5 Best Ways to Compare Two DataFrames in Python Pandas with Missing Values

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πŸ’‘ Problem Formulation: When working with data in Python, it’s common to encounter the need to compare data sets for validation, consistency, or merging purposes. This article specifically tackles the challenge of comparing two Pandas DataFrames when there are missing values present. Assume we have two DataFrames df1 and df2, each containing similar data with potential discrepancies and NaN values. Our goal is to find an efficient and clear way to identify differences between these DataFrames.

Method 1: Using equals() Method

This method provides a quick way to check if two DataFrames are entirely equal, including the positions of missing values. The equals() function in Pandas returns a Boolean value indicating whether two DataFrames are the same, accounting for NaN locations. However, this method doesn’t provide detail about where the differences lie.

Here’s an example:

import pandas as pd

# Sample DataFrames with missing values
df1 = pd.DataFrame({'A': [1, 2, pd.NA], 'B': [4, pd.NA, 6]})
df2 = pd.DataFrame({'A': [1, pd.NA, 3], 'B': [4, 5, pd.NA]})

# Compare DataFrames
are_equal = df1.equals(df2)



This code snippet uses the equals() method to quickly determine if the two DataFrames df1 and df2 are identical. Since the content, including missing values, does not match perfectly, the output is False.

Method 2: Using the compare() Method

The compare() method in Pandas is particularly useful for identifying specific differences between two DataFrames. The output is a new DataFrame that highlights the changes from df1 to df2, including handling of missing values. This method makes it easier to visualize and understand where the discrepancies are located.

Here’s an example:

# Using the same sample DataFrames from Method 1
# Comparing DataFrames and displaying differences
differences = df1.compare(df2)


     A           B      
  self other self other
1    2   NaN  NaN     5
2  NaN     3    6   NaN

The code snippet uses the compare() method to show a side-by-side comparison where differences exist. Non-matching entries are shown with ‘self’ representing df1 and ‘other’ representing df2, which makes discrepancies easy to spot.

Method 3: Subtracting DataFrames

Subtracting one DataFrame from another is a way to perform element-wise comparison, which will result in a DataFrame filled with NaNs for identical positions and the actual differences for non-matching elements. This method could be confusing if original DataFrames contain NaNs, as subtraction involving NaNs also results in NaN, which could be misinterpreted as equality.

Here’s an example:

# Using the same sample DataFrames from Method 1
# Subtracting DataFrames to find differences
differences = df1 - df2


      A    B
0   NaN  NaN
1   NaN  NaN

This code snippet demonstrates subtraction of df2 from df1, which shows NaN for all elements that either match or involve NaNs in the operation. It’s important to note that this method only indicates differences where both corresponding values are numbers and not NaN.

Method 4: Using merge() with Indicator

By merging two DataFrames with an indicator flag, we can determine if a row exists in one, both, or neither of the DataFrames. This method is beneficial for overall comparison and is often used in conjunction with other methods for detail-specific exploration. Merging can be computationally expensive for large datasets.

Here’s an example:

# Using the same sample DataFrames from Method 1
# Merging DataFrames with an indicator
comparison_df = df1.merge(df2, indicator=True, how='outer')


      A    B      _merge
0     1    4        both
1     2    left_only
2   NaN    6  left_only
3      5  right_only
4     3   right_only

The code snippet uses the merge() function with the how='outer' argument and an indicator to show where the rows originate. The output column _merge indicates which DataFrame each row is unique to, or if it’s present in both.

Bonus One-Liner Method 5: Using where() to Mask Differences

The where() function in Pandas can be used to mask the data of one DataFrame with the data from another DataFrame wherever the condition is False. This one-liner can be handy to directly spot differences, especially when combined with visual methods such as highlighting in a spreadsheet. Consider this less of a method and more of a quick check or data inspection technique.

Here’s an example:

# Using the same sample DataFrames from Method 1
# Masking df2 with df1 to highlight differences
masked_df = df1.where(df1 == df2)


     A    B
0  1.0  4.0
1  NaN  NaN
2  NaN  NaN

This code snippet masks df2 with df1 using the where() method, essentially providing a DataFrame with elements from df1 where both DataFrames match and NaN for differing values, helping to quickly spot where differences lie.


  • Method 1: Using equals(). Quick binary comparison. Does not provide details on differences. Best for quick checks.
  • Method 2: Using the compare() method. Gives a detailed overview of differences. Good for thorough analysis on small to moderate sized DataFrames.
  • Method 3: Subtracting DataFrames. Potentially confusing due to NaN handling but useful for numeric comparisons. Quick but with limitations on interpretability.
  • Method 4: Using merge() with an indicator. Helpful for comparing DataFrames at the row level. Computational cost can be high for large datasets.
  • Bonus Method 5: Using where() to mask differences. Great for spotting differences visually. Works well as a supplementary check rather than a standalone method.