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"""
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|
Basic statistics module.
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|
This module provides functions for calculating statistics of data, including
|
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averages, variance, and standard deviation.
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Calculating averages
|
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|
|
--------------------
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|
|
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|
|
|
|
================== ==================================================
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|
Function Description
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|
|
|
================== ==================================================
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|
mean Arithmetic mean (average) of data.
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fmean Fast, floating point arithmetic mean.
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geometric_mean Geometric mean of data.
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harmonic_mean Harmonic mean of data.
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median Median (middle value) of data.
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median_low Low median of data.
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median_high High median of data.
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median_grouped Median, or 50th percentile, of grouped data.
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mode Mode (most common value) of data.
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multimode List of modes (most common values of data).
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quantiles Divide data into intervals with equal probability.
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|
|
|
================== ==================================================
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|
Calculate the arithmetic mean ("the average") of data:
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>>> mean([-1.0, 2.5, 3.25, 5.75])
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2.625
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Calculate the standard median of discrete data:
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>>> median([2, 3, 4, 5])
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3.5
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Calculate the median, or 50th percentile, of data grouped into class intervals
|
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|
|
centred on the data values provided. E.g. if your data points are rounded to
|
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|
|
the nearest whole number:
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>>> median_grouped([2, 2, 3, 3, 3, 4]) #doctest: +ELLIPSIS
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2.8333333333...
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This should be interpreted in this way: you have two data points in the class
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|
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interval 1.5-2.5, three data points in the class interval 2.5-3.5, and one in
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|
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the class interval 3.5-4.5. The median of these data points is 2.8333...
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|
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Calculating variability or spread
|
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|
|
---------------------------------
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|
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|
|
|
|
================== =============================================
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|
|
|
Function Description
|
|
|
|
|
================== =============================================
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pvariance Population variance of data.
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variance Sample variance of data.
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|
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pstdev Population standard deviation of data.
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|
|
stdev Sample standard deviation of data.
|
|
|
|
|
================== =============================================
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|
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Calculate the standard deviation of sample data:
|
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|
>>> stdev([2.5, 3.25, 5.5, 11.25, 11.75]) #doctest: +ELLIPSIS
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4.38961843444...
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|
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If you have previously calculated the mean, you can pass it as the optional
|
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|
|
second argument to the four "spread" functions to avoid recalculating it:
|
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|
>>> data = [1, 2, 2, 4, 4, 4, 5, 6]
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|
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>>> mu = mean(data)
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|
|
>>> pvariance(data, mu)
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|
2.5
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Exceptions
|
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|
|
----------
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|
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A single exception is defined: StatisticsError is a subclass of ValueError.
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|
"""
|
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__all__ = [
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|
|
'NormalDist',
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|
'StatisticsError',
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|
'fmean',
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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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|
|
import math
|
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|
|
import numbers
|
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|
|
import random
|
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|
|
from fractions import Fraction
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|
|
from decimal import Decimal
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|
|
from itertools import groupby
|
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|
|
from bisect import bisect_left, bisect_right
|
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|
|
from math import hypot, sqrt, fabs, exp, erf, tau, log, fsum
|
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|
|
from operator import itemgetter
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|
|
from collections import Counter
|
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|
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|
|
|
|
# === Exceptions ===
|
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|
|
class StatisticsError(ValueError):
|
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|
|
pass
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|
|
|
|
# === Private utilities ===
|
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|
|
def _sum(data, start=0):
|
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|
|
"""_sum(data [, start]) -> (type, sum, count)
|
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|
|
Return a high-precision sum of the given numeric data as a fraction,
|
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|
|
together with the type to be converted to and the count of items.
|
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|
|
If optional argument ``start`` is given, it is added to the total.
