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| # Copyright (c) 2013, Mahmoud Hashemi | |
| # | |
| # Redistribution and use in source and binary forms, with or without | |
| # modification, are permitted provided that the following conditions are | |
| # met: | |
| # | |
| # * Redistributions of source code must retain the above copyright | |
| # notice, this list of conditions and the following disclaimer. | |
| # | |
| # * Redistributions in binary form must reproduce the above | |
| # copyright notice, this list of conditions and the following | |
| # disclaimer in the documentation and/or other materials provided | |
| # with the distribution. | |
| # | |
| # * The names of the contributors may not be used to endorse or | |
| # promote products derived from this software without specific | |
| # prior written permission. | |
| # | |
| # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS | |
| # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT | |
| # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR | |
| # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT | |
| # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, | |
| # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT | |
| # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, | |
| # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY | |
| # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | |
| # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
| # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| """``statsutils`` provides tools aimed primarily at descriptive | |
| statistics for data analysis, such as :func:`mean` (average), | |
| :func:`median`, :func:`mode`, :func:`variance`, and many others, | |
| The :class:`Stats` type provides all the main functionality of the | |
| ``statsutils`` module. A :class:`Stats` object wraps a given dataset, | |
| providing all statistical measures as property attributes. These | |
| attributes cache their results, which allows efficient computation of | |
| multiple measures, as many measures rely on other measures. For | |
| example, relative standard deviation (:attr:`Stats.rel_std_dev`) | |
| relies on both the mean and standard deviation. The Stats object | |
| caches those results so no rework is done. | |
| The :class:`Stats` type's attributes have module-level counterparts for | |
| convenience when the computation reuse advantages do not apply. | |
| stats = Stats(range(42)) | |
| stats.mean | |
| 20.5 | |
| mean(range(42)) | |
| 20.5 | |
| Statistics is a large field, and ``statsutils`` is focused on a few | |
| basic techniques that are useful in software. The following is a brief | |
| introduction to those techniques. For a more in-depth introduction, | |
| `Statistics for Software | |
| <https://www.paypal-engineering.com/2016/04/11/statistics-for-software/>`_, | |
| an article I wrote on the topic. It introduces key terminology vital | |
| to effective usage of statistics. | |
| Statistical moments | |
| ------------------- | |
| Python programmers are probably familiar with the concept of the | |
| *mean* or *average*, which gives a rough quantitiative middle value by | |
| which a sample can be can be generalized. However, the mean is just | |
| the first of four `moment`_-based measures by which a sample or | |
| distribution can be measured. | |
| The four `Standardized moments`_ are: | |
| 1. `Mean`_ - :func:`mean` - theoretical middle value | |
| 2. `Variance`_ - :func:`variance` - width of value dispersion | |
| 3. `Skewness`_ - :func:`skewness` - symmetry of distribution | |
