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Larry Hastingsf5e987b2013-10-19 11:50:09 -07001"""
2Basic statistics module.
3
4This module provides functions for calculating statistics of data, including
5averages, variance, and standard deviation.
6
7Calculating averages
8--------------------
9
Raymond Hettinger9013ccf2019-04-23 00:06:35 -070010================== ==================================================
Larry Hastingsf5e987b2013-10-19 11:50:09 -070011Function Description
Raymond Hettinger9013ccf2019-04-23 00:06:35 -070012================== ==================================================
Larry Hastingsf5e987b2013-10-19 11:50:09 -070013mean Arithmetic mean (average) of data.
Raymond Hettinger72800482019-04-23 01:35:16 -070014fmean Fast, floating point arithmetic mean.
Raymond Hettinger6463ba32019-04-07 09:20:03 -070015geometric_mean Geometric mean of data.
Steven D'Apranoa474afd2016-08-09 12:49:01 +100016harmonic_mean Harmonic mean of data.
Larry Hastingsf5e987b2013-10-19 11:50:09 -070017median Median (middle value) of data.
18median_low Low median of data.
19median_high High median of data.
20median_grouped Median, or 50th percentile, of grouped data.
21mode Mode (most common value) of data.
Raymond Hettinger6463ba32019-04-07 09:20:03 -070022multimode List of modes (most common values of data).
Raymond Hettinger9013ccf2019-04-23 00:06:35 -070023quantiles Divide data into intervals with equal probability.
24================== ==================================================
Larry Hastingsf5e987b2013-10-19 11:50:09 -070025
26Calculate the arithmetic mean ("the average") of data:
27
28>>> mean([-1.0, 2.5, 3.25, 5.75])
292.625
30
31
32Calculate the standard median of discrete data:
33
34>>> median([2, 3, 4, 5])
353.5
36
37
38Calculate the median, or 50th percentile, of data grouped into class intervals
39centred on the data values provided. E.g. if your data points are rounded to
40the nearest whole number:
41
42>>> median_grouped([2, 2, 3, 3, 3, 4]) #doctest: +ELLIPSIS
432.8333333333...
44
45This should be interpreted in this way: you have two data points in the class
46interval 1.5-2.5, three data points in the class interval 2.5-3.5, and one in
47the class interval 3.5-4.5. The median of these data points is 2.8333...
48
49
50Calculating variability or spread
51---------------------------------
52
53================== =============================================
54Function Description
55================== =============================================
56pvariance Population variance of data.
57variance Sample variance of data.
58pstdev Population standard deviation of data.
59stdev Sample standard deviation of data.
60================== =============================================
61
62Calculate the standard deviation of sample data:
63
64>>> stdev([2.5, 3.25, 5.5, 11.25, 11.75]) #doctest: +ELLIPSIS
654.38961843444...
66
67If you have previously calculated the mean, you can pass it as the optional
68second argument to the four "spread" functions to avoid recalculating it:
69
70>>> data = [1, 2, 2, 4, 4, 4, 5, 6]
71>>> mu = mean(data)
72>>> pvariance(data, mu)
732.5
74
75
76Exceptions
77----------
78
79A single exception is defined: StatisticsError is a subclass of ValueError.
80
81"""
82
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -070083__all__ = [
84 'NormalDist',
85 'StatisticsError',
86 'fmean',
87 'geometric_mean',
88 'harmonic_mean',
89 'mean',
90 'median',
91 'median_grouped',
92 'median_high',
93 'median_low',
94 'mode',
95 'multimode',
96 'pstdev',
97 'pvariance',
98 'quantiles',
99 'stdev',
100 'variance',
101]
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700102
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700103import math
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000104import numbers
Raymond Hettinger11c79532019-02-23 14:44:07 -0800105import random
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700106
107from fractions import Fraction
108from decimal import Decimal
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800109from itertools import groupby, repeat
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000110from bisect import bisect_left, bisect_right
Raymond Hettinger318d5372019-03-06 22:59:40 -0800111from math import hypot, sqrt, fabs, exp, erf, tau, log, fsum
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700112from operator import itemgetter
113from collections import Counter
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700114
115# === Exceptions ===
116
117class StatisticsError(ValueError):
118 pass
119
120
121# === Private utilities ===
122
123def _sum(data, start=0):
Steven D'Apranob28c3272015-12-01 19:59:53 +1100124 """_sum(data [, start]) -> (type, sum, count)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700125
Steven D'Apranob28c3272015-12-01 19:59:53 +1100126 Return a high-precision sum of the given numeric data as a fraction,
127 together with the type to be converted to and the count of items.
128
129 If optional argument ``start`` is given, it is added to the total.
130 If ``data`` is empty, ``start`` (defaulting to 0) is returned.
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700131
132
133 Examples
134 --------
135
136 >>> _sum([3, 2.25, 4.5, -0.5, 1.0], 0.75)
Benjamin Petersonab078e92016-07-13 21:13:29 -0700137 (<class 'float'>, Fraction(11, 1), 5)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700138
139 Some sources of round-off error will be avoided:
140
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000141 # Built-in sum returns zero.
142 >>> _sum([1e50, 1, -1e50] * 1000)
Benjamin Petersonab078e92016-07-13 21:13:29 -0700143 (<class 'float'>, Fraction(1000, 1), 3000)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700144
145 Fractions and Decimals are also supported:
146
147 >>> from fractions import Fraction as F
148 >>> _sum([F(2, 3), F(7, 5), F(1, 4), F(5, 6)])
Benjamin Petersonab078e92016-07-13 21:13:29 -0700149 (<class 'fractions.Fraction'>, Fraction(63, 20), 4)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700150
151 >>> from decimal import Decimal as D
152 >>> data = [D("0.1375"), D("0.2108"), D("0.3061"), D("0.0419")]
153 >>> _sum(data)
Benjamin Petersonab078e92016-07-13 21:13:29 -0700154 (<class 'decimal.Decimal'>, Fraction(6963, 10000), 4)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700155
Nick Coghlan73afe2a2014-02-08 19:58:04 +1000156 Mixed types are currently treated as an error, except that int is
157 allowed.
