scikit-na

scikit-na is a Python package for missing data (NA) analysis. The package includes many functions for statistical analysis, modeling, and data visualization. The latter is done using two packages — matplotlib and Altair.

Features

• Interactive report (based on ipywidgets)
• Descriptive statistics
• Regression modeling
• Hypotheses tests
• Data visualization

Donate

If you find this package useful, please consider donating any amount of money. This will help me spend more time on supporting open-source software.

Installation

Package can be installed from PyPi:

pip install scikit-na

or from this repo:

pip install git+https://github.com/maximtrp/scikit-na.git

Example

We will use Titanic dataset (from Kaggle) that contains NA values in three columns: Age, Cabin, and Embarked.

Summary

Per each column

By default, summary() function returns the results for each column.

import scikit_na as na
import pandas as pd

data = pd.read_csv('titanic_dataset.csv')

# Excluding three columns without NA to fit the table here
na.summary(data, columns=data.columns.difference(['SibSp', 'Parch', 'Ticket']))

	Age	Cabin	Embarked	Fare	Name	PassengerId	Pclass	Sex	Survived
NA count	177	687	2	0	0	0	0	0	0
NA, % (per column)	19.87	77.1	0.22	0	0	0	0	0	0
NA, % (of all NAs)	20.44	79.33	0.23	0	0	0	0	0	0
NA unique (per column)	19	529	2	0	0	0	0	0	0
NA unique, % (per column)	10.73	77	100	0	0	0	0	0	0
Rows left after dropna()	714	204	889	891	891	891	891	891	891
Rows left after dropna(), %	80.13	22.9	99.78	100	100	100	100	100	100

NA unique is the number of NA values per each column that are unique for it, i.e. do not intersect with NA values in the other columns (or that will remain in dataset if we drop NA values in the other columns).

Whole dataset

We can also get a summary of missing data for the whole dataset:

na.summary(data, per_column=False)

	dataset
Total columns	12
Total rows	891
Rows with NA	708
Rows without NA	183
Total cells	10692
Cells with NA	866
Cells with NA, %	8.1
Cells with non-missing data	9826
Cells with non-missing data, %	91.9

Correlations

To calculate correlations between columns in terms of missing data, just call correlate() function with your DataFrame as the first argument:

na.correlate(data, method="spearman").round(3)

	Embarked	Age	Cabin
Embarked	1	-0.024	-0.087
Age	-0.024	1	0.144
Cabin	-0.087	0.144	1

This method can be used to uncover hidden patterns in missing data across many columns in a dataset. Columns with no missing data are automatically excluded.

There is a function to visualize correlations with a heatmap:

na.altair\
    .plot_corr(data, corr_kws={'method': 'spearman'})
    .properties(width=150, height=150)

Visualization

Heatmap

Now, let's visualize NA values on a heatmap. We will be using Altair + Vega backend:

na.altair.plot_heatmap(data)

Droppables are those values that will be dropped if we simply use pandas.DataFrame.dropna() on the whole dataset.

Stairs plot

Stairs plot is one more useful visualization of dataset shrinkage on applying pandas.Series.dropna() method to each column sequentially (sorted by the number of NA values, by default):

na.altair.plot_stairs(data)

After dropping all NAs in Cabin column, we are left with 21 more NAs (in Age and Embarked columns). This plot also shows tooltips with exact numbers of NA values that are dropped per each column.

Histogram

You may need to adjust some parameters before a histogram starts looking as you expect:

chart = na.altair.plot_hist(data, col='Pclass', col_na='Age')\
    .properties(width=200, height=200)
chart.configure_axisX(labelAngle = 0)

Regression model

We can build a logistic regression model with Age as a dependent variable and Fare, Parch, Pclass, SibSp, Survived as independent variables. Internally, pandas.Series.isna() method is called on Age column, and the resulting boolean values are converted to integers (True/False becomes 1/0). Finally, fitting a logistic model is done by statsmodels package:

# Selecting columns with numeric data
# Dropping "PassengerId" column
subset = data.loc[:, data.dtypes != object].drop(columns=['PassengerId'])
model = na.model(subset, col_na='Age')
model.summary()

Optimization terminated successfully.
Current function value: 0.467801
Iterations 7
                        Logit Regression Results                           
===============================================================================
Dep. Variable:                    Age   No. Observations:                   891
Model:                          Logit   Df Residuals:                       885
Method:                           MLE   Df Model:                             5
Date:                Sat, 05 Jun 2021   Pseudo R-squ.:                  0.06164
Time:                        17:51:31   Log-Likelihood:                 -416.81
converged:                       True   LL-Null:                        -444.19
Covariance Type:            nonrobust   LLR p-value:                  1.463e-10
===============================================================================
                coef    std err          z      P>|z|      [0.025      0.975]
-------------------------------------------------------------------------------
(intercept)    -2.7294      0.429     -6.369      0.000      -3.569      -1.890
Fare            0.0010      0.003      0.376      0.707      -0.004       0.006
Parch          -0.8874      0.223     -3.984      0.000      -1.324      -0.451
Pclass          0.5953      0.147      4.046      0.000       0.307       0.884
SibSp           0.2548      0.095      2.684      0.007       0.069       0.441
Survived       -0.1026      0.198     -0.519      0.604      -0.490       0.285
===============================================================================

Interactive report

Use scikit_na.report() function to show interactive report interface:

na.report(data)

Contribution

Any contribution is highly appreciated: pull requests, suggestions, or bug reports.