Dealing with missing values#

Dealing with missing values is a common challenge in data analysis and modelling.

Missing data can occur for various reasons, including data entry errors, equipment failure, or simply because the data was not collected. Failing to handle missing data appropriately can lead to biased or inaccurate results. It may negatively impact the performance of machine learning models.

This notebook will explore different strategies for handling missing data in Pandas, including removing missing data, imputing missing values with means or medians, and using advanced imputation techniques.

How To#

import pandas as pd
import missingno as msno
df = pd.read_csv("data/housing.csv")
msno.matrix(df)
<Axes: >
../_images/560ed9d405563cd6dde3efd5f47c5880b2351eab9acb911e1024363d91486fba.png
df
longitude latitude housing_median_age total_rooms total_bedrooms population households median_income median_house_value ocean_proximity
0 -122.23 37.88 41.0 880.0 129.0 322.0 126.0 8.3252 452600.0 NEAR BAY
1 -122.22 37.86 21.0 7099.0 1106.0 2401.0 1138.0 8.3014 358500.0 NEAR BAY
2 -122.24 37.85 52.0 1467.0 190.0 496.0 177.0 7.2574 352100.0 NEAR BAY
3 -122.25 37.85 52.0 1274.0 235.0 558.0 219.0 5.6431 341300.0 NEAR BAY
4 -122.25 37.85 52.0 1627.0 280.0 565.0 259.0 3.8462 342200.0 NEAR BAY
... ... ... ... ... ... ... ... ... ... ...
20635 -121.09 39.48 25.0 1665.0 374.0 845.0 330.0 1.5603 78100.0 INLAND
20636 -121.21 39.49 18.0 697.0 150.0 356.0 114.0 2.5568 77100.0 INLAND
20637 -121.22 39.43 17.0 2254.0 485.0 1007.0 433.0 1.7000 92300.0 INLAND
20638 -121.32 39.43 18.0 1860.0 409.0 741.0 349.0 1.8672 84700.0 INLAND
20639 -121.24 39.37 16.0 2785.0 616.0 1387.0 530.0 2.3886 89400.0 INLAND

20640 rows Γ— 10 columns

msno.bar(df)
<Axes: >
../_images/08ded46392e18908e8b3f685fe368d3c899f4afdd4b57b1d4ffb3ef2418d00b5.png
collisions = pd.read_csv("https://raw.githubusercontent.com/ResidentMario/missingno-data/master/nyc_collision_factors.csv")
collisions.head()
DATE TIME BOROUGH ZIP CODE LATITUDE LONGITUDE LOCATION ON STREET NAME CROSS STREET NAME OFF STREET NAME ... CONTRIBUTING FACTOR VEHICLE 1 CONTRIBUTING FACTOR VEHICLE 2 CONTRIBUTING FACTOR VEHICLE 3 CONTRIBUTING FACTOR VEHICLE 4 CONTRIBUTING FACTOR VEHICLE 5 VEHICLE TYPE CODE 1 VEHICLE TYPE CODE 2 VEHICLE TYPE CODE 3 VEHICLE TYPE CODE 4 VEHICLE TYPE CODE 5
0 11/10/2016 16:11:00 BROOKLYN 11208.0 40.662514 -73.872007 (40.6625139, -73.8720068) WORTMAN AVENUE MONTAUK AVENUE NaN ... Failure to Yield Right-of-Way Unspecified NaN NaN NaN TAXI PASSENGER VEHICLE NaN NaN NaN
1 11/10/2016 05:11:00 MANHATTAN 10013.0 40.721323 -74.008344 (40.7213228, -74.0083444) HUBERT STREET HUDSON STREET NaN ... Failure to Yield Right-of-Way NaN NaN NaN NaN PASSENGER VEHICLE NaN NaN NaN NaN
2 04/16/2016 09:15:00 BROOKLYN 11201.0 40.687999 -73.997563 (40.6879989, -73.9975625) HENRY STREET WARREN STREET NaN ... Lost Consciousness Lost Consciousness NaN NaN NaN PASSENGER VEHICLE VAN NaN NaN NaN
3 04/15/2016 10:20:00 QUEENS 11375.0 40.719228 -73.854542 (40.7192276, -73.8545422) NaN NaN 67-64 FLEET STREET ... Failure to Yield Right-of-Way Failure to Yield Right-of-Way Failure to Yield Right-of-Way NaN NaN PASSENGER VEHICLE PASSENGER VEHICLE PASSENGER VEHICLE NaN NaN
4 04/15/2016 10:35:00 BROOKLYN 11210.0 40.632147 -73.952731 (40.6321467, -73.9527315) BEDFORD AVENUE CAMPUS ROAD NaN ... Failure to Yield Right-of-Way Failure to Yield Right-of-Way NaN NaN NaN PASSENGER VEHICLE PASSENGER VEHICLE NaN NaN NaN