| 4. `Kurtosis`_ - :func:`kurtosis` - "peakiness" or "long-tailed"-ness | |
| For more information check out `the Moment article on Wikipedia`_. | |
| .. _moment: https://en.wikipedia.org/wiki/Moment_(mathematics) | |
| .. _Standardized moments: https://en.wikipedia.org/wiki/Standardized_moment | |
| .. _Mean: https://en.wikipedia.org/wiki/Mean | |
| .. _Variance: https://en.wikipedia.org/wiki/Variance | |
| .. _Skewness: https://en.wikipedia.org/wiki/Skewness | |
| .. _Kurtosis: https://en.wikipedia.org/wiki/Kurtosis | |
| .. _the Moment article on Wikipedia: https://en.wikipedia.org/wiki/Moment_(mathematics) | |
| Keep in mind that while these moments can give a bit more insight into | |
| the shape and distribution of data, they do not guarantee a complete | |
| picture. Wildly different datasets can have the same values for all | |
| four moments, so generalize wisely. | |
| Robust statistics | |
| ----------------- | |
| Moment-based statistics are notorious for being easily skewed by | |
| outliers. The whole field of robust statistics aims to mitigate this | |
| dilemma. ``statsutils`` also includes several robust statistical methods: | |
| * `Median`_ - The middle value of a sorted dataset | |
| * `Trimean`_ - Another robust measure of the data's central tendency | |
| * `Median Absolute Deviation`_ (MAD) - A robust measure of | |
| variability, a natural counterpart to :func:`variance`. | |
| * `Trimming`_ - Reducing a dataset to only the middle majority of | |
| data is a simple way of making other estimators more robust. | |
| .. _Median: https://en.wikipedia.org/wiki/Median | |
| .. _Trimean: https://en.wikipedia.org/wiki/Trimean | |
| .. _Median Absolute Deviation: https://en.wikipedia.org/wiki/Median_absolute_deviation | |
| .. _Trimming: https://en.wikipedia.org/wiki/Trimmed_estimator | |
| Online and Offline Statistics | |
| ----------------------------- | |
| Unrelated to computer networking, `online`_ statistics involve | |
| calculating statistics in a `streaming`_ fashion, without all the data | |
| being available. The :class:`Stats` type is meant for the more | |
| traditional offline statistics when all the data is available. For | |
| pure-Python online statistics accumulators, look at the `Lithoxyl`_ | |
| system instrumentation package. | |
| .. _Online: https://en.wikipedia.org/wiki/Online_algorithm | |
| .. _streaming: https://en.wikipedia.org/wiki/Streaming_algorithm | |
| .. _Lithoxyl: https://github.com/mahmoud/lithoxyl | |
| """ | |
| import bisect | |
| from math import floor, ceil | |
| from collections import Counter | |
| class _StatsProperty: | |
| def __init__(self, name, func): | |
| self.name = name | |
| self.func = func | |
| self.internal_name = '_' + name | |
| doc = func.__doc__ or '' | |
| pre_doctest_doc, _, _ = doc.partition('>>>') | |
| self.__doc__ = pre_doctest_doc | |
| def __get__(self, obj, objtype=None): | |
| if obj is None: | |
| return self | |
| if not obj.data: | |
| return obj.default | |
| try: | |
| return getattr(obj, self.internal_name) | |
| except AttributeError: | |
| setattr(obj, self.internal_name, self.func(obj)) | |
| return getattr(obj, self.internal_name) | |
| class Stats: | |
| """The ``Stats`` type is used to represent a group of unordered | |
| statistical datapoints for calculations such as mean, median, and | |
| variance. | |
| Args: | |
| data (list): List or other iterable containing numeric values. | |
| default (float): A value to be returned when a given | |
| statistical measure is not defined. 0.0 by default, but | |
| ``float('nan')`` is appropriate for stricter applications. | |
