.. -*- mode: rst -*- | .. image:: https://img.shields.io/pypi/v/pingouin.svg :target: https://pypi.org/project/pingouin/ .. image:: https://img.shields.io/conda/vn/conda-forge/pingouin.svg :target: https://anaconda.org/conda-forge/pingouin .. image:: https://img.shields.io/github/license/raphaelvallat/pingouin.svg :target: https://github.com/raphaelvallat/pingouin/blob/main/LICENSE .. image:: https://github.com/raphaelvallat/pingouin/actions/workflows/pytest.yml/badge.svg :target: https://github.com/raphaelvallat/pingouin/actions .. image:: https://codecov.io/gh/raphaelvallat/pingouin/branch/main/graph/badge.svg :target: https://codecov.io/gh/raphaelvallat/pingouin .. image:: https://pepy.tech/badge/pingouin/month :target: https://pepy.tech/badge/pingouin/month .. image:: https://joss.theoj.org/papers/d2254e6d8e8478da192148e4cfbe4244/status.svg :target: https://joss.theoj.org/papers/d2254e6d8e8478da192148e4cfbe4244 ---------------- .. image:: https://raw.githubusercontent.com/raphaelvallat/pingouin/main/docs/pictures/logo_pingouin.png :align: center **Pingouin** is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy. Some of its main features are listed below. For a full list of available functions, please refer to the `API documentation `_. 1. ANOVAs: N-ways, repeated measures, mixed, ancova 2. Pairwise post-hocs tests (parametric and non-parametric) and pairwise correlations 3. Robust, partial, distance and repeated measures correlations 4. Linear/logistic regression and mediation analysis 5. Bayes Factors 6. Multivariate tests 7. Reliability and consistency 8. Effect sizes and power analysis 9. Parametric/bootstrapped confidence intervals around an effect size or a correlation coefficient 10. Circular statistics 11. Chi-squared tests 12. Plotting: Bland-Altman plot, Q-Q plot, paired plot, robust correlation... Pingouin is designed for users who want **simple yet exhaustive statistical functions**. For example, the :code:`ttest_ind` function of SciPy returns only the T-value and the p-value. By contrast, the :code:`ttest` function of Pingouin returns the T-value, the p-value, the degrees of freedom, the effect size (Cohen's d), the 95% confidence intervals of the difference in means, the statistical power and the Bayes Factor (BF10) of the test. Documentation ============= - `Link to documentation `_ Chat ==== If you have questions, please ask them in `GitHub Discussions `_. Installation ============ Dependencies ------------ The main dependencies of Pingouin are: * `NumPy `_ >= 2.2.2 * `SciPy `_ >= 1.15.0 * `Pandas `_ >= 2.3.0 * `Matplotlib `_ >= 3.10.1 * `Seaborn `_ >= 0.13.2 * `Scikit-learn `_ >= 1.6.1 * `Tabulate `_ Some functions additionally require the following optional dependencies, which can be installed with ``pip install "pingouin[extras]"``: * `Statsmodels `_ >= 0.14.5: ``ancova``, ``rm_corr`` and ``anova`` with unbalanced or N-way designs * `Mpmath `_: one-sided ``bayesfactor_pearson`` Pingouin is a Python 3 package and is currently tested for Python 3.11+. User installation ----------------- Pingouin can be easily installed using `uv `_ .. code-block:: shell uv pip install pingouin pip .. code-block:: shell pip install pingouin or conda .. code-block:: shell conda install -c conda-forge pingouin New releases are frequent so always make sure that you have the latest version: .. code-block:: shell uv pip install --upgrade pingouin Installation from source ------------------------ To build and install from source, clone this repository and install in editable mode with `uv `_ .. code-block:: shell git clone https://github.com/raphaelvallat/pingouin.git cd pingouin uv pip install --group=dev --editable . # test the package pytest --verbose Quick start ============ The `notebooks/ `_ folder contains a collection of Jupyter notebooks showing the main functionalities of Pingouin. 