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Minor whitespace, indentation, and quoting changes to improve internal consistency and appease linters (GH-14888)
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1 changed files with 74 additions and 53 deletions
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@ -80,11 +80,24 @@ A single exception is defined: StatisticsError is a subclass of ValueError.
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"""
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"""
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__all__ = [ 'StatisticsError', 'NormalDist', 'quantiles',
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__all__ = [
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'pstdev', 'pvariance', 'stdev', 'variance',
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'NormalDist',
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'median', 'median_low', 'median_high', 'median_grouped',
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'StatisticsError',
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'mean', 'mode', 'multimode', 'harmonic_mean', 'fmean',
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'fmean',
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'geometric_mean',
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'geometric_mean',
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'harmonic_mean',
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'mean',
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'median',
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'median_grouped',
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'median_high',
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'median_low',
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'mode',
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'multimode',
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'pstdev',
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'pvariance',
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'quantiles',
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'stdev',
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'variance',
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]
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]
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import math
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import math
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@ -304,6 +317,7 @@ def mean(data):
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assert count == n
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assert count == n
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return _convert(total/n, T)
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return _convert(total/n, T)
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def fmean(data):
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def fmean(data):
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"""Convert data to floats and compute the arithmetic mean.
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"""Convert data to floats and compute the arithmetic mean.
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@ -313,7 +327,6 @@ def fmean(data):
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>>> fmean([3.5, 4.0, 5.25])
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>>> fmean([3.5, 4.0, 5.25])
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4.25
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4.25
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"""
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"""
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try:
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try:
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n = len(data)
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n = len(data)
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@ -332,6 +345,7 @@ def fmean(data):
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except ZeroDivisionError:
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except ZeroDivisionError:
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raise StatisticsError('fmean requires at least one data point') from None
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raise StatisticsError('fmean requires at least one data point') from None
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def geometric_mean(data):
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def geometric_mean(data):
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"""Convert data to floats and compute the geometric mean.
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"""Convert data to floats and compute the geometric mean.
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@ -350,6 +364,7 @@ def geometric_mean(data):
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raise StatisticsError('geometric mean requires a non-empty dataset '
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raise StatisticsError('geometric mean requires a non-empty dataset '
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' containing positive numbers') from None
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' containing positive numbers') from None
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def harmonic_mean(data):
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def harmonic_mean(data):
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"""Return the harmonic mean of data.
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"""Return the harmonic mean of data.
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@ -558,12 +573,12 @@ def multimode(data):
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['b', 'd', 'f']
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['b', 'd', 'f']
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>>> multimode('')
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>>> multimode('')
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[]
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[]
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"""
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"""
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counts = Counter(iter(data)).most_common()
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counts = Counter(iter(data)).most_common()
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maxcount, mode_items = next(groupby(counts, key=itemgetter(1)), (0, []))
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maxcount, mode_items = next(groupby(counts, key=itemgetter(1)), (0, []))
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return list(map(itemgetter(0), mode_items))
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return list(map(itemgetter(0), mode_items))
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# Notes on methods for computing quantiles
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# Notes on methods for computing quantiles
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# ----------------------------------------
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# ----------------------------------------
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#
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#
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@ -601,7 +616,7 @@ def multimode(data):
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# external packages can be used for anything more advanced.
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# external packages can be used for anything more advanced.
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def quantiles(dist, /, *, n=4, method='exclusive'):
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def quantiles(dist, /, *, n=4, method='exclusive'):
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'''Divide *dist* into *n* continuous intervals with equal probability.
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"""Divide *dist* into *n* continuous intervals with equal probability.
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Returns a list of (n - 1) cut points separating the intervals.
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Returns a list of (n - 1) cut points separating the intervals.
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@ -616,7 +631,7 @@ def quantiles(dist, /, *, n=4, method='exclusive'):
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If *method* is set to *inclusive*, *dist* is treated as population
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If *method* is set to *inclusive*, *dist* is treated as population
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data. The minimum value is treated as the 0th percentile and the
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data. The minimum value is treated as the 0th percentile and the
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maximum value is treated as the 100th percentile.
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maximum value is treated as the 100th percentile.
