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Statistics in Python — Scipy lecture notes

3.1. Statistics in Python

Author: Gaël Varoquaux

Requirements
Standard scientific Python environment (numpy, scipy, matplotlib)
Pandas
Statsmodels
Seaborn

To install Python and these dependencies, we recommend that you download Anaconda Python or
Enthought Canopy, or preferably use the package manager if you are under Ubuntu or other linux.

See also:
Bayesian statistics in Python: This chapter does not cover tools for Bayesian statistics. Of par-
ticular interest for Bayesian modelling is PyMC, which implements a probabilistic programming
language in Python.
Read a statistics book: The Think stats book is available as free PDF or in print and is a great
introduction to statistics.

Why Python for statistics?

R is a language dedicated to statistics. Python is a general-purpose language with statistics modules. R has
more statistical analysis features than Python, and specialized syntaxes. However, when it comes to building
complex analysis pipelines that mix statistics with e.g. image analysis, text mining, or control of a physical ex-
periment, the richness of Python is an invaluable asset.

Contents
Data representation and interaction
Data as a table
The pandas data-frame
Hypothesis testing: comparing two groups
Student’s t-test: the simplest statistical test
Paired tests: repeated measurements on the same individuals
Linear models, multiple factors, and analysis of variance
“formulas” to specify statistical models in Python
Multiple Regression: including multiple factors
Post-hoc hypothesis testing: analysis of variance (ANOVA)
More visualization: seaborn for statistical exploration
Pairplot: scatter matrices

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lmplot: plotting a univariate regression

Testing for interactions
Full code for the figures
Solutions to this chapter’s exercises

In this document, the Python inputs are represented with the sign “>>>”.

Disclaimer: Gender questions

Some of the examples of this tutorial are chosen around gender questions. The reason is that on such ques-
tions controlling the truth of a claim actually matters to many people.

3.1.1. Data representation and interaction

3.1.1.1. Data as a table

The setting that we consider for statistical analysis is that of multiple observations or samples described
by a set of different attributes or features. The data can than be seen as a 2D table, or matrix, with col-
umns giving the different attributes of the data, and rows the observations. For instance, the data con-
tained in examples/brain_size.csv:

"";"Gender";"FSIQ";"VIQ";"PIQ";"Weight";"Height";"MRI_Count"
"1";"Female";133;132;124;"118";"64.5";816932
"2";"Male";140;150;124;".";"72.5";1001121
"3";"Male";139;123;150;"143";"73.3";1038437
"4";"Male";133;129;128;"172";"68.8";965353
"5";"Female";137;132;134;"147";"65.0";951545

3.1.1.2. The pandas data-frame

We will store and manipulate this data in a pandas.DataFrame, from the pandas module. It is the Python
equivalent of the spreadsheet table. It is different from a 2D numpy array as it has named columns, can contain
a mixture of different data types by column, and has elaborate selection and pivotal mechanisms.

Creating dataframes: reading data files or converting arrays

Separator

It is a CSV file, but the separator is “;”

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Reading from a CSV file: Using the above CSV file that gives observations of brain size and weight and
IQ (Willerman et al. 1991), the data are a mixture of numerical and categorical values:

>>> import pandas >>>

>>> data = pandas.read_csv('examples/brain_size.csv', sep=';', na_values=
".")
>>> data
Unnamed: 0 Gender FSIQ VIQ PIQ Weight Height MRI_Count
0 1 Female 133 132 124 118.0 64.5 816932
1 2 Male 140 150 124 NaN 72.5 1001121
2 3 Male 139 123 150 143.0 73.3 1038437
3 4 Male 133 129 128 172.0 68.8 965353
4 5 Female 137 132 134 147.0 65.0 951545
...

 Missing values
The weight of the second individual is missing in the CSV file. If we don’t specify the missing value (NA
= not available) marker, we will not be able to do statistical analysis.

Creating from arrays: A pandas.DataFrame can also be seen as a dictionary of 1D ‘series’, eg arrays
or lists. If we have 3 numpy arrays:

>>> import numpy as np >>>

>>> t = np.linspace(-6, 6, 20)
>>> sin_t = np.sin(t)
>>> cos_t = np.cos(t)

We can expose them as a pandas.DataFrame:

>>> pandas.DataFrame({'t': t, 'sin': sin_t, 'cos': cos_t}) >>>

t sin cos
0 -6.000000 0.279415 0.960170
1 -5.368421 0.792419 0.609977
2 -4.736842 0.999701 0.024451
3 -4.105263 0.821291 -0.570509
4 -3.473684 0.326021 -0.945363
5 -2.842105 -0.295030 -0.955488
6 -2.210526 -0.802257 -0.596979
7 -1.578947 -0.999967 -0.008151
8 -0.947368 -0.811882 0.583822
...

