Mercurial > repos > guerler > springsuite
annotate planemo/lib/python3.7/site-packages/boltons/statsutils.py @ 0:d30785e31577 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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| date | Fri, 31 Jul 2020 00:18:57 -0400 | 
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changeset | 1 # -*- coding: utf-8 -*- | 
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changeset | 2 """``statsutils`` provides tools aimed primarily at descriptive | 
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changeset | 3 statistics for data analysis, such as :func:`mean` (average), | 
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changeset | 4 :func:`median`, :func:`variance`, and many others, | 
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changeset | 5 | 
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changeset | 6 The :class:`Stats` type provides all the main functionality of the | 
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changeset | 7 ``statsutils`` module. A :class:`Stats` object wraps a given dataset, | 
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changeset | 8 providing all statistical measures as property attributes. These | 
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changeset | 9 attributes cache their results, which allows efficient computation of | 
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changeset | 10 multiple measures, as many measures rely on other measures. For | 
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changeset | 11 example, relative standard deviation (:attr:`Stats.rel_std_dev`) | 
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changeset | 12 relies on both the mean and standard deviation. The Stats object | 
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changeset | 13 caches those results so no rework is done. | 
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changeset | 14 | 
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changeset | 15 The :class:`Stats` type's attributes have module-level counterparts for | 
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changeset | 16 convenience when the computation reuse advantages do not apply. | 
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changeset | 17 | 
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changeset | 18 >>> stats = Stats(range(42)) | 
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changeset | 19 >>> stats.mean | 
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changeset | 20 20.5 | 
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changeset | 21 >>> mean(range(42)) | 
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changeset | 22 20.5 | 
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changeset | 23 | 
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changeset | 24 Statistics is a large field, and ``statsutils`` is focused on a few | 
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changeset | 25 basic techniques that are useful in software. The following is a brief | 
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changeset | 26 introduction to those techniques. For a more in-depth introduction, | 
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changeset | 27 `Statistics for Software | 
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changeset | 28 <https://www.paypal-engineering.com/2016/04/11/statistics-for-software/>`_, | 
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changeset | 29 an article I wrote on the topic. It introduces key terminology vital | 
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changeset | 30 to effective usage of statistics. | 
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changeset | 31 | 
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changeset | 32 Statistical moments | 
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changeset | 33 ------------------- | 
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changeset | 34 | 
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changeset | 35 Python programmers are probably familiar with the concept of the | 
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changeset | 36 *mean* or *average*, which gives a rough quantitiative middle value by | 
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changeset | 37 which a sample can be can be generalized. However, the mean is just | 
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changeset | 38 the first of four `moment`_-based measures by which a sample or | 
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changeset | 39 distribution can be measured. | 
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changeset | 40 | 
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changeset | 41 The four `Standardized moments`_ are: | 
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changeset | 42 | 
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changeset | 43 1. `Mean`_ - :func:`mean` - theoretical middle value | 
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changeset | 44 2. `Variance`_ - :func:`variance` - width of value dispersion | 
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changeset | 45 3. `Skewness`_ - :func:`skewness` - symmetry of distribution | 
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changeset | 46 4. `Kurtosis`_ - :func:`kurtosis` - "peakiness" or "long-tailed"-ness | 
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changeset | 47 | 
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changeset | 48 For more information check out `the Moment article on Wikipedia`_. | 
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changeset | 49 | 
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changeset | 50 .. _moment: https://en.wikipedia.org/wiki/Moment_(mathematics) | 
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changeset | 51 .. _Standardized moments: https://en.wikipedia.org/wiki/Standardized_moment | 
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changeset | 52 .. _Mean: https://en.wikipedia.org/wiki/Mean | 
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changeset | 53 .. _Variance: https://en.wikipedia.org/wiki/Variance | 
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changeset | 54 .. _Skewness: https://en.wikipedia.org/wiki/Skewness | 
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changeset | 55 .. _Kurtosis: https://en.wikipedia.org/wiki/Kurtosis | 
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changeset | 56 .. _the Moment article on Wikipedia: https://en.wikipedia.org/wiki/Moment_(mathematics) | 
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changeset | 57 | 
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changeset | 58 Keep in mind that while these moments can give a bit more insight into | 
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changeset | 59 the shape and distribution of data, they do not guarantee a complete | 
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changeset | 60 picture. Wildly different datasets can have the same values for all | 
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changeset | 61 four moments, so generalize wisely. | 
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changeset | 62 | 
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changeset | 63 Robust statistics | 
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changeset | 64 ----------------- | 
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changeset | 65 | 
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changeset | 66 Moment-based statistics are notorious for being easily skewed by | 
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changeset | 67 outliers. The whole field of robust statistics aims to mitigate this | 
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changeset | 68 dilemma. ``statsutils`` also includes several robust statistical methods: | 
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changeset | 69 | 
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changeset | 70 * `Median`_ - The middle value of a sorted dataset | 
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changeset | 71 * `Trimean`_ - Another robust measure of the data's central tendency | 
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changeset | 72 * `Median Absolute Deviation`_ (MAD) - A robust measure of | 
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changeset | 73 variability, a natural counterpart to :func:`variance`. | 
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changeset | 74 * `Trimming`_ - Reducing a dataset to only the middle majority of | 
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changeset | 75 data is a simple way of making other estimators more robust. | 
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changeset | 76 | 
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changeset | 77 .. _Median: https://en.wikipedia.org/wiki/Median | 
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changeset | 78 .. _Trimean: https://en.wikipedia.org/wiki/Trimean | 
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changeset | 79 .. _Median Absolute Deviation: https://en.wikipedia.org/wiki/Median_absolute_deviation | 
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changeset | 80 .. _Trimming: https://en.wikipedia.org/wiki/Trimmed_estimator | 
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changeset | 81 | 
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changeset | 82 | 
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changeset | 83 Online and Offline Statistics | 
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changeset | 84 ----------------------------- | 
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changeset | 85 | 
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changeset | 86 Unrelated to computer networking, `online`_ statistics involve | 
