals are also supported: + + >>> from fractions import Fraction as F + >>> _sum([F(2, 3), F(7, 5), F(1, 4), F(5, 6)]) + (<class 'fractions.Fraction'>, Fraction(63, 20), 4) + + >>> from decimal import Decimal as D + >>> data = [D("0.1375"), D("0.2108"), D("0.3061"), D("0.0419")] + >>> _sum(data) + (<class 'decimal.Decimal'>, Fraction(6963, 10000), 4) + + Mixed types are currently treated as an error, except that int is + allowed. + """ + count = 0 + n, d = _exact_ratio(start) + partials = {d: n} + partials_get = partials.get + T = _coerce(int, type(start)) + for typ, values in groupby(data, type): + T = _coerce(T, typ) # or raise TypeError + for n, d in map(_exact_ratio, values): + count += 1 + partials[d] = partials_get(d, 0) + n + if None in partials: + # The sum will be a NAN or INF. We can ignore all the finite + # partials, and just look at this special one. + total = partials[None] + assert not _isfinite(total) + else: + # Sum all the partial sums using builtin sum. + # FIXME is this faster if we sum them in order of the denominator? + total = sum(Fraction(n, d) for d, n in sorted(partials.items())) + return (T, total, count) + + +def _isfinite(x): + try: + return x.is_finite() # Likely a Decimal. + except AttributeError: + return math.isfinite(x) # Coerces to float first. + + +def _coerce(T, S): + """Coerce types T and S to a common type, or raise TypeError. + + Coercion rules are currently an implementation detail. See the CoerceTest + test class in test_statistics for details. + """ + # See http://bugs.python.org/issue24068. + assert T is not bool, "initial type T is bool" + # If the types are the same, no need to coerce anything. Put this + # first, so that the usual case (no coercion needed) happens as soon + # as possible. + if T is S: return T + # Mixed int & other coerce to the other type. + if S is int or S is bool: return T + if T is int: return S + # If one is a (strict) subclass of the other, coerce to the subclass. + if issubclass(S, T): return S + if issubclass(T, S): return T + # Ints coerce to the other type. + if issubclass(T, int): return S + if issubclass(S, int): return T + # Mixed fraction & float coerces to float (or float subclass). + if issubclass(T, Fraction) and issubclass(S, float): + return S + if issubclass(T, float) and issubclass(S, Fraction): + return T + # Any other combination is disallowed. + msg = "don't know how to coerce %s and %s" + raise TypeError(msg % (T.__name__, S.__name__)) + + +def _exact_ratio(x): + """Return Real number x to exact (numerator, denominator) pair. + + >>> _exact_ratio(0.25) + (1, 4) + + x is expected to be an int, Fraction, Decimal or float. + """ + try: + # Optimise the common case of floats. We expect that the most often + # used numeric type will be builtin floats, so try to make this as + # fast as possible. + if type(x) is float or type(x) is Decimal: + return x.as_integer_ratio() + try: + # x may be an int, Fraction, or Integral ABC. + return (x.numerator, x.denominator) + except AttributeError: + try: + # x may be a float or Decimal subclass. + return x.as_integer_ratio() + except AttributeError: + # Just give up? + pass + except (OverflowError, ValueError): + # float NAN or INF. + assert not _isfinite(x) + return (x, None) + msg = "can't convert type '{}' to numerator/denominator" + raise TypeError(msg.format(type(x).