├── .github └── workflows │ ├── build_package.yml │ └── python-publish.yml ├── .gitignore ├── LICENSE ├── README.md ├── build └── lib │ └── cliffs_delta │ ├── __init__.py │ └── test_cliff.py ├── cliffs_delta ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ └── cliffs_delta.cpython-38.pyc ├── snap │ └── snapcraft.yaml └── test_cliff.py ├── dist ├── cliffs_delta-1.0.0-py3-none-any.whl └── cliffs_delta-1.0.0.tar.gz └── setup.py /.github/workflows/build_package.yml: -------------------------------------------------------------------------------- 1 | name: Python package 2 | 3 | on: [push] 4 | 5 | jobs: 6 | build: 7 | 8 | runs-on: ubuntu-latest 9 | strategy: 10 | matrix: 11 | python-version: [3.6, 3.7, 3.8, 3.9] 12 | 13 | steps: 14 | - uses: actions/checkout@v2 15 | - name: Setup Python # Set Python version 16 | uses: actions/setup-python@v2 17 | with: 18 | python-version: ${{ matrix.python-version }} 19 | # Install pip and pytest 20 | - name: Install dependencies 21 | run: | 22 | python -m pip install --upgrade pip 23 | pip install pytest 24 | - name: Test with pytest 25 | run: pytest test_cliff.py --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml 26 | - name: Upload pytest test results 27 | uses: actions/upload-artifact@v2 28 | with: 29 | name: pytest-results-${{ matrix.python-version }} 30 | path: junit/test-results-${{ matrix.python-version }}.xml 31 | # Use always() to always run this step to publish test results when there are test failures 32 | if: ${{ always() }} 33 | -------------------------------------------------------------------------------- /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- 1 | # This workflow will upload a Python Package using Twine when a release is created 2 | # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries 3 | 4 | # This workflow uses actions that are not certified by GitHub. 5 | # They are provided by a third-party and are governed by 6 | # separate terms of service, privacy policy, and support 7 | # documentation. 8 | 9 | name: Upload Python Package 10 | 11 | on: 12 | release: 13 | types: [published] 14 | 15 | jobs: 16 | deploy: 17 | 18 | runs-on: ubuntu-latest 19 | 20 | steps: 21 | - uses: actions/checkout@v2 22 | - name: Set up Python 23 | uses: actions/setup-python@v2 24 | with: 25 | python-version: '3.x' 26 | - name: Install dependencies 27 | run: | 28 | python -m pip install --upgrade pip 29 | pip install build 30 | - name: Build package 31 | run: python -m build 32 | - name: Publish package 33 | uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 34 | with: 35 | user: __token__ 36 | password: ${{ secrets.PYPI_API_TOKEN }} 37 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | /cliffs_delta.egg-info 2 | /build 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 2, June 1991 3 | 4 | Copyright (C) 1989, 1991 Free Software Foundation, Inc., 5 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 6 | Everyone is permitted to copy and distribute verbatim copies 7 | of this license document, but changing it is not allowed. 8 | 9 | Preamble 10 | 11 | The licenses for most software are designed to take away your 12 | freedom to share and change it. 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If this is what you want to do, use the GNU Lesser General 339 | Public License instead of this License. 340 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | This is code to calculate the Cliff's Delta effect size metric, which strangely is not in NumPy/SciPy.stats. 2 | 3 | @Timm had [this as a gist](https://gist.github.com/timm/a6e759eb7d9b5f05b468), and @mtorchiano has [R code with tests](https://github.com/mtorchiano/effsize). I have merged them. Well, Marco's code does a lot more. I merged his tests. 4 | 5 | 6 | # cliffs_delta 7 | 8 | **The Cliff's Delta** statistic is a non-parametric effect size measure that quantifies the amount of difference between two groups of observations beyond p-values interpretation. This measure can be understood as a useful complementary analysis for the corresponding hypothesis testing. 9 | 10 | # Installation 11 | 12 | This package can either be installed using pip or from a tarball using the standard Python distutils. 