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changeset | 87 calculating statistics in a `streaming`_ fashion, without all the data | 
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changeset | 88 being available. The :class:`Stats` type is meant for the more | 
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changeset | 89 traditional offline statistics when all the data is available. For | 
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changeset | 90 pure-Python online statistics accumulators, look at the `Lithoxyl`_ | 
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changeset | 91 system instrumentation package. | 
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changeset | 92 | 
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changeset | 93 .. _Online: https://en.wikipedia.org/wiki/Online_algorithm | 
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changeset | 94 .. _streaming: https://en.wikipedia.org/wiki/Streaming_algorithm | 
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changeset | 95 .. _Lithoxyl: https://github.com/mahmoud/lithoxyl | 
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changeset | 96 | 
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changeset | 97 """ | 
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changeset | 98 | 
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changeset | 99 from __future__ import print_function | 
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changeset | 100 | 
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changeset | 101 import bisect | 
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changeset | 102 from math import floor, ceil | 
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changeset | 103 | 
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changeset | 104 | 
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changeset | 105 class _StatsProperty(object): | 
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changeset | 106 def __init__(self, name, func): | 
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changeset | 107 self.name = name | 
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changeset | 108 self.func = func | 
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changeset | 109 self.internal_name = '_' + name | 
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changeset | 110 | 
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changeset | 111 doc = func.__doc__ or '' | 
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changeset | 112 pre_doctest_doc, _, _ = doc.partition('>>>') | 
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changeset | 113 self.__doc__ = pre_doctest_doc | 
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changeset | 114 | 
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changeset | 115 def __get__(self, obj, objtype=None): | 
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changeset | 116 if obj is None: | 
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changeset | 117 return self | 
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changeset | 118 if not obj.data: | 
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changeset | 119 return obj.default | 
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changeset | 120 try: | 
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changeset | 121 return getattr(obj, self.internal_name) | 
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changeset | 122 except AttributeError: | 
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changeset | 123 setattr(obj, self.internal_name, self.func(obj)) | 
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changeset | 124 return getattr(obj, self.internal_name) | 
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changeset | 125 | 
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changeset | 126 | 
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changeset | 127 class Stats(object): | 
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changeset | 128 """The ``Stats`` type is used to represent a group of unordered | 
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changeset | 129 statistical datapoints for calculations such as mean, median, and | 
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changeset | 130 variance. | 
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changeset | 131 | 
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changeset | 132 Args: | 
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changeset | 133 | 
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changeset | 134 data (list): List or other iterable containing numeric values. | 
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changeset | 135 default (float): A value to be returned when a given | 
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changeset | 136 statistical measure is not defined. 0.0 by default, but | 
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changeset | 137 ``float('nan')`` is appropriate for stricter applications. | 
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changeset | 138 use_copy (bool): By default Stats objects copy the initial | 
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changeset | 139 data into a new list to avoid issues with | 
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changeset | 140 modifications. Pass ``False`` to disable this behavior. | 
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changeset | 141 is_sorted (bool): Presorted data can skip an extra sorting | 
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changeset | 142 step for a little speed boost. Defaults to False. | 
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changeset | 143 | 
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changeset | 144 """ | 
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changeset | 145 def __init__(self, data, default=0.0, use_copy=True, is_sorted=False): | 
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changeset | 146 self._use_copy = use_copy | 
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changeset | 147 self._is_sorted = is_sorted | 
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changeset | 148 if use_copy: | 
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changeset | 149 self.data = list(data) | 
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changeset | 150 else: | 
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changeset | 151 self.data = data | 
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changeset | 152 | 
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changeset | 153 self.default = default | 
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changeset | 154 cls = self.__class__ | 
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changeset | 155 self._prop_attr_names = [a for a in dir(self) | 
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changeset | 156 if isinstance(getattr(cls, a, None), | 
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changeset | 157 _StatsProperty)] | 
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changeset | 158 self._pearson_precision = 0 | 
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changeset | 159 | 
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changeset | 160 def __len__(self): | 
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changeset | 161 return len(self.data) | 
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changeset | 162 | 
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changeset | 163 def __iter__(self): | 
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changeset | 164 return iter(self.data) | 
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changeset | 165 | 
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changeset | 166 def _get_sorted_data(self): | 
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changeset | 167 """When using a copy of the data, it's better to have that copy be | 
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changeset | 168 sorted, but we do it lazily using this method, in case no | 
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changeset | 169 sorted measures are used. I.e., if median is never called, | 
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changeset | 170 sorting would be a waste. | 
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changeset | 171 | 
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changeset | 172 When not using a copy, it's presumed that all optimizations | 
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changeset | 173 are on the user. | 
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changeset | 174 """ | 
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changeset | 175 if not self._use_copy: | 
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changeset | 176 return sorted(self.data) | 
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changeset | 177 elif not self._is_sorted: | 
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changeset | 178 self.data.sort() | 
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changeset | 179 return self.data | 
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changeset | 180 | 
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changeset | 181 def clear_cache(self): | 
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changeset | 182 """``Stats`` objects automatically cache intermediary calculations | 
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changeset | 183 that can be reused. For instance, accessing the ``std_dev`` | 
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changeset | 184 attribute after the ``variance`` attribute will be | 
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changeset | 185 significantly faster for medium-to-large datasets. | 