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700158 """
Steven D'Apranob28c3272015-12-01 19:59:53 +1100159 count = 0
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700160 n, d = _exact_ratio(start)
Steven D'Apranob28c3272015-12-01 19:59:53 +1100161 partials = {d: n}
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700162 partials_get = partials.get
Steven D'Apranob28c3272015-12-01 19:59:53 +1100163 T = _coerce(int, type(start))
164 for typ, values in groupby(data, type):
165 T = _coerce(T, typ) # or raise TypeError
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700166 for n, d in map(_exact_ratio, values):
Steven D'Apranob28c3272015-12-01 19:59:53 +1100167 count += 1
168 partials[d] = partials_get(d, 0) + n
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700169 if None in partials:
Steven D'Apranob28c3272015-12-01 19:59:53 +1100170 # The sum will be a NAN or INF. We can ignore all the finite
171 # partials, and just look at this special one.
172 total = partials[None]
173 assert not _isfinite(total)
174 else:
175 # Sum all the partial sums using builtin sum.
176 # FIXME is this faster if we sum them in order of the denominator?
177 total = sum(Fraction(n, d) for d, n in sorted(partials.items()))
178 return (T, total, count)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700179
180
Steven D'Apranob28c3272015-12-01 19:59:53 +1100181def _isfinite(x):
182 try:
183 return x.is_finite() # Likely a Decimal.
184 except AttributeError:
185 return math.isfinite(x) # Coerces to float first.
186
187
188def _coerce(T, S):
189 """Coerce types T and S to a common type, or raise TypeError.
190
191 Coercion rules are currently an implementation detail. See the CoerceTest
192 test class in test_statistics for details.
193 """
194 # See http://bugs.python.org/issue24068.
195 assert T is not bool, "initial type T is bool"
196 # If the types are the same, no need to coerce anything. Put this
197 # first, so that the usual case (no coercion needed) happens as soon
198 # as possible.
199 if T is S: return T
200 # Mixed int & other coerce to the other type.
201 if S is int or S is bool: return T
202 if T is int: return S
203 # If one is a (strict) subclass of the other, coerce to the subclass.
204 if issubclass(S, T): return S
205 if issubclass(T, S): return T
206 # Ints coerce to the other type.
207 if issubclass(T, int): return S
208 if issubclass(S, int): return T
209 # Mixed fraction & float coerces to float (or float subclass).
210 if issubclass(T, Fraction) and issubclass(S, float):
211 return S
212 if issubclass(T, float) and issubclass(S, Fraction):
213 return T
214 # Any other combination is disallowed.
215 msg = "don't know how to coerce %s and %s"
216 raise TypeError(msg % (T.__name__, S.__name__))
Nick Coghlan73afe2a2014-02-08 19:58:04 +1000217
218
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700219def _exact_ratio(x):
Steven D'Apranob28c3272015-12-01 19:59:53 +1100220 """Return Real number x to exact (numerator, denominator) pair.
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700221
222 >>> _exact_ratio(0.25)
223 (1, 4)
224
225 x is expected to be an int, Fraction, Decimal or float.
226 """
227 try:
Steven D'Apranob28c3272015-12-01 19:59:53 +1100228 # Optimise the common case of floats. We expect that the most often
229 # used numeric type will be builtin floats, so try to make this as
230 # fast as possible.
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000231 if type(x) is float or type(x) is Decimal:
Steven D'Apranob28c3272015-12-01 19:59:53 +1100232 return x.as_integer_ratio()
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700233 try:
Steven D'Apranob28c3272015-12-01 19:59:53 +1100234 # x may be an int, Fraction, or Integral ABC.
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700235 return (x.numerator, x.denominator)
236 except AttributeError:
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700237 try:
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000238 # x may be a float or Decimal subclass.
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700239 return x.as_integer_ratio()
240 except AttributeError:
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000241 # Just give up?
242 pass
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700243 except (OverflowError, ValueError):
Steven D'Apranob28c3272015-12-01 19:59:53 +1100244 # float NAN or INF.
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000245 assert not _isfinite(x)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700246 return (x, None)
Steven D'Apranob28c3272015-12-01 19:59:53 +1100247 msg = "can't convert type '{}' to numerator/denominator"
248 raise TypeError(msg.format(type(x).__name__))
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700249
250
Steven D'Apranob28c3272015-12-01 19:59:53 +1100251def _convert(value, T):
252 """Convert value to given numeric type T."""
253 if type(value) is T:
254 # This covers the cases where T is Fraction, or where value is
255 # a NAN or INF (Decimal or float).
256 return value
257 if issubclass(T, int) and value.denominator != 1:
258 T = float
259 try:
260 # FIXME: what do we do if this overflows?
261 return T(value)
262 except TypeError:
263 if issubclass(T, Decimal):
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700264 return T(value.numerator) / T(value.denominator)
Steven D'Apranob28c3272015-12-01 19:59:53 +1100265 else:
266 raise
267
268
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000269def _find_lteq(a, x):
270 'Locate the leftmost value exactly equal to x'
271 i = bisect_left(a, x)
272 if i != len(a) and a[i] == x:
273 return i
274 raise ValueError
275
276
277def _find_rteq(a, l, x):
278 'Locate the rightmost value exactly equal to x'
279 i = bisect_right(a, x, lo=l)
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700280 if i != (len(a) + 1) and a[i - 1] == x:
281 return i - 1
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000282 raise ValueError
283
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000284
285def _fail_neg(values, errmsg='negative value'):
286 """Iterate over values, failing if any are less than zero."""
287 for x in values:
288 if x < 0:
289 raise StatisticsError(errmsg)
290 yield x
291
292
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700293# === Measures of central tendency (averages) ===
294
295def mean(data):
296 """Return the sample arithmetic mean of data.
297
298 >>> mean([1, 2, 3, 4, 4])
299 2.8
300
301 >>> from fractions import Fraction as F
302 >>> mean([F(3, 7), F(1, 21), F(5, 3), F(1, 3)])
303 Fraction(13, 21)
304
305 >>> from decimal import Decimal as D
306 >>> mean([D("0.5"), D("0.75"), D("0.625"), D("0.375")])
307 Decimal('0.5625')
308
309 If ``data`` is empty, StatisticsError will be raised.
310 """
311 if iter(data) is data:
312 data = list(data)
313 n = len(data)
314 if n < 1:
315 raise StatisticsError('mean requires at least one data point')
Steven D'Apranob28c3272015-12-01 19:59:53 +1100316 T, total, count = _sum(data)
317 assert count == n
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700318 return _convert(total / n, T)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700319
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700320
Raymond Hettinger47d99872019-02-21 15:06:29 -0800321def fmean(data):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700322 """Convert data to floats and compute the arithmetic mean.