13 | 14 | If you are installing using ```pip```, you don’t need to download anything as the latest version will be downloaded for you from PyPI: 15 | 16 | ``` 17 | pip install cliffs-delta 18 | ``` 19 | # Example & Usage 20 | 21 | Import the method ```cliffs_delta``` from ```cliffs_delta``` 22 | 23 | ```python 24 | from cliffs_delta import cliffs_delta 25 | 26 | x1 = [10, 20, 20, 20, 30, 30, 30, 40, 50, 100] 27 | x2 = [10, 20, 30, 40, 40, 50] 28 | d, res = cliffs_delta(x1, x2) 29 | 30 | print(d,res) 31 | 32 | -0.06666666666666667 negligible 33 | ``` -------------------------------------------------------------------------------- /build/lib/cliffs_delta/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = "1.0.0" 2 | 3 | def cliffs_delta(lst1, lst2, **dull): 4 | 5 | """Returns delta and true if there are more than 'dull' differences""" 6 | if not dull: 7 | dull = {'small': 0.147, 'medium': 0.33, 'large': 0.474} # effect sizes from (Hess and Kromrey, 2004) 8 | m, n = len(lst1), len(lst2) 9 | lst2 = sorted(lst2) 10 | j = more = less = 0 11 | for repeats, x in runs(sorted(lst1)): 12 | while j <= (n - 1) and lst2[j] < x: 13 | j += 1 14 | more += j*repeats 15 | while j <= (n - 1) and lst2[j] == x: 16 | j += 1 17 | less += (n - j)*repeats 18 | d = (more - less) / (m*n) 19 | size = lookup_size(d, dull) 20 | return d, size 21 | 22 | 23 | def lookup_size(delta: float, dull: dict) -> str: 24 | """ 25 | :type delta: float 26 | :type dull: dict, a dictionary of small, medium, large thresholds. 27 | """ 28 | delta = abs(delta) 29 | if delta < dull['small']: 30 | return 'negligible' 31 | if dull['small'] <= delta < dull['medium']: 32 | return 'small' 33 | if dull['medium'] <= delta < dull['large']: 34 | return 'medium' 35 | if delta >= dull['large']: 36 | return 'large' 37 | 38 | 39 | def runs(lst): 40 | """Iterator, chunks repeated values""" 41 | for j, two in enumerate(lst): 42 | if j == 0: 43 | one, i = two, 0 44 | if one != two: 45 | yield j - i, one 46 | i = j 47 | one = two 48 | yield j - i + 1, two 49 | -------------------------------------------------------------------------------- /build/lib/cliffs_delta/test_cliff.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | 3 | from __init__ import cliffs_delta 4 | 5 | class MyTest(unittest.TestCase): 6 | 7 | def test_small_difference(self): 8 | """ test data from Marco Torchiano R package https://github.com/mtorchiano/effsize""" 9 | treatment = [10, 10, 20, 20, 20, 30, 30, 30, 40, 50] 10 | control = [10, 20, 30, 40, 40, 50] 11 | 12 | d, res = cliffs_delta(treatment, control) 13 | # Cliff's Delta 14 | # 15 | # delta estimate: -0.25 (small) 16 | # 95 percent confidence interval: 17 | # inf sup 18 | # -0.7265846 0.3890062 19 | self.assertEqual("small", res) 20 | self.assertEqual(d, -0.25) 21 | 22 | def test_tim(self): 23 | lst1 = range(8) 24 | out = [] 25 | expected = ['negligible','negligible','small','small', 'medium'] 26 | for r in [1.01, 1.1, 1.21, 1.5, 2]: 27 | lst2 = list(map(lambda x: x * r, lst1)) 28 | d, res = cliffs_delta(lst1, lst2) 29 | out.append(res) 30 | 31 | self.assertEqual(expected,out) 32 | 33 | def test_negligible(self): #Marco 34 | x1 = [10, 20, 20, 20, 30, 30, 30, 40, 50, 100] 35 | x2 = [10, 20, 30, 40, 40, 50] 36 | d, res = cliffs_delta(x1, x2) 37 | self.assertAlmostEqual(-0.06667, d, 4) 38 | 39 | def test_nonoverlapping(self): # marco's test 40 | x1 = [10, 20, 20, 20, 30, 30, 30, 40, 50, 100] 41 | x2 = [10, 20, 30, 40, 40, 50] 42 | factor = 110 43 | x2 = [x+factor for x in x2] 44 | 45 | d, res = cliffs_delta(x1, x2) 46 | self.assertEqual(res, 'large') 47 | self.assertAlmostEqual(d, -1, 2) 48 | 49 | if __name__ == '__main__': 50 | unittest.main() -------------------------------------------------------------------------------- /cliffs_delta/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = "1.0.0" 2 | 3 | def cliffs_delta(lst1, lst2, **dull): 4 | 5 | """Returns delta and true if there are more than 'dull' differences""" 6 | if not dull: 7 | dull = {'small': 0.147, 'medium': 0.33, 'large': 0.474} # effect sizes from (Hess and Kromrey, 2004) 8 | m, n = len(lst1), len(lst2) 9 | lst2 = sorted(lst2) 10 | j = more = less = 0 11 | for repeats, x in runs(sorted(lst1)): 12 | while j <= (n - 1) and lst2[j] < x: 13 | j += 1 14 | more += j*repeats 15 | while j <= (n - 1) and lst2[j] == x: 16 | j += 1 17 | less += (n - j)*repeats 18 | d = (more - less) / (m*n) 19 | size = lookup_size(d, dull) 20 | return d, size 21 | 22 | 23 | def lookup_size(delta: float, dull: dict) -> str: 24 | """ 25 | :type delta: float 26 | :type dull: dict, a dictionary of small, medium, large thresholds. 