1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 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})'
|