5 rows Γ— 26 columns

import numpy as np
collisions = collisions.replace("nan", np.nan)

pd.read_csv(β€œβ€, na_values=[β€œnan”, -999.25])

msno.matrix(collisions)
<Axes: >
../_images/bf376a60301bb6d60aa0e3f2d47ba24c6ef0f6b99d00b88e8a5df68346b028b3.png
msno.bar(collisions)
<Axes: >
../_images/078c12cc54c72a5e3506be4250d19b55bad7166946f227d670d060569b4f46ce.png
msno.dendrogram(collisions)
<Axes: >
../_images/4a48baa214413e04242fa4f14375c4f38ac9e8b088395fd2170515be63a06f72.png

Imputing missing values#

df.head()
longitude latitude housing_median_age total_rooms total_bedrooms population households median_income median_house_value ocean_proximity
0 -122.23 37.88 41.0 880.0 129.0 322.0 126.0 8.3252 452600.0 NEAR BAY
1 -122.22 37.86 21.0 7099.0 1106.0 2401.0 1138.0 8.3014 358500.0 NEAR BAY
2 -122.24 37.85 52.0 1467.0 190.0 496.0 177.0 7.2574 352100.0 NEAR BAY
3 -122.25 37.85 52.0 1274.0 235.0 558.0 219.0 5.6431 341300.0 NEAR BAY
4 -122.25 37.85 52.0 1627.0 280.0 565.0 259.0 3.8462 342200.0 NEAR BAY
df.isnull().sum()
longitude               0
latitude                0
housing_median_age      0
total_rooms             0
total_bedrooms        207
population              0
households              0
median_income           0
median_house_value      0
ocean_proximity         0
dtype: int64
df["total_bedrooms_corrected"] = df["total_bedrooms"] # copy
df["total_bedrooms_corrected"].fillna(df["total_bedrooms"].median(), inplace=True)
df.isnull().sum()
longitude                     0
latitude                      0
housing_median_age            0
total_rooms                   0
total_bedrooms              207
population                    0
households                    0
median_income                 0
median_house_value            0
ocean_proximity               0
total_bedrooms_corrected      0
dtype: int64
df[["total_bedrooms", "total_bedrooms_corrected"]].head()
total_bedrooms total_bedrooms_corrected
0 129.0 129.0
1 1106.0 1106.0
2 190.0 190.0
3 235.0 235.0
4 280.0 280.0

Scikit Learn Imputation#

from sklearn.impute import SimpleImputer
imp = SimpleImputer(missing_values=np.nan, strategy='median')
median_imp = imp.fit_transform(df[["total_bedrooms"]])
median_imp == df[["total_bedrooms_corrected"]]
total_bedrooms_corrected
0 True
1 True
2 True
3 True
4 True
... ...
20635 True
20636 True
20637 True
20638 True
20639 True

20640 rows Γ— 1 columns

Exercise#

Explore missingno with the NYC collision dataset.

!pip install quilt
!quilt install ResidentMario/missingno_data
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[notice] A new release of pip is available: 23.0.1 -> 23.3.2
[notice] To update, run: pip install --upgrade pip
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Additional Resources#