27 | """ 28 | delta = abs(delta) 29 | if delta < dull['small']: 30 | return 'negligible' 31 | if dull['small'] <= delta < dull['medium']: 32 | return 'small' 33 | if dull['medium'] <= delta < dull['large']: 34 | return 'medium' 35 | if delta >= dull['large']: 36 | return 'large' 37 | 38 | 39 | def runs(lst): 40 | """Iterator, chunks repeated values""" 41 | for j, two in enumerate(lst): 42 | if j == 0: 43 | one, i = two, 0 44 | if one != two: 45 | yield j - i, one 46 | i = j 47 | one = two 48 | yield j - i + 1, two 49 | -------------------------------------------------------------------------------- /cliffs_delta/__pycache__/__init__.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neilernst/cliffsDelta/8f652b4d0b2c31814a1b93b8f31cc42746359c08/cliffs_delta/__pycache__/__init__.cpython-38.pyc -------------------------------------------------------------------------------- /cliffs_delta/__pycache__/cliffs_delta.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neilernst/cliffsDelta/8f652b4d0b2c31814a1b93b8f31cc42746359c08/cliffs_delta/__pycache__/cliffs_delta.cpython-38.pyc -------------------------------------------------------------------------------- /cliffs_delta/snap/snapcraft.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: cliffsdelta 3 | version: '0.1' # just for humans, typically '1.2+git' or '1.3.2' 4 | summary: Calculate Cliff's Delta 5 | description: | 6 | A test snap with a simple function. 7 | 8 | grade: devel # must be 'stable' to release into candidate/stable channels 9 | confinement: devmode # use 'strict' once you have the right plugs and slots 10 | 11 | parts: 12 | my-part: 13 | # See 'snapcraft plugins' 14 | plugin: nil 15 | 16 | -------------------------------------------------------------------------------- /cliffs_delta/test_cliff.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | 3 | from __init__ import cliffs_delta 4 | 5 | class MyTest(unittest.TestCase): 6 | 7 | def test_small_difference(self): 8 | """ test data from Marco Torchiano R package https://github.com/mtorchiano/effsize""" 9 | treatment = [10, 10, 20, 20, 20, 30, 30, 30, 40, 50] 10 | control = [10, 20, 30, 40, 40, 50] 11 | 12 | d, res = cliffs_delta(treatment, control) 13 | # Cliff's Delta 14 | # 15 | # delta estimate: -0.25 (small) 16 | # 95 percent confidence interval: 17 | # inf sup 18 | # -0.7265846 0.3890062 19 | self.assertEqual("small", res) 20 | self.assertEqual(d, -0.25) 21 | 22 | def test_tim(self): 23 | lst1 = range(8) 24 | out = [] 25 | expected = ['negligible','negligible','small','small', 'medium'] 26 | for r in [1.01, 1.1, 1.21, 1.5, 2]: 27 | lst2 = list(map(lambda x: x * r, lst1)) 28 | d, res = cliffs_delta(lst1, lst2) 29 | out.append(res) 30 | 31 | self.assertEqual(expected,out) 32 | 33 | def test_negligible(self): #Marco 34 | x1 = [10, 20, 20, 20, 30, 30, 30, 40, 50, 100] 35 | x2 = [10, 20, 30, 40, 40, 50] 36 | d, res = cliffs_delta(x1, x2) 37 | self.assertAlmostEqual(-0.06667, d, 4) 38 | 39 | def test_nonoverlapping(self): # marco's test 40 | x1 = [10, 20, 20, 20, 30, 30, 30, 40, 50, 100] 41 | x2 = [10, 20, 30, 40, 40, 50] 42 | factor = 110 43 | x2 = [x+factor for x in x2] 44 | 45 | d, res = cliffs_delta(x1, x2) 46 | self.assertEqual(res, 'large') 47 | self.assertAlmostEqual(d, -1, 2) 48 | 49 | if __name__ == '__main__': 50 | unittest.main() -------------------------------------------------------------------------------- /dist/cliffs_delta-1.0.0-py3-none-any.whl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neilernst/cliffsDelta/8f652b4d0b2c31814a1b93b8f31cc42746359c08/dist/cliffs_delta-1.0.0-py3-none-any.whl -------------------------------------------------------------------------------- /dist/cliffs_delta-1.0.0.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neilernst/cliffsDelta/8f652b4d0b2c31814a1b93b8f31cc42746359c08/dist/cliffs_delta-1.0.0.tar.gz -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import pathlib 2 | from setuptools import setup 3 | 4 | # The directory containing this file 5 | HERE = pathlib.Path(__file__).parent 6 | 7 | # The text of the README file 8 | README = (HERE / "README.md").read_text() 9 | 10 | # This call to setup() does all the work 11 | setup( 12 | name="cliffs_delta", 13 | version="1.0.0", 14 | description="Python Package to calculate Cliff's delta", 15 | long_description=README, 16 | long_description_content_type="text/markdown", 17 | url="https://github.com/neilernst/cliffsDelta", 18 | author="neilernst/prkhrv", 19 | author_email="neil@neilernst.net", 20 | license="MIT", 21 | classifiers=[ 22 | "License :: OSI Approved :: MIT License", 23 | "Programming Language :: Python :: 3", 24 | "Programming Language :: Python :: 3.7", 25 | ], 26 | packages=["cliffs_delta"], 27 | include_package_data=True, 28 | install_requires=[], 29 | ) --------------------------------------------------------------------------------