| use_copy (bool): By default Stats objects copy the initial | |
| data into a new list to avoid issues with | |
| modifications. Pass ``False`` to disable this behavior. | |
| is_sorted (bool): Presorted data can skip an extra sorting | |
| step for a little speed boost. Defaults to False. | |
| """ | |
| def __init__(self, data, default=0.0, use_copy=True, is_sorted=False): | |
| self._use_copy = use_copy | |
| self._is_sorted = is_sorted | |
| if use_copy: | |
| self.data = list(data) | |
| else: | |
| self.data = data | |
| self.default = default | |
| cls = self.__class__ | |
| self._prop_attr_names = [a for a in dir(self) | |
| if isinstance(getattr(cls, a, None), | |
| _StatsProperty)] | |
| self._pearson_precision = 0 | |
| def __len__(self): | |
| return len(self.data) | |
| def __iter__(self): | |
| return iter(self.data) | |
| def _get_sorted_data(self): | |
| """When using a copy of the data, it's better to have that copy be | |
| sorted, but we do it lazily using this method, in case no | |
| sorted measures are used. I.e., if median is never called, | |
| sorting would be a waste. | |
| When not using a copy, it's presumed that all optimizations | |
| are on the user. | |
| """ | |
| if not self._use_copy: | |
| return sorted(self.data) | |
| elif not self._is_sorted: | |
| self.data.sort() | |
| return self.data | |
| def clear_cache(self): | |
| """``Stats`` objects automatically cache intermediary calculations | |
| that can be reused. For instance, accessing the ``std_dev`` | |
| attribute after the ``variance`` attribute will be | |
| significantly faster for medium-to-large datasets. | |
| If you modify the object by adding additional data points, | |
| call this function to have the cached statistics recomputed. | |
| """ | |
| for attr_name in self._prop_attr_names: | |
| attr_name = getattr(self.__class__, attr_name).internal_name | |
| if not hasattr(self, attr_name): | |
| continue | |
| delattr(self, attr_name) | |
| return | |
| def _calc_count(self): | |
| """The number of items in this Stats object. Returns the same as | |
| :func:`len` on a Stats object, but provided for pandas terminology | |
| parallelism. | |
| >>> Stats(range(20)).count | |
| 20 | |
| """ | |
| return len(self.data) | |
| count = _StatsProperty('count', _calc_count) | |
| def _calc_mean(self): | |
| """ | |
| The arithmetic mean, or "average". Sum of the values divided by | |
| the number of values. | |
| >>> mean(range(20)) | |
| 9.5 | |
| >>> mean(list(range(19)) + [949]) # 949 is an arbitrary outlier | |
| 56.0 | |
| """ | |
| return sum(self.data, 0.0) / len(self.data) | |
| mean = _StatsProperty('mean', _calc_mean) | |
| def _calc_max(self): | |
| """ | |
| The maximum value present in the data. | |
| >>> Stats([2, 1, 3]).max | |
| 3 | |
| """ | |
| if self._is_sorted: | |
| return self.data[-1] | |
| return max(self.data) | |
| max = _StatsProperty('max', _calc_max) | |
| def _calc_min(self): | |
| """ | |
| The minimum value present in the data. | |
| >>> Stats([2, 1, 3]).min | |
| 1 | |
| """ | |
| if self._is_sorted: | |
| return self.data[0] | |
| return min(self.data) | |
| min = _StatsProperty('min', _calc_min) | |
| def _calc_median(self): | |
| """ | |
| The median is either the middle value or the average of the two | |
| middle values of a sample. Compared to the mean, it's generally | |
| more resilient to the presence of outliers in the sample. | |
| >>> median([2, 1, 3]) | |
| 2 | |
| >>> median(range(97)) | |
| 48 | |
| >>> median(list(range(96)) + [1066]) # 1066 is an arbitrary outlier | |
| 48 | |
| """ | |
| return self._get_quantile(self._get_sorted_data(), 0.5) | |