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|
|
If ``data`` is empty, ``start`` (defaulting to 0) is returned.
|
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|
|
Examples
|
|
|
|
|
--------
|
|
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|
|
>>> _sum([3, 2.25, 4.5, -0.5, 1.0], 0.75)
|
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|
|
(<class 'float'>, Fraction(11, 1), 5)
|
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|
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|
|
Some sources of round-off error will be avoided:
|
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|
|
|
|
|
|
|
# Built-in sum returns zero.
|
|
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|
|
>>> _sum([1e50, 1, -1e50] * 1000)
|
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|
|
(<class 'float'>, Fraction(1000, 1), 3000)
|
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|
|
|
|
|
|
Fractions and Decimals are also supported:
|
|
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|
|
|
|
|
|
|
>>> from fractions import Fraction as F
|
|
|
|
|
>>> _sum([F(2, 3), F(7, 5), F(1, 4), F(5, 6)])
|
|
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|
|
(<class 'fractions.Fraction'>, Fraction(63, 20), 4)
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|
|
|
|
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|
|
>>> 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)
|
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|
|
|
|
|
|
|
Mixed types are currently treated as an error, except that int is
|
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|
|
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.
|
|
|
|
|
"""
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return [self.inv_cdf(i / n) for i in range(1, n)]
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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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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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the two underlying probability density functions.
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>>> N1 = NormalDist(2.4, 1.6)
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>>> N2 = NormalDist(3.2, 2.0)
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>>> N1.overlap(N2)
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0.8035050657330205
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"""
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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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# normal densities" -- Henry F. Inman and Edwin L. Bradley Jr
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# http://dx.doi.org/10.1080/03610928908830127
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if not isinstance(other, NormalDist):
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raise TypeError('Expected another NormalDist instance')
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X, Y = self, other
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if (Y._sigma, Y._mu) < (X._sigma, X._mu): # sort to assure commutativity
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X, Y = Y, X
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X_var, Y_var = X.variance, Y.variance
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if not X_var or not Y_var:
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raise StatisticsError('overlap() not defined when sigma is zero')
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dv = Y_var - X_var
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dm = fabs(Y._mu - X._mu)
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if not dv:
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return 1.0 - erf(dm / (2.0 * X._sigma * sqrt(2.0)))
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a = X._mu * Y_var - Y._mu * X_var
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b = X._sigma * Y._sigma * sqrt(dm**2.0 + dv * log(Y_var / X_var))
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x1 = (a + b) / dv
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x2 = (a - b) / dv
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return 1.0 - (fabs(Y.cdf(x1) - X.cdf(x1)) + fabs(Y.cdf(x2) - X.cdf(x2)))
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def zscore(self, x):
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"""Compute the Standard Score. (x - mean) / stdev
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Describes *x* in terms of the number of standard deviations
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above or below the mean of the normal distribution.
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"""
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# https://www.statisticshowto.com/probability-and-statistics/z-score/
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if not self._sigma:
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raise StatisticsError('zscore() not defined when sigma is zero')
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return (x - self._mu) / self._sigma
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@property
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def mean(self):
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"Arithmetic mean of the normal distribution."
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return self._mu
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@property
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def median(self):
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"Return the median of the normal distribution"
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return self._mu
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@property
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def mode(self):
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"""Return the mode of the normal distribution
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The mode is the value x where which the probability density
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function (pdf) takes its maximum value.
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"""
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return self._mu
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@property
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|
def stdev(self):
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|
"Standard deviation of the normal distribution."
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|
|
return self._sigma
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|
@property
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|
def variance(self):
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|
"Square of the standard deviation."
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|
|
return self._sigma ** 2.0
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|
def __add__(x1, x2):
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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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|
leaving sigma unchanged.
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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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|
|
independent or if they are jointly normally distributed.
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|
|
"""
|
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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, x1._sigma)
|
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|
|
def __sub__(x1, x2):
|
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|
|
"""Subtract a constant or another NormalDist instance.
|
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|
|
|
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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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|
|
|
|
|
|
|
|
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)
|
|
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|
|
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|
|
|
|
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})'
|