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'''
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"""
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if n < 1:
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if n < 1:
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raise StatisticsError('n must be at least 1')
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raise StatisticsError('n must be at least 1')
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if hasattr(dist, 'inv_cdf'):
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if hasattr(dist, 'inv_cdf'):
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@ -646,6 +661,7 @@ def quantiles(dist, /, *, n=4, method='exclusive'):
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return result
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return result
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raise ValueError(f'Unknown method: {method!r}')
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raise ValueError(f'Unknown method: {method!r}')
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# === Measures of spread ===
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# === Measures of spread ===
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# See http://mathworld.wolfram.com/Variance.html
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# See http://mathworld.wolfram.com/Variance.html
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@ -805,18 +821,21 @@ def pstdev(data, mu=None):
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except AttributeError:
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except AttributeError:
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return math.sqrt(var)
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return math.sqrt(var)
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## Normal Distribution #####################################################
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## Normal Distribution #####################################################
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class NormalDist:
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class NormalDist:
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'Normal distribution of a random variable'
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"Normal distribution of a random variable"
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# https://en.wikipedia.org/wiki/Normal_distribution
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# https://en.wikipedia.org/wiki/Normal_distribution
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# https://en.wikipedia.org/wiki/Variance#Properties
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# https://en.wikipedia.org/wiki/Variance#Properties
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__slots__ = {'_mu': 'Arithmetic mean of a normal distribution',
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__slots__ = {
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'_sigma': 'Standard deviation of a normal distribution'}
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'_mu': 'Arithmetic mean of a normal distribution',
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'_sigma': 'Standard deviation of a normal distribution',
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}
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def __init__(self, mu=0.0, sigma=1.0):
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def __init__(self, mu=0.0, sigma=1.0):
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'NormalDist where mu is the mean and sigma is the standard deviation.'
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"NormalDist where mu is the mean and sigma is the standard deviation."
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if sigma < 0.0:
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if sigma < 0.0:
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raise StatisticsError('sigma must be non-negative')
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raise StatisticsError('sigma must be non-negative')
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self._mu = mu
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self._mu = mu
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@ -824,40 +843,42 @@ class NormalDist:
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@classmethod
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@classmethod
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def from_samples(cls, data):
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def from_samples(cls, data):
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'Make a normal distribution instance from sample data.'
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"Make a normal distribution instance from sample data."
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if not isinstance(data, (list, tuple)):
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if not isinstance(data, (list, tuple)):
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data = list(data)
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data = list(data)
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xbar = fmean(data)
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xbar = fmean(data)
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return cls(xbar, stdev(data, xbar))
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return cls(xbar, stdev(data, xbar))
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def samples(self, n, *, seed=None):
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def samples(self, n, *, seed=None):
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'Generate *n* samples for a given mean and standard deviation.'
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"Generate *n* samples for a given mean and standard deviation."
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gauss = random.gauss if seed is None else random.Random(seed).gauss
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gauss = random.gauss if seed is None else random.Random(seed).gauss
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mu, sigma = self._mu, self._sigma
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mu, sigma = self._mu, self._sigma
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return [gauss(mu, sigma) for i in range(n)]
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return [gauss(mu, sigma) for i in range(n)]
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def pdf(self, x):
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def pdf(self, x):
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'Probability density function. P(x <= X < x+dx) / dx'
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"Probability density function. P(x <= X < x+dx) / dx"
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variance = self._sigma ** 2.0
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variance = self._sigma ** 2.0
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if not variance:
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if not variance:
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raise StatisticsError('pdf() not defined when sigma is zero')
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raise StatisticsError('pdf() not defined when sigma is zero')
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return exp((x - self._mu)**2.0 / (-2.0*variance)) / sqrt(tau*variance)
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return exp((x - self._mu)**2.0 / (-2.0*variance)) / sqrt(tau*variance)
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def cdf(self, x):
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def cdf(self, x):
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'Cumulative distribution function. P(X <= x)'
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"Cumulative distribution function. P(X <= x)"
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if not self._sigma:
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if not self._sigma:
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raise StatisticsError('cdf() not defined when sigma is zero')
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raise StatisticsError('cdf() not defined when sigma is zero')
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return 0.5 * (1.0 + erf((x - self._mu) / (self._sigma * sqrt(2.0))))
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return 0.5 * (1.0 + erf((x - self._mu) / (self._sigma * sqrt(2.0))))
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def inv_cdf(self, p):
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def inv_cdf(self, p):
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'''Inverse cumulative distribution function. x : P(X <= x) = p
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"""Inverse cumulative distribution function. x : P(X <= x) = p
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Finds the value of the random variable such that the probability of the
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Finds the value of the random variable such that the probability of
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variable being less than or equal to that value equals the given probability.