| median = _StatsProperty('median', _calc_median) | |
| def _calc_mode(self): | |
| """ | |
| The mode is the value that appears most frequently in the | |
| data. Unlike the mean and median, the mode is well-defined for | |
| non-numeric, categorical data, too. | |
| >>> mode([2, 1, 3, 1]) | |
| 1 | |
| >>> mode(['a', 'b', 'b', 'c', 'c', 'c']) | |
| 'c' | |
| When several values are equally common, the one appearing | |
| first in the data is returned, matching the standard library's | |
| :func:`statistics.mode`. | |
| >>> mode([1, 1, 2, 2, 3]) | |
| 1 | |
| """ | |
| return Counter(self.data).most_common(1)[0][0] | |
| mode = _StatsProperty('mode', _calc_mode) | |
| def _calc_iqr(self): | |
| """Inter-quartile range (IQR) is the difference between the 75th | |
| percentile and 25th percentile. IQR is a robust measure of | |
| dispersion, like standard deviation, but safer to compare | |
| between datasets, as it is less influenced by outliers. | |
| >>> iqr([1, 2, 3, 4, 5]) | |
| 2 | |
| >>> iqr(range(1001)) | |
| 500 | |
| """ | |
| return self.get_quantile(0.75) - self.get_quantile(0.25) | |
| iqr = _StatsProperty('iqr', _calc_iqr) | |
| def _calc_trimean(self): | |
| """The trimean is a robust measure of central tendency, like the | |
| median, that takes the weighted average of the median and the | |
| upper and lower quartiles. | |
| >>> trimean([2, 1, 3]) | |
| 2.0 | |
| >>> trimean(range(97)) | |
| 48.0 | |
| >>> trimean(list(range(96)) + [1066]) # 1066 is an arbitrary outlier | |
| 48.0 | |
| """ | |
| sorted_data = self._get_sorted_data() | |
| gq = lambda q: self._get_quantile(sorted_data, q) | |
| return (gq(0.25) + (2 * gq(0.5)) + gq(0.75)) / 4.0 | |
| trimean = _StatsProperty('trimean', _calc_trimean) | |
| def _calc_variance(self): | |
| """\ | |
| Variance is the average of the squares of the difference between | |
| each value and the mean. | |
| >>> variance(range(97)) | |
| 784.0 | |
| """ | |
| global mean # defined elsewhere in this file | |
| return mean(self._get_pow_diffs(2)) | |
| variance = _StatsProperty('variance', _calc_variance) | |
| def _calc_std_dev(self): | |
| """\ | |
| Standard deviation. Square root of the variance. | |
| >>> std_dev(range(97)) | |
| 28.0 | |
| """ | |
| return self.variance ** 0.5 | |
| std_dev = _StatsProperty('std_dev', _calc_std_dev) | |
| def _calc_median_abs_dev(self): | |
| """\ | |
| Median Absolute Deviation is a robust measure of statistical | |
| dispersion: http://en.wikipedia.org/wiki/Median_absolute_deviation | |
| >>> median_abs_dev(range(97)) | |
| 24.0 | |
| """ | |
| global median # defined elsewhere in this file | |
| sorted_vals = sorted(self.data) | |
| x = float(median(sorted_vals)) | |
| return median([abs(x - v) for v in sorted_vals]) | |
| median_abs_dev = _StatsProperty('median_abs_dev', _calc_median_abs_dev) | |
| mad = median_abs_dev # convenience | |
| def _calc_rel_std_dev(self): | |
| """\ | |
| Standard deviation divided by the absolute value of the average. | |
| http://en.wikipedia.org/wiki/Relative_standard_deviation | |
| >>> print('%1.3f' % rel_std_dev(range(97))) | |
| 0.583 | |
| """ | |
| abs_mean = abs(self.mean) | |
| if abs_mean: | |
| return self.std_dev / abs_mean | |
| else: | |
| return self.default | |
| rel_std_dev = _StatsProperty('rel_std_dev', _calc_rel_std_dev) | |
| def _calc_skewness(self): | |
| """\ | |
| Indicates the asymmetry of a curve. Positive values mean the bulk | |
| of the values are on the left side of the average and vice versa. | |
| http://en.wikipedia.org/wiki/Skewness | |