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changeset | 186 | 
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changeset | 187 If you modify the object by adding additional data points, | 
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changeset | 188 call this function to have the cached statistics recomputed. | 
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changeset | 189 | 
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changeset | 190 """ | 
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changeset | 191 for attr_name in self._prop_attr_names: | 
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changeset | 192 attr_name = getattr(self.__class__, attr_name).internal_name | 
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changeset | 193 if not hasattr(self, attr_name): | 
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changeset | 194 continue | 
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changeset | 195 delattr(self, attr_name) | 
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changeset | 196 return | 
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changeset | 197 | 
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changeset | 198 def _calc_count(self): | 
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changeset | 199 """The number of items in this Stats object. Returns the same as | 
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changeset | 200 :func:`len` on a Stats object, but provided for pandas terminology | 
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changeset | 201 parallelism. | 
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changeset | 202 | 
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changeset | 203 >>> Stats(range(20)).count | 
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changeset | 204 20 | 
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changeset | 205 """ | 
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changeset | 206 return len(self.data) | 
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changeset | 207 count = _StatsProperty('count', _calc_count) | 
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changeset | 208 | 
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changeset | 209 def _calc_mean(self): | 
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changeset | 210 """ | 
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changeset | 211 The arithmetic mean, or "average". Sum of the values divided by | 
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changeset | 212 the number of values. | 
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changeset | 213 | 
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changeset | 214 >>> mean(range(20)) | 
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changeset | 215 9.5 | 
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changeset | 216 >>> mean(list(range(19)) + [949]) # 949 is an arbitrary outlier | 
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changeset | 217 56.0 | 
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changeset | 218 """ | 
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changeset | 219 return sum(self.data, 0.0) / len(self.data) | 
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changeset | 220 mean = _StatsProperty('mean', _calc_mean) | 
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changeset | 221 | 
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changeset | 222 def _calc_max(self): | 
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changeset | 223 """ | 
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changeset | 224 The maximum value present in the data. | 
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changeset | 225 | 
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changeset | 226 >>> Stats([2, 1, 3]).max | 
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changeset | 227 3 | 
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changeset | 228 """ | 
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changeset | 229 if self._is_sorted: | 
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changeset | 230 return self.data[-1] | 
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changeset | 231 return max(self.data) | 
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changeset | 232 max = _StatsProperty('max', _calc_max) | 
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changeset | 233 | 
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changeset | 234 def _calc_min(self): | 
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changeset | 235 """ | 
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changeset | 236 The minimum value present in the data. | 
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changeset | 237 | 
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changeset | 238 >>> Stats([2, 1, 3]).min | 
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changeset | 239 1 | 
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changeset | 240 """ | 
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changeset | 241 if self._is_sorted: | 
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changeset | 242 return self.data[0] | 
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changeset | 243 return min(self.data) | 
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changeset | 244 min = _StatsProperty('min', _calc_min) | 
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changeset | 245 | 
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changeset | 246 def _calc_median(self): | 
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changeset | 247 """ | 
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changeset | 248 The median is either the middle value or the average of the two | 
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changeset | 249 middle values of a sample. Compared to the mean, it's generally | 
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changeset | 250 more resilient to the presence of outliers in the sample. | 
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changeset | 251 | 
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changeset | 252 >>> median([2, 1, 3]) | 
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changeset | 253 2 | 
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changeset | 254 >>> median(range(97)) | 
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changeset | 255 48 | 
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changeset | 256 >>> median(list(range(96)) + [1066]) # 1066 is an arbitrary outlier | 
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changeset | 257 48 | 
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changeset | 258 """ | 
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changeset | 259 return self._get_quantile(self._get_sorted_data(), 0.5) | 
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changeset | 260 median = _StatsProperty('median', _calc_median) | 
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changeset | 261 | 
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changeset | 262 def _calc_iqr(self): | 
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changeset | 263 """Inter-quartile range (IQR) is the difference between the 75th | 
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changeset | 264 percentile and 25th percentile. IQR is a robust measure of | 
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changeset | 265 dispersion, like standard deviation, but safer to compare | 
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changeset | 266 between datasets, as it is less influenced by outliers. | 
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changeset | 267 | 
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changeset | 268 >>> iqr([1, 2, 3, 4, 5]) | 
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changeset | 269 2 | 
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changeset | 270 >>> iqr(range(1001)) | 
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changeset | 271 500 | 
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changeset | 272 """ | 
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changeset | 273 return self.get_quantile(0.75) - self.get_quantile(0.25) | 
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changeset | 274 iqr = _StatsProperty('iqr', _calc_iqr) | 
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changeset | 275 | 
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changeset | 276 def _calc_trimean(self): | 
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changeset | 277 """The trimean is a robust measure of central tendency, like the | 
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changeset | 278 median, that takes the weighted average of the median and the | 
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changeset | 279 upper and lower quartiles. | 
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changeset | 280 | 
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changeset | 281 >>> trimean([2, 1, 3]) | 
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changeset | 282 2.0 | 
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changeset | 283 >>> trimean(range(97)) | 
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changeset | 284 48.0 | 
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changeset | 285 >>> trimean(list(range(96)) + [1066]) # 1066 is an arbitrary outlier | 
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changeset | 286 48.0 | 
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changeset | 287 | 
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changeset | 288 """ | 
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changeset | 289 sorted_data = self._get_sorted_data() | 
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changeset | 290 gq = lambda q: self._get_quantile(sorted_data, q) | 