Other inputs: pandas can input data from SQL, excel files, or other formats. See the pandas documenta-
tion.

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Manipulating data

data is a pandas.DataFrame, that resembles R’s dataframe:

>>> data.shape # 40 rows and 8 columns >>>

(40, 8)

>>> data.columns # It has columns

Index([u'Unnamed: 0', u'Gender', u'FSIQ', u'VIQ', u'PIQ', u'Weight',
u'Height', u'MRI_Count'], dtype='object')

>>> print(data['Gender']) # Columns can be addressed by name

0 Female
1 Male
2 Male
3 Male
4 Female
...

>>> # Simpler selector

>>> data[data['Gender'] == 'Female']['VIQ'].mean()
109.45

Note: For a quick view on a large dataframe, use its describe method:
pandas.DataFrame.describe().

groupby: splitting a dataframe on values of categorical variables:

>>> groupby_gender = data.groupby('Gender') >>>

>>> for gender, value in groupby_gender['VIQ']:
... print((gender, value.mean()))
('Female', 109.45)
('Male', 115.25)

groupby_gender is a powerful object that exposes many operations on the resulting group of dataframes:

>>> groupby_gender.mean() >>>

Unnamed: 0 FSIQ VIQ PIQ Weight Height MRI_Count
Gender
Female 19.65 111.9 109.45 110.45 137.200000 65.765000 862654.6
Male 21.35 115.0 115.25 111.60 166.444444 71.431579 954855.4

Use tab-completion on groupby_gender to find more. Other common grouping functions are median, count
(useful for checking to see the amount of missing values in different subsets) or sum. Groupby evaluation is
lazy, no work is done until an aggregation function is applied.

Exercise

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What is the mean value for VIQ for the full

population?
How many males/females were included in this
study?

Hint use ‘tab completion’ to find out the methods

that can be called, instead of ‘mean’ in the above
example.
What is the average value of MRI counts expressed
in log units, for males and females?

Note: groupby_gender.boxplot is used for the plots above (see this example).

Plotting data

Pandas comes with some plotting tools (pandas.tools.plotting, using matplotlib behind the scene) to
display statistics of the data in dataframes:

Scatter matrices:

>>> from pandas.tools import plotting >>>

>>> plotting.scatter_matrix(data[['Weight', 'Height', 'MRI_Count']])

>>> plotting.scatter_matrix(data[['PIQ', 'VIQ', 'FSIQ']]) >>>

Two populations

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The IQ metrics are bimodal, as if there

are 2 sub-populations.

Exercise

Plot the scatter matrix for males only, and for females only. Do you think that the 2 sub-populations cor-
respond to gender?

3.1.2. Hypothesis testing: comparing two groups

For simple statistical tests, we will use the scipy.stats sub-module of scipy:

>>> from scipy import stats >>>

See also: Scipy is a vast library. For a quick summary to the whole library, see the scipy chapter.

3.1.2.1. Student’s t-test: the simplest statistical test

1-sample t-test: testing the value of a population mean

scipy.stats.ttest_1samp() tests if the population mean of data is likely to be equal to a given value
(technically if observations are drawn from a Gaussian distributions of given population mean). It returns
the T statistic, and the p-value (see the function’s help):

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>>> stats.ttest_1samp(data['VIQ'], 0) >>>

Ttest_1sampResult(statistic=30.088099970...,
pvalue=1.32891964...e-28)

With a p-value of 10^-28 we can claim that the population mean for the
IQ (VIQ measure) is not 0.

2-sample t-test: testing for difference across populations

We have seen above that the mean VIQ in the male and female populations were different. To test if this
is significant, we do a 2-sample t-test with scipy.stats.ttest_ind():

>>> female_viq = data[data['Gender'] == 'Female']['VIQ'] >>>

>>> male_viq = data[data['Gender'] == 'Male']['VIQ']
>>> stats.ttest_ind(female_viq, male_viq)
Ttest_indResult(statistic=-0.77261617232..., pvalue=0.4445287677858...)

3.1.2.2. Paired tests: repeated measurements on the same individuals

PIQ, VIQ, and FSIQ give 3 measures of IQ. Let us test if

FISQ and PIQ are significantly different. We can use a 2
sample test:

>>> stats.ttest_ind(data['FSIQ'], data[ >>>

'PIQ'])
Ttest_indResult(statistic=0.465637596
38..., pvalue=0.64277250...)