Raymond Hettinger47d99872019-02-21 15:06:29 -0800323
324 This runs faster than the mean() function and it always returns a float.
Raymond Hettinger47d99872019-02-21 15:06:29 -0800325 If the input dataset is empty, it raises a StatisticsError.
326
327 >>> fmean([3.5, 4.0, 5.25])
328 4.25
Raymond Hettinger47d99872019-02-21 15:06:29 -0800329 """
330 try:
331 n = len(data)
332 except TypeError:
333 # Handle iterators that do not define __len__().
334 n = 0
Raymond Hettinger6c01ebc2019-06-05 07:39:38 -0700335 def count(iterable):
Raymond Hettinger47d99872019-02-21 15:06:29 -0800336 nonlocal n
Raymond Hettinger6c01ebc2019-06-05 07:39:38 -0700337 for n, x in enumerate(iterable, start=1):
338 yield x
339 total = fsum(count(data))
Raymond Hettinger47d99872019-02-21 15:06:29 -0800340 else:
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700341 total = fsum(data)
Raymond Hettinger47d99872019-02-21 15:06:29 -0800342 try:
343 return total / n
344 except ZeroDivisionError:
345 raise StatisticsError('fmean requires at least one data point') from None
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700346
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700347
Raymond Hettinger6463ba32019-04-07 09:20:03 -0700348def geometric_mean(data):
349 """Convert data to floats and compute the geometric mean.
350
351 Raises a StatisticsError if the input dataset is empty,
352 if it contains a zero, or if it contains a negative value.
353
354 No special efforts are made to achieve exact results.
355 (However, this may change in the future.)
356
357 >>> round(geometric_mean([54, 24, 36]), 9)
358 36.0
359 """
360 try:
361 return exp(fmean(map(log, data)))
362 except ValueError:
363 raise StatisticsError('geometric mean requires a non-empty dataset '
364 ' containing positive numbers') from None
365
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700366
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800367def harmonic_mean(data, weights=None):
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000368 """Return the harmonic mean of data.
369
370 The harmonic mean, sometimes called the subcontrary mean, is the
371 reciprocal of the arithmetic mean of the reciprocals of the data,
372 and is often appropriate when averaging quantities which are rates
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800373 or ratios, for example speeds.
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000374
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800375 Suppose a car travels 40 km/hr for 5 km and then speeds-up to
376 60 km/hr for another 5 km. What is the average speed?
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000377
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800378 >>> harmonic_mean([40, 60])
379 48.0
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000380
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800381 Suppose a car travels 40 km/hr for 5 km, and when traffic clears,
382 speeds-up to 60 km/hr for the remaining 30 km of the journey. What
383 is the average speed?
384
385 >>> harmonic_mean([40, 60], weights=[5, 30])
386 56.0
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000387
388 If ``data`` is empty, or any element is less than zero,
389 ``harmonic_mean`` will raise ``StatisticsError``.
390 """
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000391 if iter(data) is data:
392 data = list(data)
393 errmsg = 'harmonic mean does not support negative values'
394 n = len(data)
395 if n < 1:
396 raise StatisticsError('harmonic_mean requires at least one data point')
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800397 elif n == 1 and weights is None:
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000398 x = data[0]
399 if isinstance(x, (numbers.Real, Decimal)):
400 if x < 0:
401 raise StatisticsError(errmsg)
402 return x
403 else:
404 raise TypeError('unsupported type')
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800405 if weights is None:
406 weights = repeat(1, n)
407 sum_weights = n
408 else:
409 if iter(weights) is weights:
410 weights = list(weights)
411 if len(weights) != n:
412 raise StatisticsError('Number of weights does not match data size')
413 _, sum_weights, _ = _sum(w for w in _fail_neg(weights, errmsg))
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000414 try:
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800415 data = _fail_neg(data, errmsg)
416 T, total, count = _sum(w / x if w else 0 for w, x in zip(weights, data))
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000417 except ZeroDivisionError:
418 return 0
Raymond Hettingercc3467a2020-12-23 19:52:09 -0800419 if total <= 0:
420 raise StatisticsError('Weighted sum must be positive')
421 return _convert(sum_weights / total, T)
Steven D'Apranoa474afd2016-08-09 12:49:01 +1000422
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700423# FIXME: investigate ways to calculate medians without sorting? Quickselect?
424def median(data):
425 """Return the median (middle value) of numeric data.
426
427 When the number of data points is odd, return the middle data point.
428 When the number of data points is even, the median is interpolated by
429 taking the average of the two middle values:
430
431 >>> median([1, 3, 5])
432 3
433 >>> median([1, 3, 5, 7])
434 4.0
435
436 """
437 data = sorted(data)
438 n = len(data)
439 if n == 0:
440 raise StatisticsError("no median for empty data")
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700441 if n % 2 == 1:
442 return data[n // 2]
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700443 else:
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700444 i = n // 2
445 return (data[i - 1] + data[i]) / 2
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700446
447
448def median_low(data):
449 """Return the low median of numeric data.
450
451 When the number of data points is odd, the middle value is returned.
452 When it is even, the smaller of the two middle values is returned.
453
454 >>> median_low([1, 3, 5])
455 3
456 >>> median_low([1, 3, 5, 7])
457 3
458
459 """
460 data = sorted(data)
461 n = len(data)
462 if n == 0:
463 raise StatisticsError("no median for empty data")
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700464 if n % 2 == 1:
465 return data[n // 2]
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700466 else:
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700467 return data[n // 2 - 1]
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700468
469
470def median_high(data):
471 """Return the high median of data.
472
473 When the number of data points is odd, the middle value is returned.
474 When it is even, the larger of the two middle values is returned.
475
476 >>> median_high([1, 3, 5])
477 3
478 >>> median_high([1, 3, 5, 7])
479 5
480
481 """
482 data = sorted(data)
483 n = len(data)
484 if n == 0:
485 raise StatisticsError("no median for empty data")
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700486 return data[n // 2]
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700487
488
489def median_grouped(data, interval=1):
Zachary Waredf2660e2015-10-27 22:00:41 -0500490 """Return the 50th percentile (median) of grouped continuous data.