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changeset | 291 return (gq(0.25) + (2 * gq(0.5)) + gq(0.75)) / 4.0 | 
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changeset | 292 trimean = _StatsProperty('trimean', _calc_trimean) | 
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changeset | 293 | 
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changeset | 294 def _calc_variance(self): | 
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changeset | 295 """\ | 
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changeset | 296 Variance is the average of the squares of the difference between | 
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changeset | 297 each value and the mean. | 
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changeset | 298 | 
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changeset | 299 >>> variance(range(97)) | 
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changeset | 300 784.0 | 
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changeset | 301 """ | 
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changeset | 302 global mean # defined elsewhere in this file | 
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changeset | 303 return mean(self._get_pow_diffs(2)) | 
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changeset | 304 variance = _StatsProperty('variance', _calc_variance) | 
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changeset | 305 | 
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changeset | 306 def _calc_std_dev(self): | 
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changeset | 307 """\ | 
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changeset | 308 Standard deviation. Square root of the variance. | 
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changeset | 309 | 
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changeset | 310 >>> std_dev(range(97)) | 
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changeset | 311 28.0 | 
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changeset | 312 """ | 
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changeset | 313 return self.variance ** 0.5 | 
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changeset | 314 std_dev = _StatsProperty('std_dev', _calc_std_dev) | 
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changeset | 315 | 
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changeset | 316 def _calc_median_abs_dev(self): | 
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changeset | 317 """\ | 
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changeset | 318 Median Absolute Deviation is a robust measure of statistical | 
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changeset | 319 dispersion: http://en.wikipedia.org/wiki/Median_absolute_deviation | 
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changeset | 320 | 
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changeset | 321 >>> median_abs_dev(range(97)) | 
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changeset | 322 24.0 | 
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changeset | 323 """ | 
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changeset | 324 global median # defined elsewhere in this file | 
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changeset | 325 sorted_vals = sorted(self.data) | 
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changeset | 326 x = float(median(sorted_vals)) | 
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changeset | 327 return median([abs(x - v) for v in sorted_vals]) | 
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changeset | 328 median_abs_dev = _StatsProperty('median_abs_dev', _calc_median_abs_dev) | 
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changeset | 329 mad = median_abs_dev # convenience | 
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changeset | 330 | 
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changeset | 331 def _calc_rel_std_dev(self): | 
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changeset | 332 """\ | 
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changeset | 333 Standard deviation divided by the absolute value of the average. | 
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changeset | 334 | 
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changeset | 335 http://en.wikipedia.org/wiki/Relative_standard_deviation | 
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changeset | 336 | 
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changeset | 337 >>> print('%1.3f' % rel_std_dev(range(97))) | 
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changeset | 338 0.583 | 
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changeset | 339 """ | 
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changeset | 340 abs_mean = abs(self.mean) | 
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changeset | 341 if abs_mean: | 
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changeset | 342 return self.std_dev / abs_mean | 
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changeset | 343 else: | 
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changeset | 344 return self.default | 
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changeset | 345 rel_std_dev = _StatsProperty('rel_std_dev', _calc_rel_std_dev) | 
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changeset | 346 | 
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changeset | 347 def _calc_skewness(self): | 
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changeset | 348 """\ | 
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changeset | 349 Indicates the asymmetry of a curve. Positive values mean the bulk | 
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changeset | 350 of the values are on the left side of the average and vice versa. | 
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changeset | 351 | 
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changeset | 352 http://en.wikipedia.org/wiki/Skewness | 
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changeset | 353 | 
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changeset | 354 See the module docstring for more about statistical moments. | 
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changeset | 355 | 
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changeset | 356 >>> skewness(range(97)) # symmetrical around 48.0 | 
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changeset | 357 0.0 | 
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changeset | 358 >>> left_skewed = skewness(list(range(97)) + list(range(10))) | 
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changeset | 359 >>> right_skewed = skewness(list(range(97)) + list(range(87, 97))) | 
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changeset | 360 >>> round(left_skewed, 3), round(right_skewed, 3) | 
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changeset | 361 (0.114, -0.114) | 
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changeset | 362 """ | 
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changeset | 363 data, s_dev = self.data, self.std_dev | 
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changeset | 364 if len(data) > 1 and s_dev > 0: | 
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changeset | 365 return (sum(self._get_pow_diffs(3)) / | 
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changeset | 366 float((len(data) - 1) * (s_dev ** 3))) | 
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changeset | 367 else: | 
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changeset | 368 return self.default | 
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changeset | 369 skewness = _StatsProperty('skewness', _calc_skewness) | 
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changeset | 370 | 
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changeset | 371 def _calc_kurtosis(self): | 
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changeset | 372 """\ | 
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changeset | 373 Indicates how much data is in the tails of the distribution. The | 
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changeset | 374 result is always positive, with the normal "bell-curve" | 
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changeset | 375 distribution having a kurtosis of 3. | 
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changeset | 376 | 
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changeset | 377 http://en.wikipedia.org/wiki/Kurtosis | 
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changeset | 378 | 
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changeset | 379 See the module docstring for more about statistical moments. | 
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changeset | 380 | 
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changeset | 381 >>> kurtosis(range(9)) | 
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changeset | 382 1.99125 | 
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changeset | 383 | 
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changeset | 384 With a kurtosis of 1.99125, [0, 1, 2, 3, 4, 5, 6, 7, 8] is more | 
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changeset | 385 centrally distributed than the normal curve. | 
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changeset | 386 """ | 
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changeset | 387 data, s_dev = self.data, self.std_dev | 
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changeset | 388 if len(data) > 1 and s_dev > 0: | 
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changeset | 389 return (sum(self._get_pow_diffs(4)) / | 
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changeset | 390 float((len(data) - 1) * (s_dev ** 4))) | 
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changeset | 391 else: | 