10 minutes to Pingouin ---------------------- 1. T-test ######### .. code-block:: python import numpy as np import pingouin as pg np.random.seed(123) mean, cov, n = [4, 5], [(1, .6), (.6, 1)], 30 x, y = np.random.multivariate_normal(mean, cov, n).T # T-test pg.ttest(x, y) .. table:: Output :widths: auto ====== ===== ============= ======= ============= ========= ======= ====== T dof alternative p_val CI95 cohen_d power BF10 ====== ===== ============= ======= ============= ========= ======= ====== -3.401 58 two-sided 0.001 [-1.68 -0.43] 0.878 0.917 26.155 ====== ===== ============= ======= ============= ========= ======= ====== ------------ 2. Pearson's correlation ######################## .. code-block:: python pg.corr(x, y) .. table:: Output :widths: auto === ===== =========== ======= ====== ======= n r CI95 p_val BF10 power === ===== =========== ======= ====== ======= 30 0.595 [0.3 0.79] 0.001 69.723 0.950 === ===== =========== ======= ====== ======= ------------ 3. Robust correlation ##################### .. code-block:: python # Introduce an outlier x[5] = 18 # Use the robust biweight midcorrelation pg.corr(x, y, method="bicor") .. table:: Output :widths: auto === ===== =========== ======= ======= n r CI95 p_val power === ===== =========== ======= ======= 30 0.576 [0.27 0.78] 0.001 0.933 === ===== =========== ======= ======= ------------ 4. Test the normality of the data ################################# The `pingouin.normality` function works with lists, arrays, or pandas DataFrame in wide or long-format. .. code-block:: python print(pg.normality(x)) # Univariate normality print(pg.multivariate_normality(np.column_stack((x, y)))) # Multivariate normality .. table:: Output :widths: auto ===== ====== ======== W pval normal ===== ====== ======== 0.615 0.000 False ===== ====== ======== .. parsed-literal:: HZResults(hz=1.697, pval=0.00018, normal=False) ------------ 5. One-way ANOVA using a pandas DataFrame ######################################### .. code-block:: python # Read an example dataset df = pg.read_dataset('mixed_anova') # Run the ANOVA aov = pg.anova(data=df, dv='Scores', between='Group', detailed=True) print(aov) .. table:: Output :widths: auto ======== ======= ==== ===== ======= ======= ======= Source SS DF MS F p_unc np2 ======== ======= ==== ===== ======= ======= ======= Group 5.460 1 5.460 5.244 0.023 0.029 Within 185.343 178 1.041 nan nan nan ======== ======= ==== ===== ======= ======= ======= ------------ 6. Repeated measures ANOVA ########################## .. code-block:: python pg.rm_anova(data=df, dv='Scores', within='Time', subject='Subject', detailed=True) .. table:: Output :widths: auto ======== ======= ==== ===== ======= ======= ======= ======= Source SS DF MS F p_unc ng2 eps ======== ======= ==== ===== ======= ======= ======= ======= Time 7.628 2 3.814 3.913 0.023 0.04 0.999 Error 115.027 118 0.975 nan nan nan nan ======== ======= ==== ===== ======= ======= ======= ======= ------------ 7. Post-hoc tests corrected for multiple-comparisons #################################################### .. code-block:: python # FDR-corrected post hocs with Hedges'g effect size posthoc = pg.pairwise_tests(data=df, dv='Scores', within='Time', subject='Subject', parametric=True, padjust='fdr_bh', effsize='hedges') # Pretty printing