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700491
492 >>> median_grouped([1, 2, 2, 3, 4, 4, 4, 4, 4, 5])
493 3.7
494 >>> median_grouped([52, 52, 53, 54])
495 52.5
496
497 This calculates the median as the 50th percentile, and should be
498 used when your data is continuous and grouped. In the above example,
499 the values 1, 2, 3, etc. actually represent the midpoint of classes
500 0.5-1.5, 1.5-2.5, 2.5-3.5, etc. The middle value falls somewhere in
501 class 3.5-4.5, and interpolation is used to estimate it.
502
503 Optional argument ``interval`` represents the class interval, and
504 defaults to 1. Changing the class interval naturally will change the
505 interpolated 50th percentile value:
506
507 >>> median_grouped([1, 3, 3, 5, 7], interval=1)
508 3.25
509 >>> median_grouped([1, 3, 3, 5, 7], interval=2)
510 3.5
511
512 This function does not check whether the data points are at least
513 ``interval`` apart.
514 """
515 data = sorted(data)
516 n = len(data)
517 if n == 0:
518 raise StatisticsError("no median for empty data")
519 elif n == 1:
520 return data[0]
521 # Find the value at the midpoint. Remember this corresponds to the
522 # centre of the class interval.
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700523 x = data[n // 2]
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700524 for obj in (x, interval):
525 if isinstance(obj, (str, bytes)):
526 raise TypeError('expected number but got %r' % obj)
527 try:
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700528 L = x - interval / 2 # The lower limit of the median interval.
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700529 except TypeError:
530 # Mixed type. For now we just coerce to float.
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700531 L = float(x) - float(interval) / 2
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000532
533 # Uses bisection search to search for x in data with log(n) time complexity
Martin Panterf1579822016-05-26 06:03:33 +0000534 # Find the position of leftmost occurrence of x in data
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000535 l1 = _find_lteq(data, x)
Martin Panterf1579822016-05-26 06:03:33 +0000536 # Find the position of rightmost occurrence of x in data[l1...len(data)]
Steven D'Aprano3b06e242016-05-05 03:54:29 +1000537 # Assuming always l1 <= l2
538 l2 = _find_rteq(data, l1, x)
539 cf = l1
540 f = l2 - l1 + 1
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700541 return L + interval * (n / 2 - cf) / f
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700542
543
544def mode(data):
545 """Return the most common data point from discrete or nominal data.
546
547 ``mode`` assumes discrete data, and returns a single value. This is the
548 standard treatment of the mode as commonly taught in schools:
549
Raymond Hettingere4810b22019-09-05 00:18:47 -0700550 >>> mode([1, 1, 2, 3, 3, 3, 3, 4])
551 3
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700552
553 This also works with nominal (non-numeric) data:
554
Raymond Hettingere4810b22019-09-05 00:18:47 -0700555 >>> mode(["red", "blue", "blue", "red", "green", "red", "red"])
556 'red'
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700557
Raymond Hettingere4810b22019-09-05 00:18:47 -0700558 If there are multiple modes with same frequency, return the first one
559 encountered:
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700560
561 >>> mode(['red', 'red', 'green', 'blue', 'blue'])
562 'red'
563
564 If *data* is empty, ``mode``, raises StatisticsError.
565
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700566 """
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700567 pairs = Counter(iter(data)).most_common(1)
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700568 try:
Raymond Hettinger7ce4bfa2019-09-20 21:46:52 -0700569 return pairs[0][0]
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700570 except IndexError:
571 raise StatisticsError('no mode for empty data') from None
572
573
574def multimode(data):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700575 """Return a list of the most frequently occurring values.
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700576
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700577 Will return more than one result if there are multiple modes
578 or an empty list if *data* is empty.
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700579
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700580 >>> multimode('aabbbbbbbbcc')
581 ['b']
582 >>> multimode('aabbbbccddddeeffffgg')
583 ['b', 'd', 'f']
584 >>> multimode('')
585 []
Raymond Hettingerfc06a192019-03-12 00:43:27 -0700586 """
587 counts = Counter(iter(data)).most_common()
588 maxcount, mode_items = next(groupby(counts, key=itemgetter(1)), (0, []))
589 return list(map(itemgetter(0), mode_items))
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700590
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700591
Raymond Hettingercba9f842019-06-02 21:07:43 -0700592# Notes on methods for computing quantiles
593# ----------------------------------------
594#
595# There is no one perfect way to compute quantiles. Here we offer
596# two methods that serve common needs. Most other packages
597# surveyed offered at least one or both of these two, making them
598# "standard" in the sense of "widely-adopted and reproducible".
599# They are also easy to explain, easy to compute manually, and have
600# straight-forward interpretations that aren't surprising.
601
602# The default method is known as "R6", "PERCENTILE.EXC", or "expected
603# value of rank order statistics". The alternative method is known as
604# "R7", "PERCENTILE.INC", or "mode of rank order statistics".
605
606# For sample data where there is a positive probability for values
607# beyond the range of the data, the R6 exclusive method is a
608# reasonable choice. Consider a random sample of nine values from a
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700609# population with a uniform distribution from 0.0 to 1.0. The
Raymond Hettingercba9f842019-06-02 21:07:43 -0700610# distribution of the third ranked sample point is described by
611# betavariate(alpha=3, beta=7) which has mode=0.250, median=0.286, and
612# mean=0.300. Only the latter (which corresponds with R6) gives the
613# desired cut point with 30% of the population falling below that
614# value, making it comparable to a result from an inv_cdf() function.
Raymond Hettinger7ce4bfa2019-09-20 21:46:52 -0700615# The R6 exclusive method is also idempotent.
Raymond Hettingercba9f842019-06-02 21:07:43 -0700616
617# For describing population data where the end points are known to
618# be included in the data, the R7 inclusive method is a reasonable
619# choice. Instead of the mean, it uses the mode of the beta
620# distribution for the interior points. Per Hyndman & Fan, "One nice
621# property is that the vertices of Q7(p) divide the range into n - 1
622# intervals, and exactly 100p% of the intervals lie to the left of
623# Q7(p) and 100(1 - p)% of the intervals lie to the right of Q7(p)."
624
Raymond Hettingereed5e9a2019-07-19 01:57:22 -0700625# If needed, other methods could be added. However, for now, the
626# position is that fewer options make for easier choices and that
627# external packages can be used for anything more advanced.
Raymond Hettingercba9f842019-06-02 21:07:43 -0700628
Raymond Hettinger272d0d02019-09-17 20:45:05 -0700629def quantiles(data, *, n=4, method='exclusive'):
Raymond Hettingere4810b22019-09-05 00:18:47 -0700630 """Divide *data* into *n* continuous intervals with equal probability.