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the variable being less than or equal to that value equals the given
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probability.
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This function is also called the percent point function or quantile function.
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This function is also called the percent point function or quantile
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'''
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function.
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if (p <= 0.0 or p >= 1.0):
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"""
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if p <= 0.0 or p >= 1.0:
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raise StatisticsError('p must be in the range 0.0 < p < 1.0')
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raise StatisticsError('p must be in the range 0.0 < p < 1.0')
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if self._sigma <= 0.0:
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if self._sigma <= 0.0:
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raise StatisticsError('cdf() not defined when sigma at or below zero')
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raise StatisticsError('cdf() not defined when sigma at or below zero')
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@ -933,7 +954,7 @@ class NormalDist:
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return self._mu + (x * self._sigma)
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return self._mu + (x * self._sigma)
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def overlap(self, other):
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def overlap(self, other):
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'''Compute the overlapping coefficient (OVL) between two normal distributions.
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"""Compute the overlapping coefficient (OVL) between two normal distributions.
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Measures the agreement between two normal probability distributions.
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Measures the agreement between two normal probability distributions.
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Returns a value between 0.0 and 1.0 giving the overlapping area in
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Returns a value between 0.0 and 1.0 giving the overlapping area in
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@ -943,7 +964,7 @@ class NormalDist:
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>>> N2 = NormalDist(3.2, 2.0)
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>>> N2 = NormalDist(3.2, 2.0)
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>>> N1.overlap(N2)
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>>> N1.overlap(N2)
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0.8035050657330205
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0.8035050657330205
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'''
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"""
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# See: "The overlapping coefficient as a measure of agreement between
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# See: "The overlapping coefficient as a measure of agreement between
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# probability distributions and point estimation of the overlap of two
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# probability distributions and point estimation of the overlap of two
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# normal densities" -- Henry F. Inman and Edwin L. Bradley Jr
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# normal densities" -- Henry F. Inman and Edwin L. Bradley Jr
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@ -968,21 +989,21 @@ class NormalDist:
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@property
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@property
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def mean(self):
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def mean(self):
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'Arithmetic mean of the normal distribution.'
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"Arithmetic mean of the normal distribution."
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return self._mu
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return self._mu
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@property
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@property
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def stdev(self):
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def stdev(self):
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'Standard deviation of the normal distribution.'
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"Standard deviation of the normal distribution."
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return self._sigma
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return self._sigma
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@property
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@property
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def variance(self):
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def variance(self):
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'Square of the standard deviation.'
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"Square of the standard deviation."
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return self._sigma ** 2.0
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return self._sigma ** 2.0
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def __add__(x1, x2):
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def __add__(x1, x2):
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'''Add a constant or another NormalDist instance.
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"""Add a constant or another NormalDist instance.
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If *other* is a constant, translate mu by the constant,
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If *other* is a constant, translate mu by the constant,
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leaving sigma unchanged.
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leaving sigma unchanged.
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@ -990,13 +1011,13 @@ class NormalDist:
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If *other* is a NormalDist, add both the means and the variances.
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If *other* is a NormalDist, add both the means and the variances.
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Mathematically, this works only if the two distributions are
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Mathematically, this works only if the two distributions are
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independent or if they are jointly normally distributed.
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independent or if they are jointly normally distributed.