__name__)) + + +def _convert(value, T): + """Convert value to given numeric type T.""" + if type(value) is T: + # This covers the cases where T is Fraction, or where value is + # a NAN or INF (Decimal or float). + return value + if issubclass(T, int) and value.denominator != 1: + T = float + try: + # FIXME: what do we do if this overflows? + return T(value) + except TypeError: + if issubclass(T, Decimal): + return T(value.numerator) / T(value.denominator) + else: + raise + + +def _find_lteq(a, x): + 'Locate the leftmost value exactly equal to x' + i = bisect_left(a, x) + if i != len(a) and a[i] == x: + return i + raise ValueError + + +def _find_rteq(a, l, x): + 'Locate the rightmost value exactly equal to x' + i = bisect_right(a, x, lo=l) + if i != (len(a) + 1) and a[i - 1] == x: + return i - 1 + raise ValueError + + +def _fail_neg(values, errmsg='negative value'): + """Iterate over values, failing if any are less than zero.""" + for x in values: + if x < 0: + raise StatisticsError(errmsg) + yield x + + +# === Measures of central tendency (averages) === + +def mean(data): + """Return the sample arithmetic mean of data. + + >>> mean([1, 2, 3, 4, 4]) + 2.8 + + >>> from fractions import Fraction as F + >>> mean([F(3, 7), F(1, 21), F(5, 3), F(1, 3)]) + Fraction(13, 21) + + >>> from decimal import Decimal as D + >>> mean([D("0.5"), D("0.75"), D("0.625"), D("0.375")]) + Decimal('0.5625') + + If ``data`` is empty, StatisticsError will be raised. + """ + if iter(data) is data: + data = list(data) + n = len(data) + if n < 1: + raise StatisticsError('mean requires at least one data point') + T, total, count = _sum(data) + assert count == n + return _convert(total / n, T) + + +def fmean(data): + """Convert data to floats and compute the arithmetic mean. + + This runs faster than the mean() function and it always returns a float. + If the input dataset is empty, it raises a StatisticsError. + + >>> fmean([3.5, 4.0, 5.25]) + 4.25 + """ + try: + n = len(data) + except TypeError: + # Handle iterators that do not define __len__(). + n = 0 + def count(iterable): + nonlocal n + for n, x in enumerate(iterable, start=1): + yield x + total = fsum(count(data)) + else: + total = fsum(data) + try: + return total / n + except ZeroDivisionError: + raise StatisticsError('fmean requires at least one data point') from None + + +def geometric_mean(data): + """Convert data to floats and compute the geometric mean. + + Raises a StatisticsError if the input dataset is empty, + if it contains a zero, or if it contains a negative value. + + No special efforts are made to achieve exact results. + (However, this may change in the future.) + + >>> round(geometric_mean([54, 24, 36]), 9) + 36.0 + """ + try: + return exp(fmean(map(log, data))) + except ValueError: + raise StatisticsError('geometric mean requires a non-empty dataset ' + 'containing positive numbers') from None + + +def harmonic_mean(data): + """Return the harmonic mean of data. + + The harmonic mean, sometimes called the subcontrary mean, is the + reciprocal of the arithmetic mean of the reciprocals of the data, + and is often appropriate when averaging quantities which are rates + or ratios, for example speeds. Example: + + Suppose an investor purchases an equal value of shares in each of + three companies, with P/E (price/earning) ratios of 2.5, 3 and 10. + What is the average P/E ratio for the investor's portfolio? + + >>> harmonic_mean([2.5, 3, 10]) # For an equal investment portfolio. + 3.6 + + Using the arithmetic mean would give an average of about 5.167, which + is too high. + + If ``data`` is empty, or any element is less than zero, + ``harmonic_mean`` will raise ``StatisticsError``. + """ + # For a justification for using harmonic mean for P/E ratios, see + # http://fixthepitch.pellucid.com/comps-analysis-the-missing-harmony-of-summary-statistics/ + # http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2621087 + if iter(data) is data: + data = list(data) + errmsg = 'harmonic mean does not support negative values' + n = len(data) + if n < 1: + raise StatisticsError('harmonic_mean requires at least one data point') + elif n == 1: + x = data[0] + if isinstance(x, (numbers.Real, Decimal)): + if x < 0: + raise StatisticsError(errmsg) + return x + else: + raise TypeError('unsupported type') + try: + T, total, count = _sum(1 / x for x in _fail_neg(data, errmsg)) + except ZeroDivisionError: + return 0 + assert count == n + return _convert(n / total, T) + + +# FIXME: investigate ways to calculate medians without sorting? Quickselect? +def median(data): + """Return the median (middle value) of numeric data. + + When the number of data points is odd, return the middle data point. + When the number of data points is even, the median is interpolated by + taking the average of the two middle values: + + >>> median([1, 3, 5]) + 3 + >>> median([1, 3, 5, 7]) + 4.0 + + """ + data = sorted(data) + n = len(data) + if n == 0: + raise StatisticsError("no median for empty data") + if n % 2 == 1: + return data[n // 2] + else: + i = n // 2 + return (data[i - 1] + data[i]) / 2 + + +def median_low(data): + """Return the low median of numeric data. + + When the number of data points is odd, the middle value is returned. + When it is even, the smaller of the two middle values is returned. + + >>> median_low([1, 3, 5]) + 3 + >>> median_low([1, 3, 5, 7]) + 3 + + """ + data = sorted(data) + n = len(data) + if n == 0: + raise StatisticsError("no median for empty data") + if n % 2 == 1: + return data[n // 2] + else: + return data[n // 2 - 1] + + +def median_high(data): + """Return the high median of data. + + When the number of data points is odd, the middle value is returned. + When it is even, the larger of the two middle values is returned. + + >>> median_high([1, 3, 5]) + 3 + >>> median_high([1, 3, 5, 7]) + 5 + + """ + data = sorted(data) + n = len(data) + if n == 0: + raise StatisticsError("no median for empty data") + return data[n // 2] + + +def median_grouped(data, interval=1): + """Return the 50th percentile (median) of grouped continuous data. + + >>> median_grouped([1, 2, 2, 3, 4, 4, 4, 4, 4, 5]) + 3.7 + >>> median_grouped([52, 52, 53, 54]) + 52.5 + + This calculates the median as the 50th percentile, and should be + used when your data is continuous and grouped. In the above example, + the values 1, 2, 3, etc. actually represent the midpoint of classes + 0.5-1.5, 1.5-2.5, 2.5-3.5, etc. The middle value falls somewhere in + class 3.5-4.5, and interpolation is used to estimate it. + + Optional argument ``interval`` represents the class interval, and + defaults to 1. Changing the class interval naturally will change the + interpolated 50th percentile value: + + >>> median_grouped([1, 3, 3, 5, 7], interval=1) + 3.25 + >>> median_grouped([1, 3, 3, 5, 7], interval=2) + 3.5 + + This function does not check whether the data points are at least + ``interval`` apart. + """ + data = sorted(data) + n = len(data) + if n == 0: + raise StatisticsError("no median for empty data") + elif n == 1: + return data[0] + # Find the value at the midpoint. Remember this corresponds to the + # centre of the class interval. + x = data[n // 2] + for obj in (x, interval): + if isinstance(obj, (str, bytes)): + raise TypeError('expected number but got %r' % obj) + try: + L = x - interval / 2 # The lower limit of the median interval. + except TypeError: + # Mixed type. For now we just coerce to float. + L = float(x) - float(interval) / 2 + + # Uses bisection search to search for x in data with log(n) time complexity + # Find the position of leftmost occurrence of x in data + l1 = _find_lteq(data, x) + # Find the position of rightmost occurrence of x in data[l1...len(data)] + # Assuming always l1 <= l2 + l2 = _find_rteq(data, l1, x) + cf = l1 + f = l2 - l1 + 1 + return L + interval * (n / 2 - cf) / f + + +def mode(data): + """Return the most common data point from discrete or nominal data. + + ``mode`` assumes discrete data, and returns a single value. This is the + standard treatment of the mode as commonly taught in schools: + + >>> mode([1, 1, 2, 3, 3, 3, 3, 4]) + 3 + + This also works with nominal (non-numeric) data: + + >>> mode(["red", "blue", "blue", "red", "green", "red", "red"]) + 'red' + + If there are multiple modes with same frequency, return the first one + encountered: + + >>> mode(['red', 'red', 'green', 'blue', 'blue']) + 'red' + + If *data* is empty, ``mode``, raises StatisticsError. + + """ + pairs = Counter(iter(data)).most_common(1) + try: + return pairs[0][0] + except IndexError: + raise StatisticsError('no mode for empty data') from None + + +def multimode(data): + """Return a list of the most frequently occurring values. + + Will return more than one result if there are multiple modes + or an empty list if *data* is empty. + + >>> multimode('aabbbbbbbbcc') + ['b'] + >>> multimode('aabbbbccddddeeffffgg') + ['b', 'd', 'f'] + >>> multimode('') + [] + """ + counts = Counter(iter(data)).most_common() + maxcount, mode_items = next(groupby(counts, key=itemgetter(1)), (0, [])) + return list(map(itemgetter(0), mode_items)) + + +# Notes on methods for computing quantiles +# ---------------------------------------- +# +# There is no one perfect way to compute quantiles. Here we offer +# two methods that serve common needs. Most other packages +# surveyed offered at least one or both of these two, making them +# "standard" in the sense of "widely-adopted and reproducible". +# They are also easy to explain, easy to compute manually, and have +# straight-forward interpretations that aren't surprising. + +# The default method is known as "R6", "PERCENTILE.EXC", or "expected +# value of rank order statistics". The alternative method is known as +# "R7", "PERCENTILE.INC", or "mode of rank order statistics". + +# For sample data where there is a positive probability for values +# beyond the range of the data, the R6 exclusive method is a +# reasonable choice. Consider a random sample of nine values from a +# population with a uniform distribution from 0.0 to 1.0. The +# distribution of the third ranked sample point is described by +# betavariate(alpha=3, beta=7) which has mode=0.250, median=0.286, and +# mean=0.300. Only the latter (which corresponds with R6) gives the +# desired cut point with 30% of the population falling below that +# value, making it comparable to a result from an inv_cdf() function. +# The R6 exclusive method is also idempotent. + +# For describing population data where the end points are known to +# be included in the data, the R7 inclusive method is a reasonable +# choice. Instead of the mean, it uses the mode of the beta +# distribution for the interior points. Per Hyndman & Fan, "One nice +# property is that the vertices of Q7(p) divide the range into n - 1 +# intervals, and exactly 100p% of the intervals lie to the left of +# Q7(p) and 100(1 - p)% of the intervals lie to the right of Q7(p)." + +# If needed, other methods could be added. However, for now, the +# position is that fewer options make for easier choices and that +# external packages can be used for anything more advanced. + +def quantiles(data, *, n=4, method='exclusive'): + """Divide *data* into *n* continuous intervals with equal probability. + + Returns a list of (n - 1) cut points separating the intervals. + + Set *n* to 4 for quartiles (the default). Set *n* to 10 for deciles. + Set *n* to 100 for percentiles which gives the 99 cuts points that + separate *data* in to 100 equal sized groups. + + The *data* can be any iterable containing sample. + The cut points are linearly interpolated between data points. + + If *method* is set to *inclusive*, *data* is treated as population + data. The minimum value is treated as the 0th percentile and the + maximum value is treated as the 100th percentile. + """ + if n < 1: + raise StatisticsError('n must be at least 1') + data = sorted(data) + ld = len(data) + if ld < 2: + raise StatisticsError('must have at least two data points') + if