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700631
632 Returns a list of (n - 1) cut points separating the intervals.
633
634 Set *n* to 4 for quartiles (the default). Set *n* to 10 for deciles.
635 Set *n* to 100 for percentiles which gives the 99 cuts points that
Raymond Hettingere4810b22019-09-05 00:18:47 -0700636 separate *data* in to 100 equal sized groups.
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700637
Raymond Hettinger4db25d52019-09-08 16:57:58 -0700638 The *data* can be any iterable containing sample.
639 The cut points are linearly interpolated between data points.
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700640
Raymond Hettingere4810b22019-09-05 00:18:47 -0700641 If *method* is set to *inclusive*, *data* is treated as population
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700642 data. The minimum value is treated as the 0th percentile and the
643 maximum value is treated as the 100th percentile.
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700644 """
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700645 if n < 1:
646 raise StatisticsError('n must be at least 1')
Raymond Hettingere4810b22019-09-05 00:18:47 -0700647 data = sorted(data)
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700648 ld = len(data)
649 if ld < 2:
650 raise StatisticsError('must have at least two data points')
651 if method == 'inclusive':
652 m = ld - 1
653 result = []
654 for i in range(1, n):
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700655 j, delta = divmod(i * m, n)
656 interpolated = (data[j] * (n - delta) + data[j + 1] * delta) / n
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700657 result.append(interpolated)
658 return result
659 if method == 'exclusive':
660 m = ld + 1
661 result = []
662 for i in range(1, n):
663 j = i * m // n # rescale i to m/n
664 j = 1 if j < 1 else ld-1 if j > ld-1 else j # clamp to 1 .. ld-1
665 delta = i*m - j*n # exact integer math
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700666 interpolated = (data[j - 1] * (n - delta) + data[j] * delta) / n
Raymond Hettinger9013ccf2019-04-23 00:06:35 -0700667 result.append(interpolated)
668 return result
669 raise ValueError(f'Unknown method: {method!r}')
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700670
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700671
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700672# === Measures of spread ===
673
674# See http://mathworld.wolfram.com/Variance.html
675# http://mathworld.wolfram.com/SampleVariance.html
676# http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance
677#
678# Under no circumstances use the so-called "computational formula for
679# variance", as that is only suitable for hand calculations with a small
680# amount of low-precision data. It has terrible numeric properties.
681#
682# See a comparison of three computational methods here:
683# http://www.johndcook.com/blog/2008/09/26/comparing-three-methods-of-computing-standard-deviation/
684
685def _ss(data, c=None):
686 """Return sum of square deviations of sequence data.
687
688 If ``c`` is None, the mean is calculated in one pass, and the deviations
689 from the mean are calculated in a second pass. Otherwise, deviations are
690 calculated from ``c`` as given. Use the second case with care, as it can
691 lead to garbage results.
692 """
Raymond Hettingerd71ab4f2020-06-13 15:55:52 -0700693 if c is not None:
694 T, total, count = _sum((x-c)**2 for x in data)
695 return (T, total)
696 c = mean(data)
Steven D'Apranob28c3272015-12-01 19:59:53 +1100697 T, total, count = _sum((x-c)**2 for x in data)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700698 # The following sum should mathematically equal zero, but due to rounding
699 # error may not.
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700700 U, total2, count2 = _sum((x - c) for x in data)
Steven D'Apranob28c3272015-12-01 19:59:53 +1100701 assert T == U and count == count2
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700702 total -= total2 ** 2 / len(data)
Steven D'Apranob28c3272015-12-01 19:59:53 +1100703 assert not total < 0, 'negative sum of square deviations: %f' % total
704 return (T, total)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700705
706
707def variance(data, xbar=None):
708 """Return the sample variance of data.
709
710 data should be an iterable of Real-valued numbers, with at least two
711 values. The optional argument xbar, if given, should be the mean of
712 the data. If it is missing or None, the mean is automatically calculated.
713
714 Use this function when your data is a sample from a population. To
715 calculate the variance from the entire population, see ``pvariance``.
716
717 Examples:
718
719 >>> data = [2.75, 1.75, 1.25, 0.25, 0.5, 1.25, 3.5]
720 >>> variance(data)
721 1.3720238095238095
722
723 If you have already calculated the mean of your data, you can pass it as
724 the optional second argument ``xbar`` to avoid recalculating it:
725
726 >>> m = mean(data)
727 >>> variance(data, m)
728 1.3720238095238095
729
730 This function does not check that ``xbar`` is actually the mean of
731 ``data``. Giving arbitrary values for ``xbar`` may lead to invalid or
732 impossible results.
733
734 Decimals and Fractions are supported:
735
736 >>> from decimal import Decimal as D
737 >>> variance([D("27.5"), D("30.25"), D("30.25"), D("34.5"), D("41.75")])
738 Decimal('31.01875')
739
740 >>> from fractions import Fraction as F
741 >>> variance([F(1, 6), F(1, 2), F(5, 3)])
742 Fraction(67, 108)
743
744 """
745 if iter(data) is data:
746 data = list(data)
747 n = len(data)
748 if n < 2:
749 raise StatisticsError('variance requires at least two data points')
Steven D'Apranob28c3272015-12-01 19:59:53 +1100750 T, ss = _ss(data, xbar)
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700751 return _convert(ss / (n - 1), T)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700752
753
754def pvariance(data, mu=None):
755 """Return the population variance of ``data``.
756
Raymond Hettinger733b9a32019-11-11 23:35:06 -0800757 data should be a sequence or iterable of Real-valued numbers, with at least one
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700758 value. The optional argument mu, if given, should be the mean of
759 the data. If it is missing or None, the mean is automatically calculated.
760
761 Use this function to calculate the variance from the entire population.
762 To estimate the variance from a sample, the ``variance`` function is
763 usually a better choice.
