Finding Missing Data After a Pandas Merge

What will you learn?

In this tutorial, you will master the art of pinpointing and retrieving rows that do not align after executing a merge operation in pandas. By understanding the intricacies of merging datasets and utilizing pandas’ functionalities effectively, you will be equipped to identify missing data accurately.

Introduction to the Problem and Solution

When working with datasets and performing merging operations using tools like pandas in Python, it is common to encounter mismatches where some rows do not align due to non-matching keys in the datasets. This discrepancy can hinder your data analysis efforts or prevent you from gaining a complete understanding of your data.

The solution lies in comprehending how the merge function operates and leveraging its parameters efficiently to locate these missing rows. By employing methods such as outer joins and utilizing indicator flags provided by pandas during merge operations, you can effectively identify and extract the unmatched rows. This tutorial will guide you through practical examples, enabling you not only to merge datasets but also to detect any discrepancies seamlessly.


import pandas as pd

# Example DataFrames
df1 = pd.DataFrame({'Key': ['A', 'B', 'C', 'D'],
                    'Value1': [1, 2, 3, 4]})
df2 = pd.DataFrame({'Key': ['B', 'C', 'E'],
                    'Value2': [5, 6, 7]})

# Merging with an indicator
merged_df = df1.merge(df2, on='Key', how='outer', indicator=True)

# Filtering out only those rows exclusive to either DataFrame
excluded_data = merged_df[merged_df['_merge'] != 'both']

# Copyright PHD


In the code snippet above:

  • Step 1: Create two sample DataFrames, df1 and df2, for merging.

  • Step 2: Perform an outer merge using .merge() with key arguments:

    • on=’Key’: Specifies the column used for merging.
    • how=’outer’: Includes all records from both DataFrames.
    • indicator=True: Adds a special column _merge indicating if each row is from one DataFrame (‘left_only’ or ‘right_only’) or both (‘both’).
  • Step 3: Filter out exclusively unmatched rows by checking where _merge does not equal ‘both’.

This method efficiently identifies excluded data post-merge without complex comparisons.

  1. How can I perform an inner join instead?

  2. To perform an inner join, change how=’outer’ in .merge() to how=’inner’.

  3. Can I apply this method with more than two DataFrames?

  4. Yes! However, successive merges and checks are required for each additional DataFrame.

  5. What if my DataFrames have different key column names?

  6. Use left_on= and right_on= instead of “on=” in .merge(), specifying respective columns.

  7. How do I maintain indexes after merging?

  8. Set ignore_index=False.

  9. What other types of joins are available besides outer and inner?

  10. You can use ‘left’, ‘right’, or even a cross join using ‘cross’.


Identifying excluded data rows post-merging is essential for thorough data analysis. Mastering techniques such as outer joins and indicators in pandas empowers you to ensure data integrity and completeness during transformation processes. Enhance your skills as a data professional by mastering these powerful features offered by pandas.

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