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changeset | 392 return 0.0 | 
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changeset | 393 kurtosis = _StatsProperty('kurtosis', _calc_kurtosis) | 
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changeset | 394 | 
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changeset | 395 def _calc_pearson_type(self): | 
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changeset | 396 precision = self._pearson_precision | 
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changeset | 397 skewness = self.skewness | 
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changeset | 398 kurtosis = self.kurtosis | 
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changeset | 399 beta1 = skewness ** 2.0 | 
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changeset | 400 beta2 = kurtosis * 1.0 | 
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changeset | 401 | 
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changeset | 402 # TODO: range checks? | 
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changeset | 403 | 
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changeset | 404 c0 = (4 * beta2) - (3 * beta1) | 
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changeset | 405 c1 = skewness * (beta2 + 3) | 
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changeset | 406 c2 = (2 * beta2) - (3 * beta1) - 6 | 
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changeset | 407 | 
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changeset | 408 if round(c1, precision) == 0: | 
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changeset | 409 if round(beta2, precision) == 3: | 
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changeset | 410 return 0 # Normal | 
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changeset | 411 else: | 
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changeset | 412 if beta2 < 3: | 
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changeset | 413 return 2 # Symmetric Beta | 
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changeset | 414 elif beta2 > 3: | 
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changeset | 415 return 7 | 
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changeset | 416 elif round(c2, precision) == 0: | 
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changeset | 417 return 3 # Gamma | 
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changeset | 418 else: | 
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changeset | 419 k = c1 ** 2 / (4 * c0 * c2) | 
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changeset | 420 if k < 0: | 
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changeset | 421 return 1 # Beta | 
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changeset | 422 raise RuntimeError('missed a spot') | 
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changeset | 423 pearson_type = _StatsProperty('pearson_type', _calc_pearson_type) | 
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changeset | 424 | 
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changeset | 425 @staticmethod | 
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changeset | 426 def _get_quantile(sorted_data, q): | 
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changeset | 427 data, n = sorted_data, len(sorted_data) | 
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changeset | 428 idx = q / 1.0 * (n - 1) | 
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changeset | 429 idx_f, idx_c = int(floor(idx)), int(ceil(idx)) | 
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changeset | 430 if idx_f == idx_c: | 
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changeset | 431 return data[idx_f] | 
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changeset | 432 return (data[idx_f] * (idx_c - idx)) + (data[idx_c] * (idx - idx_f)) | 
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changeset | 433 | 
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changeset | 434 def get_quantile(self, q): | 
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changeset | 435 """Get a quantile from the dataset. Quantiles are floating point | 
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changeset | 436 values between ``0.0`` and ``1.0``, with ``0.0`` representing | 
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changeset | 437 the minimum value in the dataset and ``1.0`` representing the | 
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changeset | 438 maximum. ``0.5`` represents the median: | 
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changeset | 439 | 
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changeset | 440 >>> Stats(range(100)).get_quantile(0.5) | 
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changeset | 441 49.5 | 
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changeset | 442 """ | 
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changeset | 443 q = float(q) | 
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changeset | 444 if not 0.0 <= q <= 1.0: | 
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changeset | 445 raise ValueError('expected q between 0.0 and 1.0, not %r' % q) | 
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changeset | 446 elif not self.data: | 
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changeset | 447 return self.default | 
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changeset | 448 return self._get_quantile(self._get_sorted_data(), q) | 
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changeset | 449 | 
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changeset | 450 def get_zscore(self, value): | 
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changeset | 451 """Get the z-score for *value* in the group. If the standard deviation | 
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changeset | 452 is 0, 0 inf or -inf will be returned to indicate whether the value is | 
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changeset | 453 equal to, greater than or below the group's mean. | 
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changeset | 454 """ | 
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changeset | 455 mean = self.mean | 
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changeset | 456 if self.std_dev == 0: | 
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changeset | 457 if value == mean: | 
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changeset | 458 return 0 | 
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changeset | 459 if value > mean: | 
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changeset | 460 return float('inf') | 
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changeset | 461 if value < mean: | 
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changeset | 462 return float('-inf') | 
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changeset | 463 return (float(value) - mean) / self.std_dev | 
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changeset | 464 | 
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changeset | 465 def trim_relative(self, amount=0.15): | 
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changeset | 466 """A utility function used to cut a proportion of values off each end | 
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changeset | 467 of a list of values. This has the effect of limiting the | 
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changeset | 468 effect of outliers. | 
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changeset | 469 | 
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changeset | 470 Args: | 
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changeset | 471 amount (float): A value between 0.0 and 0.5 to trim off of | 
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changeset | 472 each side of the data. | 
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changeset | 473 | 
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changeset | 474 .. note: | 
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changeset | 475 | 
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changeset | 476 This operation modifies the data in-place. It does not | 
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changeset | 477 make or return a copy. | 
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changeset | 478 | 
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changeset | 479 """ | 
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changeset | 480 trim = float(amount) | 
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changeset | 481 if not 0.0 <= trim < 0.5: | 
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changeset | 482 raise ValueError('expected amount between 0.0 and 0.5, not %r' | 
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changeset | 483 % trim) | 
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changeset | 484 size = len(self.data) | 
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changeset | 485 size_diff = int(size * trim) | 
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changeset | 486 if size_diff == 0.0: | 
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changeset | 487 return | 
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changeset | 488 self.data = self._get_sorted_data()[size_diff:-size_diff] | 
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changeset | 489 self.clear_cache() | 
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changeset | 490 | 
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changeset | 491 def _get_pow_diffs(self, power): | 
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changeset | 492 """ | 
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changeset | 493 A utility function used for calculating statistical moments. | 