764
765 Examples:
766
767 >>> data = [0.0, 0.25, 0.25, 1.25, 1.5, 1.75, 2.75, 3.25]
768 >>> pvariance(data)
769 1.25
770
771 If you have already calculated the mean of the data, you can pass it as
772 the optional second argument to avoid recalculating it:
773
774 >>> mu = mean(data)
775 >>> pvariance(data, mu)
776 1.25
777
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700778 Decimals and Fractions are supported:
779
780 >>> from decimal import Decimal as D
781 >>> pvariance([D("27.5"), D("30.25"), D("30.25"), D("34.5"), D("41.75")])
782 Decimal('24.815')
783
784 >>> from fractions import Fraction as F
785 >>> pvariance([F(1, 4), F(5, 4), F(1, 2)])
786 Fraction(13, 72)
787
788 """
789 if iter(data) is data:
790 data = list(data)
791 n = len(data)
792 if n < 1:
793 raise StatisticsError('pvariance requires at least one data point')
Steven D'Apranob28c3272015-12-01 19:59:53 +1100794 T, ss = _ss(data, mu)
Raymond Hettinger5aad0272020-06-13 19:17:28 -0700795 return _convert(ss / n, T)
Larry Hastingsf5e987b2013-10-19 11:50:09 -0700796
797
798def stdev(data, xbar=None):
799 """Return the square root of the sample variance.
800
801 See ``variance`` for arguments and other details.
802
803 >>> stdev([1.5, 2.5, 2.5, 2.75, 3.25, 4.75])
804 1.0810874155219827
805
806 """
807 var = variance(data, xbar)
808 try:
809 return var.sqrt()
810 except AttributeError:
811 return math.sqrt(var)
812
813
814def pstdev(data, mu=None):
815 """Return the square root of the population variance.
816
817 See ``pvariance`` for arguments and other details.
818
819 >>> pstdev([1.5, 2.5, 2.5, 2.75, 3.25, 4.75])
820 0.986893273527251
821
822 """
823 var = pvariance(data, mu)
824 try:
825 return var.sqrt()
826 except AttributeError:
827 return math.sqrt(var)
Raymond Hettinger11c79532019-02-23 14:44:07 -0800828
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700829
Raymond Hettinger11c79532019-02-23 14:44:07 -0800830## Normal Distribution #####################################################
831
Dong-hee Na0a18ee42019-08-24 07:20:30 +0900832
833def _normal_dist_inv_cdf(p, mu, sigma):
834 # There is no closed-form solution to the inverse CDF for the normal
835 # distribution, so we use a rational approximation instead:
836 # Wichura, M.J. (1988). "Algorithm AS241: The Percentage Points of the
837 # Normal Distribution". Applied Statistics. Blackwell Publishing. 37
838 # (3): 477–484. doi:10.2307/2347330. JSTOR 2347330.
839 q = p - 0.5
840 if fabs(q) <= 0.425:
841 r = 0.180625 - q * q
842 # Hash sum: 55.88319_28806_14901_4439
843 num = (((((((2.50908_09287_30122_6727e+3 * r +
844 3.34305_75583_58812_8105e+4) * r +
845 6.72657_70927_00870_0853e+4) * r +
846 4.59219_53931_54987_1457e+4) * r +
847 1.37316_93765_50946_1125e+4) * r +
848 1.97159_09503_06551_4427e+3) * r +
849 1.33141_66789_17843_7745e+2) * r +
850 3.38713_28727_96366_6080e+0) * q
851 den = (((((((5.22649_52788_52854_5610e+3 * r +
852 2.87290_85735_72194_2674e+4) * r +
853 3.93078_95800_09271_0610e+4) * r +
854 2.12137_94301_58659_5867e+4) * r +
855 5.39419_60214_24751_1077e+3) * r +
856 6.87187_00749_20579_0830e+2) * r +
857 4.23133_30701_60091_1252e+1) * r +
858 1.0)
859 x = num / den
860 return mu + (x * sigma)
861 r = p if q <= 0.0 else 1.0 - p
862 r = sqrt(-log(r))
863 if r <= 5.0:
864 r = r - 1.6
865 # Hash sum: 49.33206_50330_16102_89036
866 num = (((((((7.74545_01427_83414_07640e-4 * r +
867 2.27238_44989_26918_45833e-2) * r +
868 2.41780_72517_74506_11770e-1) * r +
869 1.27045_82524_52368_38258e+0) * r +
870 3.64784_83247_63204_60504e+0) * r +
871 5.76949_72214_60691_40550e+0) * r +
872 4.63033_78461_56545_29590e+0) * r +
873 1.42343_71107_49683_57734e+0)
874 den = (((((((1.05075_00716_44416_84324e-9 * r +
875 5.47593_80849_95344_94600e-4) * r +
876 1.51986_66563_61645_71966e-2) * r +
877 1.48103_97642_74800_74590e-1) * r +
878 6.89767_33498_51000_04550e-1) * r +
879 1.67638_48301_83803_84940e+0) * r +
880 2.05319_16266_37758_82187e+0) * r +
881 1.0)
882 else:
883 r = r - 5.0
884 # Hash sum: 47.52583_31754_92896_71629
885 num = (((((((2.01033_43992_92288_13265e-7 * r +
886 2.71155_55687_43487_57815e-5) * r +
887 1.24266_09473_88078_43860e-3) * r +
888 2.65321_89526_57612_30930e-2) * r +
889 2.96560_57182_85048_91230e-1) * r +
890 1.78482_65399_17291_33580e+0) * r +
891 5.46378_49111_64114_36990e+0) * r +
892 6.65790_46435_01103_77720e+0)
893 den = (((((((2.04426_31033_89939_78564e-15 * r +
894 1.42151_17583_16445_88870e-7) * r +
895 1.84631_83175_10054_68180e-5) * r +
896 7.86869_13114_56132_59100e-4) * r +
897 1.48753_61290_85061_48525e-2) * r +
898 1.36929_88092_27358_05310e-1) * r +
899 5.99832_20655_58879_37690e-1) * r +
900 1.0)
901 x = num / den
902 if q < 0.0:
903 x = -x
904 return mu + (x * sigma)
905
906
Raymond Hettinger0400a7f2020-05-02 19:30:24 -0700907# If available, use C implementation
908try:
909 from _statistics import _normal_dist_inv_cdf
910except ImportError:
911 pass
912
913
Raymond Hettinger11c79532019-02-23 14:44:07 -0800914class NormalDist:
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700915 "Normal distribution of a random variable"
Raymond Hettinger11c79532019-02-23 14:44:07 -0800916 # https://en.wikipedia.org/wiki/Normal_distribution
917 # https://en.wikipedia.org/wiki/Variance#Properties
918
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700919 __slots__ = {
920 '_mu': 'Arithmetic mean of a normal distribution',
921 '_sigma': 'Standard deviation of a normal distribution',
922 }
Raymond Hettinger11c79532019-02-23 14:44:07 -0800923
924 def __init__(self, mu=0.0, sigma=1.0):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700925 "NormalDist where mu is the mean and sigma is the standard deviation."