method == 'inclusive': + m = ld - 1 + result = [] + for i in range(1, n): + j, delta = divmod(i * m, n) + interpolated = (data[j] * (n - delta) + data[j + 1] * delta) / n + result.append(interpolated) + return result + if method == 'exclusive': + m = ld + 1 + result = [] + for i in range(1, n): + j = i * m // n # rescale i to m/n + j = 1 if j < 1 else ld-1 if j > ld-1 else j # clamp to 1 .. ld-1 + delta = i*m - j*n # exact integer math + interpolated = (data[j - 1] * (n - delta) + data[j] * delta) / n + result.append(interpolated) + return result + raise ValueError(f'Unknown method: {method!r}') + + +# === Measures of spread === + +# See http://mathworld.wolfram.com/Variance.html +# http://mathworld.wolfram.com/SampleVariance.html +# http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance +# +# Under no circumstances use the so-called "computational formula for +# variance", as that is only suitable for hand calculations with a small +# amount of low-precision data. It has terrible numeric properties. +# +# See a comparison of three computational methods here: +# http://www.johndcook.com/blog/2008/09/26/comparing-three-methods-of-computing-standard-deviation/ + +def _ss(data, c=None): + """Return sum of square deviations of sequence data. + + If ``c`` is None, the mean is calculated in one pass, and the deviations + from the mean are calculated in a second pass. Otherwise, deviations are + calculated from ``c`` as given. Use the second case with care, as it can + lead to garbage results. + """ + if c is not None: + T, total, count = _sum((x-c)**2 for x in data) + return (T, total) + c = mean(data) + T, total, count = _sum((x-c)**2 for x in data) + # The following sum should mathematically equal zero, but due to rounding + # error may not. + U, total2, count2 = _sum((x - c) for x in data) + assert T == U and count == count2 + total -= total2 ** 2 / len(data) + assert not total < 0, 'negative sum of square deviations: %f' % total + return (T, total) + + +def variance(data, xbar=None): + """Return the sample variance of data. + + data should be an iterable of Real-valued numbers, with at least two + values. The optional argument xbar, if given, should be the mean of + the data. If it is missing or None, the mean is automatically calculated. + + Use this function when your data is a sample from a population. To + calculate the variance from the entire population, see ``pvariance``. + + Examples: + + >>> data = [2.75, 1.75, 1.25, 0.25, 0.5, 1.25, 3.5] + >>> variance(data) + 1.3720238095238095 + + If you have already calculated the mean of your data, you can pass it as + the optional second argument ``xbar`` to avoid recalculating it: + + >>> m = mean(data) + >>> variance(data, m) + 1.3720238095238095 + + This function does not check that ``xbar`` is actually the mean of + ``data``. Giving arbitrary values for ``xbar`` may lead to invalid or + impossible results. + + Decimals and Fractions are supported: + + >>> from decimal import Decimal as D + >>> variance([D("27.5"), D("30.25"), D("30.25"), D("34.5"), D("41.75")]) + Decimal('31.01875') + + >>> from fractions import Fraction as F + >>> variance([F(1, 6), F(1, 2), F(5, 3)]) + Fraction(67, 108) + + """ + if iter(data) is data: + data = list(data) + n = len(data) + if n < 2: + raise StatisticsError('variance requires at least two data points') + T, ss = _ss(data, xbar) + return _convert(ss / (n - 1), T) + + +def pvariance(data, mu=None): + """Return the population variance of ``data``. + + data should be a sequence or iterable of Real-valued numbers, with at least one + value. The optional argument mu, if given, should be the mean of + the data. If it is missing or None, the mean is automatically calculated. + + Use this function to calculate the variance from the entire population. + To estimate the variance