| See the module docstring for more about statistical moments. | |
| >>> skewness(range(97)) # symmetrical around 48.0 | |
| 0.0 | |
| >>> left_skewed = skewness(list(range(97)) + list(range(10))) | |
| >>> right_skewed = skewness(list(range(97)) + list(range(87, 97))) | |
| >>> round(left_skewed, 3), round(right_skewed, 3) | |
| (0.114, -0.114) | |
| """ | |
| data, s_dev = self.data, self.std_dev | |
| if len(data) > 1 and s_dev > 0: | |
| return (sum(self._get_pow_diffs(3)) / | |
| float((len(data) - 1) * (s_dev ** 3))) | |
| else: | |
| return self.default | |
| skewness = _StatsProperty('skewness', _calc_skewness) | |
| def _calc_kurtosis(self): | |
| """\ | |
| Indicates how much data is in the tails of the distribution. The | |
| result is always positive, with the normal "bell-curve" | |
| distribution having a kurtosis of 3. | |
| http://en.wikipedia.org/wiki/Kurtosis | |
| See the module docstring for more about statistical moments. | |
| >>> kurtosis(range(9)) | |
| 1.99125 | |
| With a kurtosis of 1.99125, [0, 1, 2, 3, 4, 5, 6, 7, 8] is more | |
| centrally distributed than the normal curve. | |
| """ | |
| data, s_dev = self.data, self.std_dev | |
| if len(data) > 1 and s_dev > 0: | |
| return (sum(self._get_pow_diffs(4)) / | |
| float((len(data) - 1) * (s_dev ** 4))) | |
| else: | |
| return 0.0 | |
| kurtosis = _StatsProperty('kurtosis', _calc_kurtosis) | |
| def _calc_pearson_type(self): | |
| precision = self._pearson_precision | |
| skewness = self.skewness | |
| kurtosis = self.kurtosis | |
| beta1 = skewness ** 2.0 | |
| beta2 = kurtosis * 1.0 | |
| # TODO: range checks? | |
| c0 = (4 * beta2) - (3 * beta1) | |
| c1 = skewness * (beta2 + 3) | |
| c2 = (2 * beta2) - (3 * beta1) - 6 | |
| if round(c1, precision) == 0: | |
| if round(beta2, precision) == 3: | |
| return 0 # Normal | |
| else: | |
| if beta2 < 3: | |
| return 2 # Symmetric Beta | |
| elif beta2 > 3: | |
| return 7 | |
| elif round(c2, precision) == 0: | |
| return 3 # Gamma | |
| else: | |
| k = c1 ** 2 / (4 * c0 * c2) | |
| if k < 0: | |
| return 1 # Beta | |
| raise RuntimeError('missed a spot') | |
| pearson_type = _StatsProperty('pearson_type', _calc_pearson_type) | |
| def _get_quantile(sorted_data, q): | |
| data, n = sorted_data, len(sorted_data) | |
| idx = q / 1.0 * (n - 1) | |
| idx_f, idx_c = int(floor(idx)), int(ceil(idx)) | |
| if idx_f == idx_c: | |
| return data[idx_f] | |
| return (data[idx_f] * (idx_c - idx)) + (data[idx_c] * (idx - idx_f)) | |
| def get_quantile(self, q): | |
| """Get a quantile from the dataset. Quantiles are floating point | |
| values between ``0.0`` and ``1.0``, with ``0.0`` representing | |
| the minimum value in the dataset and ``1.0`` representing the | |
| maximum. ``0.5`` represents the median: | |
| >>> Stats(range(100)).get_quantile(0.5) | |
| 49.5 | |
| """ | |
| q = float(q) | |
| if not 0.0 <= q <= 1.0: | |
| raise ValueError('expected q between 0.0 and 1.0, not %r' % q) | |
| elif not self.data: | |
| return self.default | |
| return self._get_quantile(self._get_sorted_data(), q) | |
| def get_zscore(self, value): | |
| """Get the z-score for *value* in the group. If the standard deviation | |
| is 0, 0 inf or -inf will be returned to indicate whether the value is | |
| equal to, greater than or below the group's mean. | |
| """ | |
| mean = self.mean | |
| if self.std_dev == 0: | |
| if value == mean: | |
| return 0 | |
| if value > mean: | |
| return float('inf') | |
| if value < mean: | |
| return float('-inf') | |
| return (float(value) - mean) / self.std_dev | |
| def trim_relative(self, amount=0.15): | |
| """A utility function used to cut a proportion of values off each end | |