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changeset | 494 """ | 
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changeset | 495 m = self.mean | 
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changeset | 496 return [(v - m) ** power for v in self.data] | 
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changeset | 497 | 
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changeset | 498 def _get_bin_bounds(self, count=None, with_max=False): | 
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changeset | 499 if not self.data: | 
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changeset | 500 return [0.0] # TODO: raise? | 
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changeset | 501 | 
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changeset | 502 data = self.data | 
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changeset | 503 len_data, min_data, max_data = len(data), min(data), max(data) | 
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changeset | 504 | 
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changeset | 505 if len_data < 4: | 
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changeset | 506 if not count: | 
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changeset | 507 count = len_data | 
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changeset | 508 dx = (max_data - min_data) / float(count) | 
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changeset | 509 bins = [min_data + (dx * i) for i in range(count)] | 
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changeset | 510 elif count is None: | 
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changeset | 511 # freedman algorithm for fixed-width bin selection | 
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changeset | 512 q25, q75 = self.get_quantile(0.25), self.get_quantile(0.75) | 
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changeset | 513 dx = 2 * (q75 - q25) / (len_data ** (1 / 3.0)) | 
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changeset | 514 bin_count = max(1, int(ceil((max_data - min_data) / dx))) | 
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changeset | 515 bins = [min_data + (dx * i) for i in range(bin_count + 1)] | 
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changeset | 516 bins = [b for b in bins if b < max_data] | 
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changeset | 517 else: | 
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changeset | 518 dx = (max_data - min_data) / float(count) | 
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changeset | 519 bins = [min_data + (dx * i) for i in range(count)] | 
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changeset | 520 | 
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changeset | 521 if with_max: | 
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changeset | 522 bins.append(float(max_data)) | 
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changeset | 523 | 
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changeset | 524 return bins | 
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changeset | 525 | 
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changeset | 526 def get_histogram_counts(self, bins=None, **kw): | 
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changeset | 527 """Produces a list of ``(bin, count)`` pairs comprising a histogram of | 
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changeset | 528 the Stats object's data, using fixed-width bins. See | 
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changeset | 529 :meth:`Stats.format_histogram` for more details. | 
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changeset | 530 | 
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changeset | 531 Args: | 
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changeset | 532 bins (int): maximum number of bins, or list of | 
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changeset | 533 floating-point bin boundaries. Defaults to the output of | 
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changeset | 534 Freedman's algorithm. | 
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changeset | 535 bin_digits (int): Number of digits used to round down the | 
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changeset | 536 bin boundaries. Defaults to 1. | 
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changeset | 537 | 
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changeset | 538 The output of this method can be stored and/or modified, and | 
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changeset | 539 then passed to :func:`statsutils.format_histogram_counts` to | 
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changeset | 540 achieve the same text formatting as the | 
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changeset | 541 :meth:`~Stats.format_histogram` method. This can be useful for | 
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changeset | 542 snapshotting over time. | 
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changeset | 543 """ | 
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changeset | 544 bin_digits = int(kw.pop('bin_digits', 1)) | 
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changeset | 545 if kw: | 
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changeset | 546 raise TypeError('unexpected keyword arguments: %r' % kw.keys()) | 
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changeset | 547 | 
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changeset | 548 if not bins: | 
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changeset | 549 bins = self._get_bin_bounds() | 
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changeset | 550 else: | 
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changeset | 551 try: | 
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changeset | 552 bin_count = int(bins) | 
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changeset | 553 except TypeError: | 
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changeset | 554 try: | 
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changeset | 555 bins = [float(x) for x in bins] | 
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changeset | 556 except Exception: | 
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changeset | 557 raise ValueError('bins expected integer bin count or list' | 
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changeset | 558 ' of float bin boundaries, not %r' % bins) | 
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changeset | 559 if self.min < bins[0]: | 
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changeset | 560 bins = [self.min] + bins | 
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changeset | 561 else: | 
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changeset | 562 bins = self._get_bin_bounds(bin_count) | 
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changeset | 563 | 
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changeset | 564 # floor and ceil really should have taken ndigits, like round() | 
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changeset | 565 round_factor = 10.0 ** bin_digits | 
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changeset | 566 bins = [floor(b * round_factor) / round_factor for b in bins] | 
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changeset | 567 bins = sorted(set(bins)) | 
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changeset | 568 | 
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changeset | 569 idxs = [bisect.bisect(bins, d) - 1 for d in self.data] | 
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changeset | 570 count_map = {} # would have used Counter, but py26 support | 
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changeset | 571 for idx in idxs: | 
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changeset | 572 try: | 
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changeset | 573 count_map[idx] += 1 | 
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changeset | 574 except KeyError: | 
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changeset | 575 count_map[idx] = 1 | 
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changeset | 576 | 
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changeset | 577 bin_counts = [(b, count_map.get(i, 0)) for i, b in enumerate(bins)] | 
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changeset | 578 | 
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changeset | 579 return bin_counts | 
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changeset | 580 | 
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changeset | 581 def format_histogram(self, bins=None, **kw): | 
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changeset | 582 """Produces a textual histogram of the data, using fixed-width bins, | 
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changeset | 583 allowing for simple visualization, even in console environments. | 
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changeset | 584 | 
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changeset | 585 >>> data = list(range(20)) + list(range(5, 15)) + [10] | 
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changeset | 586 >>> print(Stats(data).format_histogram(width=30)) | 
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changeset | 587 0.0: 5 ######### | 
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changeset | 588 4.4: 8 ############### | 
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changeset | 589 8.9: 11 #################### | 
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changeset | 590 13.3: 5 ######### | 
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changeset | 591 17.8: 2 #### | 
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changeset | 592 | 