from a sample, the ``variance`` function is + usually a better choice. + + Examples: + + >>> data = [0.0, 0.25, 0.25, 1.25, 1.5, 1.75, 2.75, 3.25] + >>> pvariance(data) + 1.25 + + If you have already calculated the mean of the data, you can pass it as + the optional second argument to avoid recalculating it: + + >>> mu = mean(data) + >>> pvariance(data, mu) + 1.25 + + Decimals and Fractions are supported: + + >>> from decimal import Decimal as D + >>> pvariance([D("27.5"), D("30.25"), D("30.25"), D("34.5"), D("41.75")]) + Decimal('24.815') + + >>> from fractions import Fraction as F + >>> pvariance([F(1, 4), F(5, 4), F(1, 2)]) + Fraction(13, 72) + + """ + if iter(data) is data: + data = list(data) + n = len(data) + if n < 1: + raise StatisticsError('pvariance requires at least one data point') + T, ss = _ss(data, mu) + return _convert(ss / n, T) + + +def stdev(data, xbar=None): + """Return the square root of the sample variance. + + See ``variance`` for arguments and other details. + + >>> stdev([1.5, 2.5, 2.5, 2.75, 3.25, 4.75]) + 1.0810874155219827 + + """ + var = variance(data, xbar) + try: + return var.sqrt() + except AttributeError: + return math.sqrt(var) + + +def pstdev(data, mu=None): + """Return the square root of the population variance. + + See ``pvariance`` for arguments and other details. + + >>> pstdev([1.5, 2.5, 2.5, 2.75, 3.25, 4.75]) + 0.986893273527251 + + """ + var = pvariance(data, mu) + try: + return var.sqrt() + except AttributeError: + return math.sqrt(var) + + +## Normal Distribution ##################################################### + + +def _normal_dist_inv_cdf(p, mu, sigma): + # There is no closed-form solution to the inverse CDF for the normal + # distribution, so we use a rational approximation instead: + # Wichura, M.J. (1988). "Algorithm AS241: The Percentage Points of the + # Normal Distribution". Applied Statistics. Blackwell Publishing. 37 + # (3): 477–484. doi:10.2307/2347330. JSTOR 2347330. + q = p - 0.5 + if fabs(q) <= 0.425: + r = 0.180625 - q * q + # Hash sum: 55.88319_28806_14901_4439 + num = (((((((2.50908_09287_30122_6727e+3 * r + + 3.34305_75583_58812_8105e+4) * r + + 6.72657_70927_00870_0853e+4) * r + + 4.59219_53931_54987_1457e+4) * r + + 1.37316_93765_50946_1125e+4) * r + + 1.97159_09503_06551_4427e+3) * r + + 1.33141_66789_17843_7745e+2) * r + + 3.38713_28727_96366_6080e+0) * q + den = (((((((5.22649_52788_52854_5610e+3 * r + + 2.87290_85735_72194_2674e+4) * r + + 3.93078_95800_09271_0610e+4) * r + + 2.12137_94301_58659_5867e+4) * r + + 5.39419_60214_24751_1077e+3) * r + + 6.87187_00749_20579_0830e+2) * r + + 4.23133_30701_60091_1252e+1) * r + + 1.0) + x = num / den + return mu + (x * sigma) + r = p if q <= 0.0 else 1.0 - p + r = sqrt(-log(r)) + if r <= 5.0: + r = r - 1.6 + # Hash sum: 49.33206_50330_16102_89036 + num = (((((((7.74545_01427_83414_07640e-4 * r + + 2.27238_44989_26918_45833e-2) * r + + 2.41780_72517_74506_11770e-1) * r + + 1.27045_82524_52368_38258e+0) * r + + 3.64784_83247_63204_60504e+0) * r + + 5.76949_72214_60691_40550e+0) * r + + 4.63033_78461_56545_29590e+0) * r + + 1.42343_71107_49683_57734e+0) + den = (((((((1.05075_00716_44416_84324e-9 * r + + 5.47593_80849_95344_94600e-4) * r + + 1.51986_66563_61645_71966e-2) * r + + 1.48103_97642_74800_74590e-1) * r + + 6.89767_33498_51000_04550e-1) * r + + 1.67638_48301_83803_84940e+0) * r + + 2.05319_16266_37758_82187e+0) * r + + 1.0) + else: + r = r - 5.0 + # Hash sum: 47.52583_31754_92896_71629 + num = (((((((2.01033_43992_92288_13265e-7 * r + + 2.71155_55687_43487_57815e-5) * r + + 1.24266_09473_88078_43860e-3) * r + + 2.65321_89526_57612_30930e-2) * r + + 2.96560_57182_85048_91230e-1) * r + + 1.78482_65399_17291_33580e+0) * r + + 5.46378_49111_64114_36990e+0) * r + + 6.65790_46435_01103_77720e+0) + den = (((((((2.04426_31033_89939_78564e-15 * r + + 1.42151_17583_16445_88870e-7) * r + + 1.84631_83175_10054_68180e-5) * r + + 7.86869_13114_56132_59100e-4) * r + + 1.48753_61290_85061_48525e-2) * r + + 1.36929_88092_27358_05310e-1) * r + + 5.99832_20655_58879_37690e-1) * r + + 1.0) + x = num / den + if q < 0.0: + x = -x + return mu + (x * sigma) + + +# If available, use C implementation +try: + from _statistics import _normal_dist_inv_cdf +except ImportError: + pass + + +class NormalDist: + "Normal distribution of a random variable" + # https://en.wikipedia.org/wiki/Normal_distribution + # https://en.wikipedia.org/wiki/Variance#Properties + + __slots__ = { + '_mu': 'Arithmetic mean of a normal distribution', + '_sigma': 'Standard deviation of a normal distribution', + } + + def __init__(self, mu=0.0, sigma=1.0): + "NormalDist where mu is the mean and sigma is the standard deviation." + if sigma < 0.0: + raise StatisticsError('sigma must be non-negative') + self._mu = float(mu) + self._sigma = float(sigma) + + @classmethod + def from_samples(cls, data): + "Make a normal distribution instance from sample data." + if not isinstance(data, (list, tuple)): + data = list(data) + xbar = fmean(data) + return cls(xbar, stdev(data, xbar)) + + def samples(self, n, *, seed=None): + "Generate *n* samples for a given mean and standard deviation." + gauss = random.gauss if seed is None else random.Random(seed).gauss + mu, sigma = self._mu, self._sigma + return [gauss(mu, sigma) for i in range(n)] + + def pdf(self, x): + "Probability density function. P(x <= X < x+dx) / dx" + variance = self._sigma ** 2.0 + if not variance: + raise StatisticsError('pdf() not defined when sigma is zero') + return exp((x - self._mu)**2.0 / (-2.0*variance)) / sqrt(tau*variance) + + def cdf(self, x): + "Cumulative distribution function. P(X <= x)" + if not self._sigma: + raise StatisticsError('cdf() not defined when sigma is zero') + return 0.5 * (1.0 + erf((x - self._mu) / (self._sigma * sqrt(2.0)))) + + def inv_cdf(self, p): + """Inverse cumulative distribution function. x : P(X <= x) = p + + Finds the value of the random variable such that the probability of + the variable being less than or equal to that value equals the given + probability. + + This function is also called the percent point function or quantile + function. + """ + if p <= 0.0 or p >= 1.0: + raise StatisticsError('p must be in the range 0.0 < p < 1.0') + if self._sigma <= 0.0: + raise StatisticsError('cdf() not defined when sigma at or below zero') + return _normal_dist_inv_cdf(p, self._mu, self._sigma) + + def quantiles(self, n=4): + """Divide into *n* continuous intervals with equal probability. + + Returns a list of (n - 1) cut points separating the intervals. + + Set *n* to 4 for quartiles (the default). Set *n* to 10 for deciles. + Set *n* to 100 for percentiles which gives the 99 cuts points that + separate the normal distribution in to 100 equal sized groups. + """ + return [self.inv_cdf(i / n) for i in range(1, n)] + + def overlap(self, other): + """Compute the overlapping coefficient (OVL) between two normal distributions. + + Measures the agreement between two normal probability distributions. + Returns a value between 0.0 and 1.0 giving the overlapping area in + the two underlying probability density functions. + + >>> N1 = NormalDist(2.4, 1.6) + >>> N2 = NormalDist(3.2, 2.0) + >>> N1.overlap(N2) + 0.8035050657330205 + """ + # See: "The overlapping coefficient as a measure of agreement between + # probability distributions and point estimation of the overlap of two + # normal densities" -- Henry F. Inman and Edwin L. Bradley Jr + # http://dx.doi.org/10.1080/03610928908830127 + if not isinstance(other, NormalDist): + raise TypeError('Expected another NormalDist instance') + X, Y = self, other + if (Y._sigma, Y._mu) < (X._sigma, X._mu): # sort to assure commutativity + X, Y = Y, X + X_var, Y_var = X.variance, Y.variance + if not X_var or not Y_var: + raise StatisticsError('overlap() not defined when sigma is zero') + dv = Y_var - X_var + dm = fabs(Y._mu - X._mu) + if not dv: + return 1.0 - erf(dm / (2.0 * X._sigma * sqrt(2.0))) + a = X._mu * Y_var - Y._mu * X_var + b = X._sigma * Y._sigma * sqrt(dm**2.0 + dv * log(Y_var / X_var)) + x1 = (a + b) / dv + x2 = (a - b) / dv + return 1.0 - (fabs(Y.cdf(x1) - X.cdf(x1)) + fabs(Y.cdf(x2) - X.cdf(x2))) + + def zscore(self, x): + """Compute the Standard Score. (x - mean) / stdev + + Describes *x* in terms of the number of standard deviations + above or below the mean of the normal distribution. + """ + # https://www.statisticshowto.com/probability-and-statistics/z-score/ + if not self._sigma: + raise StatisticsError('zscore() not defined when sigma is zero') + return (x - self._mu) / self._sigma + + @property + def mean(self): + "Arithmetic mean of the normal distribution." + return self._mu + + @property + def median(self): + "Return the median of the normal distribution" + return self._mu + + @property + def mode(self): + """Return the mode of the normal distribution + + The mode is the value x where which the probability density + function (pdf) takes its maximum value. + """ + return self._mu + + @property + def stdev(self): + "Standard deviation of the normal distribution." + return self._sigma + + @property + def variance(self): + "Square of the standard deviation." + return self._sigma ** 2.0 + + def __add__(x1, x2): + """Add a constant or another NormalDist instance. + + If *other* is a constant, translate mu by the constant, + leaving sigma unchanged. + + If *other* is a NormalDist, add both the means and the variances. + Mathematically, this works only if the two distributions are + independent or if they are jointly normally distributed. + """ + if isinstance(x2, NormalDist): + return NormalDist(x1._mu + x2._mu, hypot(x1._sigma, x2._sigma)) + return NormalDist(x1._mu + x2, x1._sigma) + + def __sub__(x1, x2): + """Subtract a constant or another NormalDist instance. + + If *other* is a constant, translate by the constant mu, + leaving sigma unchanged. + + If *other* is a NormalDist, subtract the means and add the variances. + Mathematically, this works only if the two distributions are + independent or if they are jointly normally distributed. + """ + if isinstance(x2, NormalDist): + return NormalDist(x1._mu - x2._mu, hypot(x1._sigma, x2._sigma)) + return NormalDist(x1._mu - x2, x1._sigma) + + def __mul__(x1, x2): + """Multiply both mu and sigma by a constant. + + Used for rescaling, perhaps to change measurement units. + Sigma is scaled with the absolute value of the constant. + """ + return NormalDist(x1._mu * x2, x1._sigma * fabs(x2)) + + def __truediv__(x1, x2): + """Divide both mu and sigma by a constant. + + Used for rescaling, perhaps to change measurement units. + Sigma is scaled with the absolute value of the constant. + """ + return NormalDist(x1._mu / x2, x1._sigma / fabs(x2)) + + def __pos__(x1): + "Return a copy of the instance." + return NormalDist(x1._mu, x1._sigma) + + def __neg__(x1): + "Negates mu while keeping sigma the same." + return NormalDist(-x1._mu, x1._sigma) + + __radd__ = __add__ + + def __rsub__(x1, x2): + "Subtract a NormalDist from a constant or another NormalDist." + return -(x1 - x2) + + __rmul__ = __mul__ + + def __eq__(x1, x2): + "Two NormalDist objects are equal if their mu and sigma are both equal." + if not isinstance(x2, NormalDist): + return NotImplemented + return x1._mu == x2._mu and x1._sigma == x2._sigma + + def __hash__(self): + "NormalDist objects hash equal if their mu and sigma are both equal." + return hash((self._mu, self._sigma)) + + def __repr__(self): + return f'{type(self).__name__}(mu={self._mu!r}, sigma={self._sigma!r})' |