| of a list of values. This has the effect of limiting the | |
| effect of outliers. | |
| Args: | |
| amount (float): A value between 0.0 and 0.5 to trim off of | |
| each side of the data. | |
| .. note: | |
| This operation modifies the data in-place. It does not | |
| make or return a copy. | |
| """ | |
| trim = float(amount) | |
| if not 0.0 <= trim < 0.5: | |
| raise ValueError('expected amount between 0.0 and 0.5, not %r' | |
| % trim) | |
| size = len(self.data) | |
| size_diff = int(size * trim) | |
| if size_diff == 0.0: | |
| return | |
| self.data = self._get_sorted_data()[size_diff:-size_diff] | |
| self.clear_cache() | |
| def _get_pow_diffs(self, power): | |
| """ | |
| A utility function used for calculating statistical moments. | |
| """ | |
| m = self.mean | |
| return [(v - m) ** power for v in self.data] | |
| def _get_bin_bounds(self, count=None, with_max=False): | |
| if not self.data: | |
| return [0.0] # TODO: raise? | |
| data = self.data | |
| len_data, min_data, max_data = len(data), min(data), max(data) | |
| if len_data < 4: | |
| if not count: | |
| count = len_data | |
| dx = (max_data - min_data) / float(count) | |
| bins = [min_data + (dx * i) for i in range(count)] | |
| elif count is None: | |
| # freedman algorithm for fixed-width bin selection | |
| q25, q75 = self.get_quantile(0.25), self.get_quantile(0.75) | |
| dx = 2 * (q75 - q25) / (len_data ** (1 / 3.0)) | |
| bin_count = max(1, int(ceil((max_data - min_data) / dx))) | |
| bins = [min_data + (dx * i) for i in range(bin_count + 1)] | |
| bins = [b for b in bins if b < max_data] | |
| else: | |
| dx = (max_data - min_data) / float(count) | |
| bins = [min_data + (dx * i) for i in range(count)] | |
| if with_max: | |
| bins.append(float(max_data)) | |
| return bins | |
| def get_histogram_counts(self, bins=None, **kw): | |
| """Produces a list of ``(bin, count)`` pairs comprising a histogram of | |
| the Stats object's data, using fixed-width bins. See | |
| :meth:`Stats.format_histogram` for more details. | |
| Args: | |
| bins (int): maximum number of bins, or list of | |
| floating-point bin boundaries. Defaults to the output of | |
| Freedman's algorithm. | |
| bin_digits (int): Number of digits used to round down the | |
| bin boundaries. Defaults to 1. | |
| The output of this method can be stored and/or modified, and | |
| then passed to :func:`statsutils.format_histogram_counts` to | |
| achieve the same text formatting as the | |
| :meth:`~Stats.format_histogram` method. This can be useful for | |
| snapshotting over time. | |
| """ | |
| bin_digits = int(kw.pop('bin_digits', 1)) | |
| if kw: | |
| raise TypeError('unexpected keyword arguments: %r' % kw.keys()) | |
| if not bins: | |
| bins = self._get_bin_bounds() | |
| else: | |
| try: | |
| bin_count = int(bins) | |
| except TypeError: | |
| try: | |
| bins = [float(x) for x in bins] | |
| except Exception: | |
| raise ValueError('bins expected integer bin count or list' | |
| ' of float bin boundaries, not %r' % bins) | |
| if self.min < bins[0]: | |
| bins = [self.min] + bins | |
| else: | |
| bins = self._get_bin_bounds(bin_count) | |
| # floor and ceil really should have taken ndigits, like round() | |
| round_factor = 10.0 ** bin_digits | |
| bins = [floor(b * round_factor) / round_factor for b in bins] | |
| bins = sorted(set(bins)) | |
| idxs = [bisect.bisect(bins, d) - 1 for d in self.data] | |
| count_map = Counter(idxs) | |
| bin_counts = [(b, count_map.get(i, 0)) for i, b in enumerate(bins)] | |
| return bin_counts | |
| def format_histogram(self, bins=None, **kw): | |