of table pg.print_table(posthoc, floatfmt='.3f') .. table:: Output :widths: auto ========== ======= ======= ======== ============ ====== ====== ============= ======= ======== ========== ====== ======== Contrast A B Paired Parametric T dof alternative p_unc p_corr p_adjust BF10 hedges ========== ======= ======= ======== ============ ====== ====== ============= ======= ======== ========== ====== ======== Time August January True True -1.740 59.000 two-sided 0.087 0.131 fdr_bh 0.582 -0.328 Time August June True True -2.743 59.000 two-sided 0.008 0.024 fdr_bh 4.232 -0.483 Time January June True True -1.024 59.000 two-sided 0.310 0.310 fdr_bh 0.232 -0.170 ========== ======= ======= ======== ============ ====== ====== ============= ======= ======== ========== ====== ======== ------------ 8. Two-way mixed ANOVA ###################### .. code-block:: python # Compute the two-way mixed ANOVA aov = pg.mixed_anova(data=df, dv='Scores', between='Group', within='Time', subject='Subject', correction=False, effsize="np2") pg.print_table(aov) .. table:: Output :widths: auto =========== ===== ===== ===== ===== ===== ======= ===== ======= Source SS DF1 DF2 MS F p_unc np2 eps =========== ===== ===== ===== ===== ===== ======= ===== ======= Group 5.460 1 58 5.460 5.052 0.028 0.080 nan Time 7.628 2 116 3.814 4.027 0.020 0.065 0.998 Interaction 5.167 2 116 2.584 2.728 0.070 0.045 0.998 =========== ===== ===== ===== ===== ===== ======= ===== ======= ------------ 9. Pairwise correlations between columns of a dataframe ####################################################### .. code-block:: python import pandas as pd np.random.seed(123) z = np.random.normal(5, 1, 30) data = pd.DataFrame({'X': x, 'Y': y, 'Z': z}) pg.pairwise_corr(data, columns=['X', 'Y', 'Z'], method='pearson') .. table:: Output :widths: auto === === ======== ============= === ===== ============= ======= ====== ======= X Y method alternative n r CI95 p_unc BF10 power === === ======== ============= === ===== ============= ======= ====== ======= X Y pearson two-sided 30 0.366 [0.01 0.64] 0.047 1.500 0.525 X Z pearson two-sided 30 0.251 [-0.12 0.56] 0.181 0.534 0.272 Y Z pearson two-sided 30 0.020 [-0.34 0.38] 0.916 0.228 0.051 === === ======== ============= === ===== ============= ======= ====== ======= ------------ 10. Pairwise T-test between columns of a dataframe ################################################### .. code-block:: python data.ptests(paired=True, stars=False) .. table:: Pairwise T-tests, with T-values on the lower triangle and p-values on the upper triangle :widths: auto ==== ====== ====== ===== .. X Y Z ==== ====== ====== ===== X - 0.226 0.165 Y -1.238 - 0.658 Z -1.424 -0.447 - ==== ====== ====== ===== ------------ 11. Multiple linear regression ############################## .. code-block:: python pg.linear_regression(data[['X', 'Z']], data['Y']) .. table:: Linear regression summary :widths: auto ========= ====== ===== ====== ====== ===== ======== ========== =========== names coef se T pval r2 adj_r2 CI2.5 CI97.5 ========= ====== ===== ====== ====== ===== ======== ========== =========== Intercept 4.650 0.841 5.530 0.000 0.139 0.076 2.925 6.376 X 0.143 0.068 2.089 0.046 0.139 0.076 0.003 0.283 Z -0.069 0.167 -0.416 0.681 0.139 0.076 -0.412 0.273 ========= ====== ===== ====== ====== ===== ======== ========== =========== ------------ 12. Mediation analysis ###################### .. code-block:: python pg.mediation_analysis(data=data, x='X', m='Z', y='Y', seed=42, n_boot=1000) .. table:: Mediation summary :widths: auto ======== ====== ===== ====== ========== =========== ===== path