Raymond Hettinger11c79532019-02-23 14:44:07 -0800926 if sigma < 0.0:
927 raise StatisticsError('sigma must be non-negative')
Raymond Hettingere4810b22019-09-05 00:18:47 -0700928 self._mu = float(mu)
929 self._sigma = float(sigma)
Raymond Hettinger11c79532019-02-23 14:44:07 -0800930
931 @classmethod
932 def from_samples(cls, data):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700933 "Make a normal distribution instance from sample data."
Raymond Hettinger11c79532019-02-23 14:44:07 -0800934 if not isinstance(data, (list, tuple)):
935 data = list(data)
936 xbar = fmean(data)
937 return cls(xbar, stdev(data, xbar))
938
Raymond Hettingerfb8c7d52019-04-23 01:46:18 -0700939 def samples(self, n, *, seed=None):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700940 "Generate *n* samples for a given mean and standard deviation."
Raymond Hettinger11c79532019-02-23 14:44:07 -0800941 gauss = random.gauss if seed is None else random.Random(seed).gauss
Raymond Hettinger02c91f52019-07-21 00:34:47 -0700942 mu, sigma = self._mu, self._sigma
Raymond Hettinger11c79532019-02-23 14:44:07 -0800943 return [gauss(mu, sigma) for i in range(n)]
944
945 def pdf(self, x):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700946 "Probability density function. P(x <= X < x+dx) / dx"
Raymond Hettinger02c91f52019-07-21 00:34:47 -0700947 variance = self._sigma ** 2.0
Raymond Hettinger11c79532019-02-23 14:44:07 -0800948 if not variance:
949 raise StatisticsError('pdf() not defined when sigma is zero')
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700950 return exp((x - self._mu)**2.0 / (-2.0*variance)) / sqrt(tau*variance)
Raymond Hettinger11c79532019-02-23 14:44:07 -0800951
952 def cdf(self, x):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700953 "Cumulative distribution function. P(X <= x)"
Raymond Hettinger02c91f52019-07-21 00:34:47 -0700954 if not self._sigma:
Raymond Hettinger11c79532019-02-23 14:44:07 -0800955 raise StatisticsError('cdf() not defined when sigma is zero')
Raymond Hettinger02c91f52019-07-21 00:34:47 -0700956 return 0.5 * (1.0 + erf((x - self._mu) / (self._sigma * sqrt(2.0))))
Raymond Hettinger11c79532019-02-23 14:44:07 -0800957
Raymond Hettinger714c60d2019-03-18 20:17:14 -0700958 def inv_cdf(self, p):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700959 """Inverse cumulative distribution function. x : P(X <= x) = p
Raymond Hettinger714c60d2019-03-18 20:17:14 -0700960
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700961 Finds the value of the random variable such that the probability of
962 the variable being less than or equal to that value equals the given
963 probability.
Raymond Hettinger714c60d2019-03-18 20:17:14 -0700964
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700965 This function is also called the percent point function or quantile
966 function.
967 """
968 if p <= 0.0 or p >= 1.0:
Raymond Hettinger714c60d2019-03-18 20:17:14 -0700969 raise StatisticsError('p must be in the range 0.0 < p < 1.0')
Raymond Hettinger02c91f52019-07-21 00:34:47 -0700970 if self._sigma <= 0.0:
Raymond Hettinger714c60d2019-03-18 20:17:14 -0700971 raise StatisticsError('cdf() not defined when sigma at or below zero')
Dong-hee Na0a18ee42019-08-24 07:20:30 +0900972 return _normal_dist_inv_cdf(p, self._mu, self._sigma)
Raymond Hettinger714c60d2019-03-18 20:17:14 -0700973
Raymond Hettinger4db25d52019-09-08 16:57:58 -0700974 def quantiles(self, n=4):
975 """Divide into *n* continuous intervals with equal probability.
976
977 Returns a list of (n - 1) cut points separating the intervals.
978
979 Set *n* to 4 for quartiles (the default). Set *n* to 10 for deciles.
980 Set *n* to 100 for percentiles which gives the 99 cuts points that
981 separate the normal distribution in to 100 equal sized groups.
982 """
983 return [self.inv_cdf(i / n) for i in range(1, n)]
984
Raymond Hettinger318d5372019-03-06 22:59:40 -0800985 def overlap(self, other):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700986 """Compute the overlapping coefficient (OVL) between two normal distributions.
Raymond Hettinger318d5372019-03-06 22:59:40 -0800987
988 Measures the agreement between two normal probability distributions.
989 Returns a value between 0.0 and 1.0 giving the overlapping area in
990 the two underlying probability density functions.
991
992 >>> N1 = NormalDist(2.4, 1.6)
993 >>> N2 = NormalDist(3.2, 2.0)
994 >>> N1.overlap(N2)
995 0.8035050657330205
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -0700996 """
Raymond Hettinger318d5372019-03-06 22:59:40 -0800997 # See: "The overlapping coefficient as a measure of agreement between
998 # probability distributions and point estimation of the overlap of two
999 # normal densities" -- Henry F. Inman and Edwin L. Bradley Jr
1000 # http://dx.doi.org/10.1080/03610928908830127
1001 if not isinstance(other, NormalDist):
1002 raise TypeError('Expected another NormalDist instance')
1003 X, Y = self, other
Raymond Hettinger5aad0272020-06-13 19:17:28 -07001004 if (Y._sigma, Y._mu) < (X._sigma, X._mu): # sort to assure commutativity
Raymond Hettinger318d5372019-03-06 22:59:40 -08001005 X, Y = Y, X
1006 X_var, Y_var = X.variance, Y.variance
1007 if not X_var or not Y_var:
1008 raise StatisticsError('overlap() not defined when sigma is zero')
1009 dv = Y_var - X_var
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001010 dm = fabs(Y._mu - X._mu)
Raymond Hettinger318d5372019-03-06 22:59:40 -08001011 if not dv:
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001012 return 1.0 - erf(dm / (2.0 * X._sigma * sqrt(2.0)))
1013 a = X._mu * Y_var - Y._mu * X_var
1014 b = X._sigma * Y._sigma * sqrt(dm**2.0 + dv * log(Y_var / X_var))
Raymond Hettinger318d5372019-03-06 22:59:40 -08001015 x1 = (a + b) / dv
1016 x2 = (a - b) / dv
1017 return 1.0 - (fabs(Y.cdf(x1) - X.cdf(x1)) + fabs(Y.cdf(x2) - X.cdf(x2)))
1018
Raymond Hettinger70f027d2020-04-16 10:25:14 -07001019 def zscore(self, x):
1020 """Compute the Standard Score. (x - mean) / stdev
1021
1022 Describes *x* in terms of the number of standard deviations
1023 above or below the mean of the normal distribution.