| """Produces a textual histogram of the data, using fixed-width bins, | |
| allowing for simple visualization, even in console environments. | |
| >>> data = list(range(20)) + list(range(5, 15)) + [10] | |
| >>> print(Stats(data).format_histogram(width=30)) | |
| 0.0: 5 ######### | |
| 4.4: 8 ############### | |
| 8.9: 11 #################### | |
| 13.3: 5 ######### | |
| 17.8: 2 #### | |
| In this histogram, five values are between 0.0 and 4.4, eight | |
| are between 4.4 and 8.9, and two values lie between 17.8 and | |
| the max. | |
| You can specify the number of bins, or provide a list of | |
| bin boundaries themselves. If no bins are provided, as in the | |
| example above, `Freedman's algorithm`_ for bin selection is | |
| used. | |
| Args: | |
| bins (int): Maximum number of bins for the | |
| histogram. Also accepts a list of floating-point | |
| bin boundaries. If the minimum boundary is still | |
| greater than the minimum value in the data, that | |
| boundary will be implicitly added. Defaults to the bin | |
| boundaries returned by `Freedman's algorithm`_. | |
| bin_digits (int): Number of digits to round each bin | |
| to. Note that bins are always rounded down to avoid | |
| clipping any data. Defaults to 1. | |
| width (int): integer number of columns in the longest line | |
| in the histogram. Defaults to console width on Python | |
| 3.3+, or 80 if that is not available. | |
| format_bin (callable): Called on each bin to create a | |
| label for the final output. Use this function to add | |
| units, such as "ms" for milliseconds. | |
| Should you want something more programmatically reusable, see | |
| the :meth:`~Stats.get_histogram_counts` method, the output of | |
| is used by format_histogram. The :meth:`~Stats.describe` | |
| method is another useful summarization method, albeit less | |
| visual. | |
| .. _Freedman's algorithm: https://en.wikipedia.org/wiki/Freedman%E2%80%93Diaconis_rule | |
| """ | |
| width = kw.pop('width', None) | |
| format_bin = kw.pop('format_bin', None) | |
| bin_counts = self.get_histogram_counts(bins=bins, **kw) | |
| return format_histogram_counts(bin_counts, | |
| width=width, | |
| format_bin=format_bin) | |
| def describe(self, quantiles=None, format=None): | |
| """Provides standard summary statistics for the data in the Stats | |
| object, in one of several convenient formats. | |
| Args: | |
| quantiles (list): A list of numeric values to use as | |
| quantiles in the resulting summary. All values must be | |
| 0.0-1.0, with 0.5 representing the median. Defaults to | |
| ``[0.25, 0.5, 0.75]``, representing the standard | |
| quartiles. | |
| format (str): Controls the return type of the function, | |
| with one of three valid values: ``"dict"`` gives back | |
| a :class:`dict` with the appropriate keys and | |
| values. ``"list"`` is a list of key-value pairs in an | |
| order suitable to pass to an OrderedDict or HTML | |
| table. ``"text"`` converts the values to text suitable | |
| for printing, as seen below. | |
| Here is the information returned by a default ``describe``, as | |
| presented in the ``"text"`` format: | |
| >>> stats = Stats(range(1, 8)) | |
| >>> print(stats.describe(format='text')) | |
| count: 7 | |
| mean: 4.0 | |
| std_dev: 2.0 | |
| mad: 2.0 | |
| min: 1 | |
| 0.25: 2.5 | |
| 0.5: 4 | |
| 0.75: 5.5 | |
| max: 7 | |
| For more advanced descriptive statistics, check out my blog | |
| post on the topic `Statistics for Software | |
| <https://www.paypal-engineering.com/2016/04/11/statistics-for-software/>`_. | |
| """ | |
| if format is None: | |
| format = 'dict' | |