The problem with this approach is that it forgets that there

are links between observations: FSIQ and PIQ are mea-
sured on the same individuals. Thus the variance due to inter-subject variability is confounding, and can
be removed, using a “paired test”, or “repeated measures test”:

>>> stats.ttest_rel(data['FSIQ'], data['PIQ']) >>>

Ttest_relResult(statistic=1.784201940..., pvalue=0.082172638183...)

This is equivalent to a 1-sample test on the difference:

>>> stats.ttest_1samp(data['FSIQ'] - data['PIQ'], 0) >>>

Ttest_1sampResult(statistic=1.784201940..., pvalue=0.082172638...)

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T-tests assume Gaussian errors. We can use a Wilcoxon signed-

rank test, that relaxes this assumption:

>>> stats.wilcoxon(data['FSIQ'], data['PIQ']) >>>

WilcoxonResult(statistic=274.5,
pvalue=0.106594927...)

Note: The corresponding test in the non paired case is the

Mann–Whitney U test, scipy.stats.mannwhitneyu().

Exercise
Test the difference between weights in males and females.
Use non parametric statistics to test the difference between VIQ in males and females.

Conclusion: we find that the data does not support the hypothesis that males and females have differ-
ent VIQ.

3.1.3. Linear models, multiple factors, and analysis of

variance

3.1.3.1. “formulas” to specify statistical models in Python

A simple linear regression

Given two set of observations, x and y, we want to test

the hypothesis that y is a linear function of x. In other
terms:

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where e is observation noise. We will use the statsmodels module to:

1. Fit a linear model. We will use the simplest strategy, ordinary least squares (OLS).
2. Test that coef is non zero.

First, we generate simulated data according to the model:

>>> import numpy as np >>>

>>> x = np.linspace(-5, 5, 20)
>>> np.random.seed(1)
>>> # normal distributed noise
>>> y = -5 + 3*x + 4 * np.random.normal(size=x.shape)
>>> # Create a data frame containing all the relevant variables
>>> data = pandas.DataFrame({'x': x, 'y': y})

“formulas” for statistics in Python

See the statsmodels documentation

Then we specify an OLS model and fit it:

>>> from statsmodels.formula.api import ols >>>

>>> model = ols("y ~ x", data).fit()

We can inspect the various statistics derived from the fit:

>>> print(model.summary()) >>>

OLS Regression Results
==========================...
Dep. Variable: y R-squared:
0.804
Model: OLS Adj. R-squared:
0.794
Method: Least Squares F-statistic:
74.03
Date: ... Prob (F-statistic): 8.56e-
08
Time: ... Log-Likelihood:
-57.988
No. Observations: 20 AIC:
120.0
Df Residuals: 18 BIC:
122.0
Df Model: 1
Covariance Type: nonrobust
==========================...
coef std err t P>|t| [0.025
0.975]
------------------------------------------...
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Intercept -5.5335 1.036 -5.342 0.000 -7.710

-3.357
x 2.9369 0.341 8.604 0.000 2.220
3.654
==========================...
Omnibus: 0.100 Durbin-Watson:
2.956
Prob(Omnibus): 0.951 Jarque-Bera (JB):
0.322
Skew: -0.058 Prob(JB):
0.851
Kurtosis: 2.390 Cond. No.
3.03
==========================...

Warnings:
[1] Standard Errors assume that the covariance matrix of the errors is cor-
rectly specified.

Terminology:

Statsmodels uses a statistical terminology: the y variable in statsmodels is called ‘endogenous’ while
the x variable is called exogenous. This is discussed in more detail here.

To simplify, y (endogenous) is the value you are trying to predict, while x (exogenous) represents the
features you are using to make the prediction.

Exercise

Retrieve the estimated parameters from the model above. Hint: use tab-completion to find the relevent
attribute.

Categorical variables: comparing groups or multiple categories

Let us go back the data on brain size:

>>> data = pandas.read_csv('examples/brain_size.csv', sep=';', na_values= >>>

".")

We can write a comparison between IQ of male and female using a linear model:

>>> model = ols("VIQ ~ Gender + 1", data).fit() >>>

>>> print(model.summary())
OLS Regression Results
==========================...
Dep. Variable: VIQ R-squared:
0.015
Model: OLS Adj. R-squared:
-0.010
Method: Least Squares F-statistic:
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0.5969
Date: ... Prob (F-statistic):
0.445
Time: ... Log-Likelihood:
-182.42
No. Observations: 40 AIC:
368.8
Df Residuals: 38 BIC:
372.2
Df Model: 1
Covariance Type: nonrobust
==========================...
coef std err t P>|t| [0.025 0.975]
-----------------------------------------------------------------------...
Intercept 109.4500 5.308 20.619 0.000 98.704
120.196
Gender[T.Male] 5.8000 7.507 0.773 0.445 -9.397
20.997
==========================...
Omnibus: 26.188 Durbin-Watson:
1.709
Prob(Omnibus): 0.000 Jarque-Bera (JB):
3.703
Skew: 0.010 Prob(JB):
0.157
Kurtosis: 1.510 Cond. No.
2.62
==========================...