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changeset | 593 In this histogram, five values are between 0.0 and 4.4, eight | 
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changeset | 594 are between 4.4 and 8.9, and two values lie between 17.8 and | 
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changeset | 595 the max. | 
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changeset | 596 | 
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changeset | 597 You can specify the number of bins, or provide a list of | 
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changeset | 598 bin boundaries themselves. If no bins are provided, as in the | 
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changeset | 599 example above, `Freedman's algorithm`_ for bin selection is | 
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changeset | 600 used. | 
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changeset | 601 | 
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changeset | 602 Args: | 
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changeset | 603 bins (int): Maximum number of bins for the | 
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changeset | 604 histogram. Also accepts a list of floating-point | 
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changeset | 605 bin boundaries. If the minimum boundary is still | 
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changeset | 606 greater than the minimum value in the data, that | 
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changeset | 607 boundary will be implicitly added. Defaults to the bin | 
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changeset | 608 boundaries returned by `Freedman's algorithm`_. | 
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changeset | 609 bin_digits (int): Number of digits to round each bin | 
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changeset | 610 to. Note that bins are always rounded down to avoid | 
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changeset | 611 clipping any data. Defaults to 1. | 
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changeset | 612 width (int): integer number of columns in the longest line | 
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changeset | 613 in the histogram. Defaults to console width on Python | 
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changeset | 614 3.3+, or 80 if that is not available. | 
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changeset | 615 format_bin (callable): Called on each bin to create a | 
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changeset | 616 label for the final output. Use this function to add | 
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changeset | 617 units, such as "ms" for milliseconds. | 
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changeset | 618 | 
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changeset | 619 Should you want something more programmatically reusable, see | 
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changeset | 620 the :meth:`~Stats.get_histogram_counts` method, the output of | 
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changeset | 621 is used by format_histogram. The :meth:`~Stats.describe` | 
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changeset | 622 method is another useful summarization method, albeit less | 
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changeset | 623 visual. | 
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changeset | 624 | 
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changeset | 625 .. _Freedman's algorithm: https://en.wikipedia.org/wiki/Freedman%E2%80%93Diaconis_rule | 
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changeset | 626 """ | 
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changeset | 627 width = kw.pop('width', None) | 
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changeset | 628 format_bin = kw.pop('format_bin', None) | 
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changeset | 629 bin_counts = self.get_histogram_counts(bins=bins, **kw) | 
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changeset | 630 return format_histogram_counts(bin_counts, | 
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changeset | 631 width=width, | 
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changeset | 632 format_bin=format_bin) | 
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changeset | 633 | 
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changeset | 634 def describe(self, quantiles=None, format=None): | 
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changeset | 635 """Provides standard summary statistics for the data in the Stats | 
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changeset | 636 object, in one of several convenient formats. | 
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changeset | 637 | 
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changeset | 638 Args: | 
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changeset | 639 quantiles (list): A list of numeric values to use as | 
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changeset | 640 quantiles in the resulting summary. All values must be | 
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changeset | 641 0.0-1.0, with 0.5 representing the median. Defaults to | 
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changeset | 642 ``[0.25, 0.5, 0.75]``, representing the standard | 
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changeset | 643 quartiles. | 
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changeset | 644 format (str): Controls the return type of the function, | 
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changeset | 645 with one of three valid values: ``"dict"`` gives back | 
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changeset | 646 a :class:`dict` with the appropriate keys and | 
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changeset | 647 values. ``"list"`` is a list of key-value pairs in an | 
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changeset | 648 order suitable to pass to an OrderedDict or HTML | 
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changeset | 649 table. ``"text"`` converts the values to text suitable | 
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changeset | 650 for printing, as seen below. | 
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changeset | 651 | 
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changeset | 652 Here is the information returned by a default ``describe``, as | 
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changeset | 653 presented in the ``"text"`` format: | 
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changeset | 654 | 
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changeset | 655 >>> stats = Stats(range(1, 8)) | 
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changeset | 656 >>> print(stats.describe(format='text')) | 
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changeset | 657 count: 7 | 
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changeset | 658 mean: 4.0 | 
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changeset | 659 std_dev: 2.0 | 
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changeset | 660 mad: 2.0 | 
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changeset | 661 min: 1 | 
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changeset | 662 0.25: 2.5 | 
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changeset | 663 0.5: 4 | 
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changeset | 664 0.75: 5.5 | 
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changeset | 665 max: 7 | 
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changeset | 666 | 
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changeset | 667 For more advanced descriptive statistics, check out my blog | 
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changeset | 668 post on the topic `Statistics for Software | 
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changeset | 669 <https://www.paypal-engineering.com/2016/04/11/statistics-for-software/>`_. | 
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changeset | 670 | 
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changeset | 671 """ | 
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changeset | 672 if format is None: | 
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changeset | 673 format = 'dict' | 
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changeset | 674 elif format not in ('dict', 'list', 'text'): | 
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changeset | 675 raise ValueError('invalid format for describe,' | 
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changeset | 676 ' expected one of "dict"/"list"/"text", not %r' | 
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changeset | 677 % format) | 
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changeset | 678 quantiles = quantiles or [0.25, 0.5, 0.75] | 
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changeset | 679 q_items = [] | 
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changeset | 680 for q in quantiles: | 
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changeset | 681 q_val = self.get_quantile(q) | 
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changeset | 682 q_items.append((str(q), q_val)) | 
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changeset | 683 | 
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changeset | 684 items = [('count', self.count), | 
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changeset | 685 ('mean', self.mean), | 
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changeset | 686 ('std_dev', self.std_dev), | 
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changeset | 687 ('mad', self.mad), | 