| elif format not in ('dict', 'list', 'text'): | |
| raise ValueError('invalid format for describe,' | |
| ' expected one of "dict"/"list"/"text", not %r' | |
| % format) | |
| quantiles = quantiles or [0.25, 0.5, 0.75] | |
| q_items = [] | |
| for q in quantiles: | |
| q_val = self.get_quantile(q) | |
| q_items.append((str(q), q_val)) | |
| items = [('count', self.count), | |
| ('mean', self.mean), | |
| ('std_dev', self.std_dev), | |
| ('mad', self.mad), | |
| ('min', self.min)] | |
| items.extend(q_items) | |
| items.append(('max', self.max)) | |
| if format == 'dict': | |
| ret = dict(items) | |
| elif format == 'list': | |
| ret = items | |
| elif format == 'text': | |
| ret = '\n'.join(['{}{}'.format((label + ':').ljust(10), val) | |
| for label, val in items]) | |
| return ret | |
| def describe(data, quantiles=None, format=None): | |
| """A convenience function to get standard summary statistics useful | |
| for describing most data. See :meth:`Stats.describe` for more | |
| details. | |
| >>> print(describe(range(7), format='text')) | |
| count: 7 | |
| mean: 3.0 | |
| std_dev: 2.0 | |
| mad: 2.0 | |
| min: 0 | |
| 0.25: 1.5 | |
| 0.5: 3 | |
| 0.75: 4.5 | |
| max: 6 | |
| See :meth:`Stats.format_histogram` for another very useful | |
| summarization that uses textual visualization. | |
| """ | |
| return Stats(data).describe(quantiles=quantiles, format=format) | |
| def _get_conv_func(attr_name): | |
| def stats_helper(data, default=0.0): | |
| return getattr(Stats(data, default=default, use_copy=False), | |
| attr_name) | |
| return stats_helper | |
| for attr_name, attr in list(Stats.__dict__.items()): | |
| if isinstance(attr, _StatsProperty): | |
| if attr_name in ('max', 'min', 'count'): # don't shadow builtins | |
| continue | |
| if attr_name in ('mad',): # convenience aliases | |
| continue | |
| func = _get_conv_func(attr_name) | |
| func.__doc__ = attr.func.__doc__ | |
| globals()[attr_name] = func | |
| delattr(Stats, '_calc_' + attr_name) | |
| # cleanup | |
| del attr | |
| del attr_name | |
| del func | |
| def format_histogram_counts(bin_counts, width=None, format_bin=None): | |
| """The formatting logic behind :meth:`Stats.format_histogram`, which | |
| takes the output of :meth:`Stats.get_histogram_counts`, and passes | |
| them to this function. | |
| Args: | |
| bin_counts (list): A list of bin values to counts. | |
| width (int): Number of character columns in the text output, | |
| defaults to 80 or console width in Python 3.3+. | |
| format_bin (callable): Used to convert bin values into string | |
| labels. | |
| """ | |
| lines = [] | |
| if not format_bin: | |
| format_bin = lambda v: v | |
| if not width: | |
| try: | |
| import shutil # python 3 convenience | |
| width = shutil.get_terminal_size()[0] | |
| except Exception: | |
| width = 80 | |
| bins = [b for b, _ in bin_counts] | |
| count_max = max([count for _, count in bin_counts]) | |
| count_cols = len(str(count_max)) | |
| labels = ['%s' % format_bin(b) for b in bins] | |
| label_cols = max([len(l) for l in labels]) | |
| tmp_line = '{}: {} #'.format('x' * label_cols, count_max) | |
| bar_cols = max(width - len(tmp_line), 3) | |
| line_k = float(bar_cols) / count_max | |
| tmpl = "{label:>{label_cols}}: {count:>{count_cols}} {bar}" | |
| for label, (bin_val, count) in zip(labels, bin_counts): | |
| bar_len = int(round(count * line_k)) | |
| bar = ('#' * bar_len) or '|' | |
| line = tmpl.format(label=label, | |
| label_cols=label_cols, | |
| count=count, | |
| count_cols=count_cols, | |
| bar=bar) | |
| lines.append(line) | |
| return '\n'.join(lines) | |