coef se pval CI2.5 CI97.5 sig ======== ====== ===== ====== ========== =========== ===== Z ~ X 0.103 0.075 0.181 -0.051 0.256 No Y ~ Z 0.018 0.171 0.916 -0.332 0.369 No Total 0.136 0.065 0.047 0.002 0.269 Yes Direct 0.143 0.068 0.046 0.003 0.283 Yes Indirect -0.007 0.025 0.898 -0.069 0.029 No ======== ====== ===== ====== ========== =========== ===== ------------ 13. Contingency analysis ######################## .. code-block:: python data = pg.read_dataset('chi2_independence') expected, observed, stats = pg.chi2_independence(data, x='sex', y='target') stats .. table:: Chi-squared tests summary :widths: auto ================== ======== ====== ===== ===== ======== ======= test lambda chi2 dof pval cramer power ================== ======== ====== ===== ===== ======== ======= pearson 1.000 22.717 1.000 0.000 0.274 0.997 cressie-read 0.667 22.931 1.000 0.000 0.275 0.998 log-likelihood 0.000 23.557 1.000 0.000 0.279 0.998 freeman-tukey -0.500 24.220 1.000 0.000 0.283 0.998 mod-log-likelihood -1.000 25.071 1.000 0.000 0.288 0.999 neyman -2.000 27.458 1.000 0.000 0.301 0.999 ================== ======== ====== ===== ===== ======== ======= Integration with Pandas ----------------------- Several functions of Pingouin can be used directly as pandas DataFrame methods. Try for yourself with the code below: .. code-block:: python import pingouin as pg # Example 1 | ANOVA df = pg.read_dataset('mixed_anova') df.anova(dv='Scores', between='Group', detailed=True) # Example 2 | Pairwise correlations data = pg.read_dataset('mediation') data.pairwise_corr(columns=['X', 'M', 'Y'], covar=['Mbin']) # Example 3 | Partial correlation matrix data.pcorr() The functions that are currently supported as pandas method are: * ANOVAs: `anova `_, `ancova `_, `rm_anova `_, `mixed_anova `_, `welch_anova `_ * Non-parametric: `kruskal `_, `friedman `_, `cochran `_ * Post-hocs: `pairwise_tests `_, `pairwise_tukey `_, `pairwise_gameshowell `_, `ptests `_ * Correlations: `pairwise_corr `_, `partial_corr `_, `pcorr `_, `rcorr `_, `rm_corr `_ * Distribution: `normality `_, `homoscedasticity `_, `sphericity `_, `epsilon `_, `box_m `_ * Contingency: `chi2_independence `_, `chi2_mcnemar `_, `dichotomous_crosstab `_ * Regression: `linear_regression `_, `logistic_regression `_, `mediation_analysis `_ * Reliability: `cronbach_alpha `_, `intraclass_corr `_ Contributing ============ Pingouin was created and is maintained by `Raphael Vallat `_, mostly during his spare time. Contributions are more than welcome so feel free to contact me, open an issue or submit a pull request! To see the code or report a bug, please visit the `GitHub repository `_. This program is provided with NO WARRANTY OF ANY KIND. Pingouin is still under heavy development and there are likely hidden bugs. Always double check the results with another statistical software. **Contributors** - Nicolas Legrand - `Richard Höchenberger `_ - `Arthur Paulino `_ - `Eelke Spaak `_ - `Johannes Elfner `_ - `Stefan Appelhoff `_ How to cite Pingouin? ===================== If you want to cite Pingouin, please use the publication in JOSS: * Vallat, R. (2018). Pingouin: statistics in Python. *Journal of Open Source Software*, 3(31), 1026, `https://doi.org/10.21105/joss.01026 `_ Acknowledgement =============== Several functions of Pingouin were inspired from R or Matlab toolboxes, including: - `effsize package (R) `_ - `ezANOVA package (R) `_ - `pwr package (R) `_ - `circular statistics (Matlab) `_ - `robust correlations (Matlab) `_ - `repeated-measure correlation (R) `_ - `real-statistics.com `_