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'''
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"""
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if isinstance(x2, NormalDist):
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if isinstance(x2, NormalDist):
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return NormalDist(x1._mu + x2._mu, hypot(x1._sigma, x2._sigma))
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return NormalDist(x1._mu + x2._mu, hypot(x1._sigma, x2._sigma))
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return NormalDist(x1._mu + x2, x1._sigma)
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return NormalDist(x1._mu + x2, x1._sigma)
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def __sub__(x1, x2):
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def __sub__(x1, x2):
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'''Subtract a constant or another NormalDist instance.
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"""Subtract a constant or another NormalDist instance.
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If *other* is a constant, translate by the constant mu,
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If *other* is a constant, translate by the constant mu,
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leaving sigma unchanged.
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leaving sigma unchanged.
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@ -1004,51 +1025,51 @@ class NormalDist:
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If *other* is a NormalDist, subtract the means and add the variances.
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If *other* is a NormalDist, subtract the means and add the variances.
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Mathematically, this works only if the two distributions are
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Mathematically, this works only if the two distributions are
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independent or if they are jointly normally distributed.
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independent or if they are jointly normally distributed.
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'''
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"""
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if isinstance(x2, NormalDist):
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if isinstance(x2, NormalDist):
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return NormalDist(x1._mu - x2._mu, hypot(x1._sigma, x2._sigma))
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return NormalDist(x1._mu - x2._mu, hypot(x1._sigma, x2._sigma))
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return NormalDist(x1._mu - x2, x1._sigma)
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return NormalDist(x1._mu - x2, x1._sigma)
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def __mul__(x1, x2):
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def __mul__(x1, x2):
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'''Multiply both mu and sigma by a constant.
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"""Multiply both mu and sigma by a constant.
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Used for rescaling, perhaps to change measurement units.
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Used for rescaling, perhaps to change measurement units.
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Sigma is scaled with the absolute value of the constant.
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Sigma is scaled with the absolute value of the constant.
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'''
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"""
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return NormalDist(x1._mu * x2, x1._sigma * fabs(x2))
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return NormalDist(x1._mu * x2, x1._sigma * fabs(x2))
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def __truediv__(x1, x2):
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def __truediv__(x1, x2):
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'''Divide both mu and sigma by a constant.
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"""Divide both mu and sigma by a constant.
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Used for rescaling, perhaps to change measurement units.
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Used for rescaling, perhaps to change measurement units.
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Sigma is scaled with the absolute value of the constant.
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Sigma is scaled with the absolute value of the constant.
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'''
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"""
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return NormalDist(x1._mu / x2, x1._sigma / fabs(x2))
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return NormalDist(x1._mu / x2, x1._sigma / fabs(x2))
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def __pos__(x1):
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def __pos__(x1):
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'Return a copy of the instance.'
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"Return a copy of the instance."
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return NormalDist(x1._mu, x1._sigma)
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return NormalDist(x1._mu, x1._sigma)
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def __neg__(x1):
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def __neg__(x1):
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'Negates mu while keeping sigma the same.'
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"Negates mu while keeping sigma the same."
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return NormalDist(-x1._mu, x1._sigma)
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return NormalDist(-x1._mu, x1._sigma)
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__radd__ = __add__
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__radd__ = __add__
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def __rsub__(x1, x2):
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def __rsub__(x1, x2):
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'Subtract a NormalDist from a constant or another NormalDist.'
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"Subtract a NormalDist from a constant or another NormalDist."
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return -(x1 - x2)
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return -(x1 - x2)
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__rmul__ = __mul__
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__rmul__ = __mul__
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def __eq__(x1, x2):
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def __eq__(x1, x2):
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'Two NormalDist objects are equal if their mu and sigma are both equal.'
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"Two NormalDist objects are equal if their mu and sigma are both equal."
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if not isinstance(x2, NormalDist):
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if not isinstance(x2, NormalDist):
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return NotImplemented
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return NotImplemented
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return (x1._mu, x2._sigma) == (x2._mu, x2._sigma)
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return (x1._mu, x2._sigma) == (x2._mu, x2._sigma)
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def __hash__(self):
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def __hash__(self):
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'NormalDist objects hash equal if their mu and sigma are both equal.'
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"NormalDist objects hash equal if their mu and sigma are both equal."
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return hash((self._mu, self._sigma))
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return hash((self._mu, self._sigma))
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def __repr__(self):
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def __repr__(self):
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