1024 """
1025 # https://www.statisticshowto.com/probability-and-statistics/z-score/
1026 if not self._sigma:
1027 raise StatisticsError('zscore() not defined when sigma is zero')
1028 return (x - self._mu) / self._sigma
1029
Raymond Hettinger11c79532019-02-23 14:44:07 -08001030 @property
Raymond Hettinger9e456bc2019-02-24 11:44:55 -08001031 def mean(self):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001032 "Arithmetic mean of the normal distribution."
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001033 return self._mu
Raymond Hettinger9e456bc2019-02-24 11:44:55 -08001034
1035 @property
Raymond Hettinger4db25d52019-09-08 16:57:58 -07001036 def median(self):
1037 "Return the median of the normal distribution"
1038 return self._mu
1039
1040 @property
1041 def mode(self):
1042 """Return the mode of the normal distribution
1043
1044 The mode is the value x where which the probability density
1045 function (pdf) takes its maximum value.
1046 """
1047 return self._mu
1048
1049 @property
Raymond Hettinger9e456bc2019-02-24 11:44:55 -08001050 def stdev(self):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001051 "Standard deviation of the normal distribution."
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001052 return self._sigma
Raymond Hettinger9e456bc2019-02-24 11:44:55 -08001053
1054 @property
Raymond Hettinger11c79532019-02-23 14:44:07 -08001055 def variance(self):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001056 "Square of the standard deviation."
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001057 return self._sigma ** 2.0
Raymond Hettinger11c79532019-02-23 14:44:07 -08001058
1059 def __add__(x1, x2):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001060 """Add a constant or another NormalDist instance.
Raymond Hettinger5f1e8b42019-03-18 22:24:15 -07001061
1062 If *other* is a constant, translate mu by the constant,
1063 leaving sigma unchanged.
1064
1065 If *other* is a NormalDist, add both the means and the variances.
1066 Mathematically, this works only if the two distributions are
1067 independent or if they are jointly normally distributed.
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001068 """
Raymond Hettinger11c79532019-02-23 14:44:07 -08001069 if isinstance(x2, NormalDist):
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001070 return NormalDist(x1._mu + x2._mu, hypot(x1._sigma, x2._sigma))
1071 return NormalDist(x1._mu + x2, x1._sigma)
Raymond Hettinger11c79532019-02-23 14:44:07 -08001072
1073 def __sub__(x1, x2):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001074 """Subtract a constant or another NormalDist instance.
Raymond Hettinger5f1e8b42019-03-18 22:24:15 -07001075
1076 If *other* is a constant, translate by the constant mu,
1077 leaving sigma unchanged.
1078
1079 If *other* is a NormalDist, subtract the means and add the variances.
1080 Mathematically, this works only if the two distributions are
1081 independent or if they are jointly normally distributed.
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001082 """
Raymond Hettinger11c79532019-02-23 14:44:07 -08001083 if isinstance(x2, NormalDist):
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001084 return NormalDist(x1._mu - x2._mu, hypot(x1._sigma, x2._sigma))
1085 return NormalDist(x1._mu - x2, x1._sigma)
Raymond Hettinger11c79532019-02-23 14:44:07 -08001086
1087 def __mul__(x1, x2):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001088 """Multiply both mu and sigma by a constant.
Raymond Hettinger5f1e8b42019-03-18 22:24:15 -07001089
1090 Used for rescaling, perhaps to change measurement units.
1091 Sigma is scaled with the absolute value of the constant.
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001092 """
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001093 return NormalDist(x1._mu * x2, x1._sigma * fabs(x2))
Raymond Hettinger11c79532019-02-23 14:44:07 -08001094
1095 def __truediv__(x1, x2):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001096 """Divide both mu and sigma by a constant.
Raymond Hettinger5f1e8b42019-03-18 22:24:15 -07001097
1098 Used for rescaling, perhaps to change measurement units.
1099 Sigma is scaled with the absolute value of the constant.
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001100 """
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001101 return NormalDist(x1._mu / x2, x1._sigma / fabs(x2))
Raymond Hettinger11c79532019-02-23 14:44:07 -08001102
1103 def __pos__(x1):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001104 "Return a copy of the instance."
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001105 return NormalDist(x1._mu, x1._sigma)
Raymond Hettinger11c79532019-02-23 14:44:07 -08001106
1107 def __neg__(x1):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001108 "Negates mu while keeping sigma the same."
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001109 return NormalDist(-x1._mu, x1._sigma)
Raymond Hettinger11c79532019-02-23 14:44:07 -08001110
1111 __radd__ = __add__
1112
1113 def __rsub__(x1, x2):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001114 "Subtract a NormalDist from a constant or another NormalDist."
Raymond Hettinger11c79532019-02-23 14:44:07 -08001115 return -(x1 - x2)
1116
1117 __rmul__ = __mul__
1118
1119 def __eq__(x1, x2):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001120 "Two NormalDist objects are equal if their mu and sigma are both equal."
Raymond Hettinger11c79532019-02-23 14:44:07 -08001121 if not isinstance(x2, NormalDist):
1122 return NotImplemented
Raymond Hettinger5eabec02019-10-18 14:20:35 -07001123 return x1._mu == x2._mu and x1._sigma == x2._sigma
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001124
1125 def __hash__(self):
Raymond Hettinger1c0e9bb2019-07-21 12:13:07 -07001126 "NormalDist objects hash equal if their mu and sigma are both equal."
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001127 return hash((self._mu, self._sigma))
Raymond Hettinger11c79532019-02-23 14:44:07 -08001128
1129 def __repr__(self):
Raymond Hettinger02c91f52019-07-21 00:34:47 -07001130 return f'{type(self).__name__}(mu={self._mu!r}, sigma={self._sigma!r})'