Warnings:
[1] Standard Errors assume that the covariance matrix of the errors is cor-
rectly specified.

Tips on specifying model

Forcing categorical: the ‘Gender’ is automatically detected as a categorical variable, and thus each of
its different values are treated as different entities.

An integer column can be forced to be treated as categorical using:

>>> model = ols('VIQ ~ C(Gender)', data).fit() >>>

Intercept: We can remove the intercept using - 1 in the formula, or force the use of an intercept using
+ 1.
By default, statsmodels treats a categorical variable with K possible values as K-1 ‘dummy’ boolean vari-
ables (the last level being absorbed into the intercept term). This is almost always a good default choice -
however, it is possible to specify different encodings for categorical variables
(http://statsmodels.sourceforge.net/devel/contrasts.html).

Link to t-tests between different FSIQ and PIQ

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To compare different types of IQ, we need to create a “long-form” table, listing IQs, where the type of
IQ is indicated by a categorical variable:

>>> data_fisq = pandas.DataFrame({'iq': data['FSIQ'], 'type': 'fsiq'}) >>>

>>> data_piq = pandas.DataFrame({'iq': data['PIQ'], 'type': 'piq'})
>>> data_long = pandas.concat((data_fisq, data_piq))
>>> print(data_long)
iq type
0 133 fsiq
1 140 fsiq
2 139 fsiq
...
31 137 piq
32 110 piq
33 86 piq
...

>>> model = ols("iq ~ type", data_long).fit()

>>> print(model.summary())
OLS Regression Results
...
==========================...
coef std err t P>|t| [0.025
0.975]
------------------------------------------...
Intercept 113.4500 3.683 30.807 0.000 106.119
120.781
type[T.piq] -2.4250 5.208 -0.466 0.643 -12.793
7.943
...

We can see that we retrieve the same values for t-test and corresponding p-values for the effect of the
type of iq than the previous t-test:

>>> stats.ttest_ind(data['FSIQ'], data['PIQ']) >>>

Ttest_indResult(statistic=0.46563759638..., pvalue=0.64277250...)

3.1.3.2. Multiple Regression: including multiple factors

Consider a linear model explaining a variable z (the de-

pendent variable) with 2 variables x and y:

Such a model can be seen in 3D as fitting a plane to a

cloud of (x, y, z) points.

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Example: the iris data (examples/iris.csv)

Sepal and petal size tend to be related: bigger flowers are bigger! But is there in addition a systematic effect of
species?

>>> data = pandas.read_csv('examples/iris.csv') >>>

>>> model = ols('sepal_width ~ name + petal_length', data).fit()
>>> print(model.summary())
OLS Regression Results
==========================...
Dep. Variable: sepal_width R-squared:
0.478
Model: OLS Adj. R-squared:
0.468
Method: Least Squares F-statistic:
44.63
Date: ... Prob (F-statistic): 1.58e-
20
Time: ... Log-Likelihood:
-38.185
No. Observations: 150 AIC:
84.37
Df Residuals: 146 BIC:
96.41
Df Model: 3
Covariance Type: nonrobust
==========================...
coef std err t P>|t| [0.025
0.975]
------------------------------------------...
Intercept 2.9813 0.099 29.989 0.000 2.785
3.178
name[T.versicolor] -1.4821 0.181 -8.190 0.000 -1.840
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-1.124
name[T.virginica] -1.6635 0.256 -6.502 0.000 -2.169
-1.158
petal_length 0.2983 0.061 4.920 0.000 0.178
0.418
==========================...
Omnibus: 2.868 Durbin-Watson:
1.753
Prob(Omnibus): 0.238 Jarque-Bera (JB):
2.885
Skew: -0.082 Prob(JB):
0.236
Kurtosis: 3.659 Cond. No.
54.0
==========================...

Warnings:
[1] Standard Errors assume that the covariance matrix of the errors is cor-
rectly specified.