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changeset | 688 ('min', self.min)] | 
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changeset | 689 | 
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changeset | 690 items.extend(q_items) | 
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changeset | 691 items.append(('max', self.max)) | 
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changeset | 692 if format == 'dict': | 
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changeset | 693 ret = dict(items) | 
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changeset | 694 elif format == 'list': | 
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changeset | 695 ret = items | 
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changeset | 696 elif format == 'text': | 
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changeset | 697 ret = '\n'.join(['%s%s' % ((label + ':').ljust(10), val) | 
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changeset | 698 for label, val in items]) | 
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changeset | 699 return ret | 
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changeset | 700 | 
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changeset | 701 | 
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changeset | 702 def describe(data, quantiles=None, format=None): | 
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changeset | 703 """A convenience function to get standard summary statistics useful | 
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changeset | 704 for describing most data. See :meth:`Stats.describe` for more | 
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changeset | 705 details. | 
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changeset | 706 | 
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changeset | 707 >>> print(describe(range(7), format='text')) | 
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changeset | 708 count: 7 | 
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changeset | 709 mean: 3.0 | 
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changeset | 710 std_dev: 2.0 | 
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changeset | 711 mad: 2.0 | 
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changeset | 712 min: 0 | 
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changeset | 713 0.25: 1.5 | 
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changeset | 714 0.5: 3 | 
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changeset | 715 0.75: 4.5 | 
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changeset | 716 max: 6 | 
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changeset | 717 | 
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changeset | 718 See :meth:`Stats.format_histogram` for another very useful | 
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changeset | 719 summarization that uses textual visualization. | 
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changeset | 720 """ | 
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changeset | 721 return Stats(data).describe(quantiles=quantiles, format=format) | 
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changeset | 722 | 
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changeset | 723 | 
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changeset | 724 def _get_conv_func(attr_name): | 
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changeset | 725 def stats_helper(data, default=0.0): | 
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changeset | 726 return getattr(Stats(data, default=default, use_copy=False), | 
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changeset | 727 attr_name) | 
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changeset | 728 return stats_helper | 
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changeset | 729 | 
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changeset | 730 | 
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changeset | 731 for attr_name, attr in list(Stats.__dict__.items()): | 
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changeset | 732 if isinstance(attr, _StatsProperty): | 
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changeset | 733 if attr_name in ('max', 'min', 'count'): # don't shadow builtins | 
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changeset | 734 continue | 
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changeset | 735 if attr_name in ('mad',): # convenience aliases | 
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changeset | 736 continue | 
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changeset | 737 func = _get_conv_func(attr_name) | 
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changeset | 738 func.__doc__ = attr.func.__doc__ | 
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changeset | 739 globals()[attr_name] = func | 
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changeset | 740 delattr(Stats, '_calc_' + attr_name) | 
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changeset | 741 # cleanup | 
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changeset | 742 del attr | 
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changeset | 743 del attr_name | 
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changeset | 744 del func | 
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changeset | 745 | 
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changeset | 746 | 
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changeset | 747 def format_histogram_counts(bin_counts, width=None, format_bin=None): | 
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changeset | 748 """The formatting logic behind :meth:`Stats.format_histogram`, which | 
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changeset | 749 takes the output of :meth:`Stats.get_histogram_counts`, and passes | 
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changeset | 750 them to this function. | 
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changeset | 751 | 
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changeset | 752 Args: | 
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changeset | 753 bin_counts (list): A list of bin values to counts. | 
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changeset | 754 width (int): Number of character columns in the text output, | 
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changeset | 755 defaults to 80 or console width in Python 3.3+. | 
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changeset | 756 format_bin (callable): Used to convert bin values into string | 
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changeset | 757 labels. | 
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changeset | 758 """ | 
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changeset | 759 lines = [] | 
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changeset | 760 if not format_bin: | 
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changeset | 761 format_bin = lambda v: v | 
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changeset | 762 if not width: | 
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changeset | 763 try: | 
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changeset | 764 import shutil # python 3 convenience | 
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changeset | 765 width = shutil.get_terminal_size()[0] | 
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changeset | 766 except Exception: | 
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changeset | 767 width = 80 | 
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changeset | 768 | 
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changeset | 769 bins = [b for b, _ in bin_counts] | 
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changeset | 770 count_max = max([count for _, count in bin_counts]) | 
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changeset | 771 count_cols = len(str(count_max)) | 
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changeset | 772 | 
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changeset | 773 labels = ['%s' % format_bin(b) for b in bins] | 
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changeset | 774 label_cols = max([len(l) for l in labels]) | 
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changeset | 775 tmp_line = '%s: %s #' % ('x' * label_cols, count_max) | 
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changeset | 776 | 
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changeset | 777 bar_cols = max(width - len(tmp_line), 3) | 
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changeset | 778 line_k = float(bar_cols) / count_max | 
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changeset | 779 tmpl = "{label:>{label_cols}}: {count:>{count_cols}} {bar}" | 
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changeset | 780 for label, (bin_val, count) in zip(labels, bin_counts): | 
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changeset | 781 bar_len = int(round(count * line_k)) | 
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changeset | 782 bar = ('#' * bar_len) or '|' | 
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changeset | 783 line = tmpl.format(label=label, | 
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changeset | 784 label_cols=label_cols, | 
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changeset | 785 count=count, | 
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changeset | 786 count_cols=count_cols, | 
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changeset | 787 bar=bar) | 
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changeset | 788 lines.append(line) | 
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changeset | 789 | 
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changeset | 790 return '\n'.join(lines) | 
