pingouin: A Python repository from inonchiu

https://travis-ci.org/raphaelvallat/pingouin.svg?branch=master

https://ci.appveyor.com/api/projects/status/v7fhavoqj8ig1bs2?svg=true

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.

ANOVAs: N-ways, repeated measures, mixed, ancova
Pairwise post-hocs tests (parametric and non-parametric) and pairwise correlations
Robust, partial, distance and repeated measures correlations
Linear/logistic regression and mediation analysis
Bayes Factors
Multivariate tests
Reliability and consistency
Effect sizes and power analysis
Parametric/bootstrapped confidence intervals around an effect size or a correlation coefficient
Circular statistics
Chi-squared tests
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 ttest_ind function of SciPy returns only the T-value and the p-value. By contrast, the 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 the public Gitter chat

Installation

Dependencies

The main dependencies of Pingouin are :

NumPy (>= 1.15)
SciPy (>= 1.3.0)
Pandas (>= 0.24)
Matplotlib (>= 3.0.2)
Seaborn (>= 0.9.0)

In addition, some functions require :

Statsmodels
Scikit-learn
Mpmath

Pingouin is a Python 3 package and is currently tested for Python 3.5, 3.6 and 3.7. Pingouin does not work with Python 2.7.

User installation

Pingouin can be easily installed using pip

pip install pingouin

or conda

conda install -c conda-forge pingouin

New releases are frequent so always make sure that you have the latest version:

pip install --upgrade pingouin

Quick start

Click on the link below and navigate to the notebooks/ folder to run a collection of interactive Jupyter notebooks showing the main functionalities of Pingouin. No need to install Pingouin beforehand, the notebooks run in a Binder environment.

10 minutes to Pingouin

1. T-test

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)

Output

T	dof	tail	p-val	CI95%	cohen-d	BF10	power
-3.401	58	two-sided	0.001	[-1.68 -0.43]	0.878	26.155	0.917

2. Pearson's correlation

pg.corr(x, y)

Output

n	r	CI95%	r2	adj_r2	p-val	BF10	power
30	0.595	[0.3 0.79]	0.354	0.306	0.001	69.723	0.95

3. Robust correlation

# Introduce an outlier
x[5] = 18
# Use the robust Shepherd's pi correlation
pg.corr(x, y, method="shepherd")

Output

n	r	CI95%	r2	adj_r2	p-val	power
30	0.561	[0.25 0.77]	0.315	0.264	0.002	0.917

4. Test the normality of the data

The pingouin.normality function works with lists, arrays, or pandas DataFrame in wide or long-format.

print(pg.normality(x))                                    # Univariate normality
print(pg.multivariate_normality(np.column_stack((x, y)))) # Multivariate normality

Output

W	pval	normal
0.615	0.000	False

(False, 0.00018)

5. One-way ANOVA using a pandas DataFrame

# 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)

Output

Source	SS	DF	MS	F	p-unc	np2
Group	5.460	1	5.460	5.244	0.02320	0.029
Within	185.343	178	1.041

6. Repeated measures ANOVA

pg.rm_anova(data=df, dv='Scores', within='Time', subject='Subject', detailed=True)

Output

Source	SS	DF	MS	F	p-unc	np2	eps
Time	7.628	2	3.814	3.913	0.022629	0.062	0.999
Error	115.027	118	0.975

7. Post-hoc tests corrected for multiple-comparisons

# FDR-corrected post hocs with Hedges'g effect size
posthoc = pg.pairwise_ttests(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')

Output

Contrast	A	B	Paired	Parametric	T	dof	tail	p-unc	p-corr	p-adjust	BF10	CLES	hedges
Time	August	January	True	True	-1.740	59.000	two-sided	0.087	0.131	fdr_bh	0.582	0.585	-0.328
Time	August	June	True	True	-2.743	59.000	two-sided	0.008	0.024	fdr_bh	4.232	0.644	-0.485
Time	January	June	True	True	-1.024	59.000	two-sided	0.310	0.310	fdr_bh	0.232	0.571	-0.170