3.1.3.3. Post-hoc hypothesis testing: analysis of variance (ANOVA)

In the above iris example, we wish to test if the petal length is different between versicolor and virginica,
after removing the effect of sepal width. This can be formulated as testing the difference between the co-
efficient associated to versicolor and virginica in the linear model estimated above (it is an Analysis of
Variance, ANOVA). For this, we write a vector of ‘contrast’ on the parameters estimated: we want to test
"name[T.versicolor] - name[T.virginica]", with an F-test:

>>> print(model.f_test([0, 1, -1, 0])) >>>

<F test: F=array([[3.24533535]]), p=0.07369..., df_denom=146, df_num=1>

Is this difference significant?

Exercise

Going back to the brain size + IQ data, test if the VIQ of male and female are different after removing
the effect of brain size, height and weight.

3.1.4. More visualization: seaborn for statistical exploration

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Seaborn combines simple statistical fits with plotting on pandas dataframes.

Let us consider a data giving wages and many other personal information on 500 individuals (Berndt, ER.
The Practice of Econometrics. 1991. NY: Addison-Wesley).
The full code loading and plotting of the wages data is found in corresponding example.
>>> print(data) >>>
EDUCATION SOUTH SEX EXPERIENCE UNION WAGE AGE RACE \
0 8 0 1 21 0 0.707570 35 2
1 9 0 1 42 0 0.694605 57 3
2 12 0 0 1 0 0.824126 19 3
3 12 0 0 4 0 0.602060 22 3
...

3.1.4.1. Pairplot: scatter matrices

We can easily have an intuition on the interactions between continuous variables using
seaborn.pairplot() to display a scatter matrix:

>>> import seaborn >>>

>>> seaborn.pairplot(data, vars=['WAGE', 'AGE', 'EDUCATION'],
... kind='reg')

Categorical variables can be plotted as the hue:

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>>> seaborn.pairplot(data, vars=['WAGE', 'AGE', 'EDUCATION'], >>>

... kind='reg', hue='SEX')

Look and feel and matplotlib settings

Seaborn changes the default of matplotlib figures to achieve a more “modern”, “excel-like” look. It does
that upon import. You can reset the default using:

>>> from matplotlib import pyplot as plt >>>

>>> plt.rcdefaults()

To switch back to seaborn settings, or understand better styling in seaborn, see the relevent section of the
seaborn documentation.

3.1.4.2. lmplot: plotting a univariate regression

A regression capturing the relation between one variable and another, eg wage and eduction, can be
plotted using seaborn.lmplot():

>>> seaborn.lmplot(y='WAGE', x='EDUCATION', data=data) >>>

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Robust regression
Given that, in the above plot, there seems to be a couple of data points that are outside of the main cloud to
the right, they might be outliers, not representative of the population, but driving the regression.

To compute a regression that is less sentive to outliers, one must use a robust model. This is done in
seaborn using robust=True in the plotting functions, or in statsmodels by replacing the use of the
OLS by a “Robust Linear Model”, statsmodels.formula.api.rlm().

3.1.5. Testing for interactions

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Do wages increase more with education for males than females?

The plot above is made of two different fits. We need to formulate a single model that tests for a variance of
slope across the two populations. This is done via an “interaction”.
>>>
>>> result = sm.ols(formula='wage ~ education + gender + education * gender',
... data=data).fit()
>>> print(result.summary())
...
coef std err t P>|t| [0.025
0.975]
-----------------------------------------------------------------------------
-
Intercept 0.2998 0.072 4.173 0.000 0.159 0.441
gender[T.male] 0.2750 0.093 2.972 0.003 0.093 0.457
education 0.0415 0.005 7.647 0.000 0.031 0.052
education:gender[T.male] -0.0134 0.007 -1.919 0.056 -0.027 0.000
==========================...
...

Can we conclude that education benefits males more than females?

Take home messages

Hypothesis testing and p-values give you the significance of an effect / difference.
Formulas (with categorical variables) enable you to express rich links in your data.
Visualizing your data and fitting simple models give insight into the data.
Conditionning (adding factors that can explain all or part of the variation) is an important model-
ing aspect that changes the interpretation.

3.1.6. Full code for the figures

Code examples for the statistics chapter.

Boxplots and paired Plotting simple quantities Analysis of Iris petal and
differences of a pandas dataframe sepal sizes

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Simple Regression Multiple Regression Test for an

education/gender interac-
tion in wages

Visualizing factors influenc- Air fares before and after

ing wages 9/11

3.1.7. Solutions to this chapter’s exercises

Relating Gender and IQ

Download all examples in Python source code: auto_examples_python.zip

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Download all examples in Jupyter notebooks: auto_examples_jupyter.zip

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