8. Two-way mixed ANOVA

# Compute the two-way mixed ANOVA and export to a .csv file
aov = pg.mixed_anova(data=df, dv='Scores', between='Group', within='Time',
                     subject='Subject', correction=False,
                     export_filename='mixed_anova.csv')
pg.print_table(aov)

Output

Source	SS	DF1	DF2	MS	F	p-unc	np2	eps
Group	5.460	1	58	5.460	5.052	0.028	0.080
Time	7.628	2	116	3.814	4.027	0.020	0.065	0.999
Interaction	5.168	2	116	2.584	2.728	0.070	0.045

9. Pairwise correlations between columns of a dataframe

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'])

Output

X	Y	method	tail	n	r	CI95%	r2	adj_r2	z	p-unc	BF10	power
X	Y	pearson	two-sided	30	0.366	[0.01 0.64]	0.134	0.070	0.384	0.047	1.500	0.525
X	Z	pearson	two-sided	30	0.251	[-0.12 0.56]	0.063	-0.006	0.256	0.181	0.534	0.272
Y	Z	pearson	two-sided	30	0.020	[-0.34 0.38]	0.000	-0.074	0.020	0.916	0.228	0.051

10. Convert between effect sizes

# Convert from Cohen's d to Hedges' g
pg.convert_effsize(0.4, 'cohen', 'hedges', nx=10, ny=12)

0.384

11. Multiple linear regression

pg.linear_regression(data[['X', 'Z']], data['Y'])

Linear regression summary

names	coef	se	T	pval	r2	adj_r2	CI[2.5%]	CI[97.5%]
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

pg.mediation_analysis(data=data, x='X', m='Z', y='Y', seed=42, n_boot=1000)

Mediation summary

path	coef	se	pval	CI[2.5%]	CI[97.5%]	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	-0.070	0.029	No

13. Contingency analysis

data = pg.read_dataset('chi2_independence')
expected, observed, stats = pg.chi2_independence(data, x='sex', y='target')
stats

Chi-squared tests summary

test	lambda	chi2	dof	cramer	power
pearson	1.000	22.717	1.000	0.274	0.997
cressie-read	0.667	22.931	1.000	0.275	0.998
log-likelihood	0.000	23.557	1.000	0.279	0.998
freeman-tukey	-0.500	24.220	1.000	0.283	0.998
mod-log-likelihood	-1.000	25.071	1.000	0.288	0.999
neyman	-2.000	27.458	1.000	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:

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:

Development

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.

Note that this program is provided with NO WARRANTY OF ANY KIND. If you can, always double check the results with another statistical software.

Contributors

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

@ARTICLE{Vallat2018,
  title    = "Pingouin: statistics in Python",
  author   = "Vallat, Raphael",
  journal  = "The Journal of Open Source Software",
  volume   =  3,
  number   =  31,
  pages    = "1026",
  month    =  nov,
  year     =  2018
}

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) (Berens 2009)
robust correlations (Matlab) (Pernet, Wilcox & Rousselet, 2012)
repeated-measure correlation (R) (Bakdash & Marusich, 2017)

I am also grateful to Charles Zaiontz and his website www.real-statistics.com which has been useful to understand the practical implementation of several functions.

inonchiu/pingouin

Documentation

Chat

Installation

Dependencies

User installation

Quick start

10 minutes to Pingouin

1. T-test

2. Pearson's correlation

3. Robust correlation

4. Test the normality of the data

5. One-way ANOVA using a pandas DataFrame

6. Repeated measures ANOVA

7. Post-hoc tests corrected for multiple-comparisons

8. Two-way mixed ANOVA

9. Pairwise correlations between columns of a dataframe

10. Convert between effect sizes

11. Multiple linear regression

12. Mediation analysis

13. Contingency analysis

Integration with Pandas

Development

Contributors

How to cite Pingouin?

Acknowledgement