5 Best Ways to Merge Dataframes of Different Lengths in Python

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πŸ’‘ Problem Formulation: When working with data in Python, analysts often face the challenge of merging two datasets (dataframes) of varying lengths. Consider having a dataframe of customer information and another of order details; these two dataframes may have a different number of rows. How can you merge these effectively to analyze the data together? This article provides a guiding example with input dataframes of different lengths and demonstrates how to merge them to obtain a combined dataset.

Method 1: Concatenation with pd.concat()

Concatenation with pd.concat() allows you to stack dataframes vertically or horizontally. When merging dataframes of different lengths, often you’ll want to stack them vertically. It’s an efficient way to combine dataframes even when they don’t have the same columns or row counts.

Here’s an example:

import pandas as pd

# Create two dataframes of different lengths
df1 = pd.DataFrame({'A': [1, 2], 'B': [3, 4]})
df2 = pd.DataFrame({'A': [5, 6, 7], 'B': [8, 9, 10]})

# Concatenate dataframes vertically
result = pd.concat([df1, df2], ignore_index=True)


   A   B
0  1   3
1  2   4
2  5   8
3  6   9
4  7  10

This code snippet uses pd.concat() to combine two dataframes df1 and df2 along the rows, which is specified by not setting the axis parameter (as the default is 0, for rows). The ignore_index=True parameter is used to reindex the combined dataframe, ensuring it has a proper sequence of index labels.

Method 2: Merge with pd.merge()

Using pd.merge() is the go-to method for joining two datasets based on a common column or index, analogous to SQL JOIN operations. It’s beneficial when the dataframes share a key and you want to merge them side-by-side, matching the rows by this key.

Here’s an example:

import pandas as pd

# DataFrames with a common column 'Key'
df1 = pd.DataFrame({'Key': ['A', 'B'], 'Data1': [1, 2]})
df2 = pd.DataFrame({'Key': ['A', 'B', 'C'], 'Data2': [3, 4, 5]})

# Merge dataframes on 'Key'
result = pd.merge(df1, df2, on='Key', how='outer')


  Key  Data1  Data2
0   A    1.0      3
1   B    2.0      4
2   C    NaN      5

The example showcases how pd.merge() method merges two dataframes df1 and df2 on a shared column ‘Key’. The how='outer' argument specifies an outer join, ensuring that all keys from both dataframes are included, with NaN for missing values.

Method 3: Custom merge with pd.DataFrame.append()

Appending dataframes with pd.DataFrame.append() is a quick way to stack rows from one dataframe to another. It doesn’t require creating a separate concatenated object and can be used for swiftly adding new records. However, it doesn’t align the dataframes based on keys or indexes like merge does.

Here’s an example:

import pandas as pd

# DataFrames of different lengths
df1 = pd.DataFrame({'Col1': [1, 2]})
df2 = pd.DataFrame({'Col1': [3, 4, 5]})

# Append df2 to df1
result = df1.append(df2, ignore_index=True)


0     1
1     2
2     3
3     4
4     5

This snippet implements df1.append(df2) to stack df2 underneath df1. The ignore_index=True flag reassigns index numbers for the new combined dataframe, creating a continuous range from 0 to n-1.

Method 4: Use of pd.DataFrame.join()

The pd.DataFrame.join() method is convenient for combining different dataframes while aligning them on their indexes. It is especially useful if the dataframes have the same indexes but different columns. It provides a single-join interface to simplify the operation.

Here’s an example:

import pandas as pd

# Two DataFrames with same index but different columns
df1 = pd.DataFrame({'Data1': [1, 2]}, index=['X', 'Y'])
df2 = pd.DataFrame({'Data2': [3, 4, 5]}, index=['X', 'Y', 'Z'])

# Join df2 to df1 aligned by index
result = df1.join(df2, how='outer')


   Data1  Data2
X    1.0      3
Y    2.0      4
Z    NaN      5

Here, df1.join(df2, how='outer') merges the dataframes based on their index. The how='outer' ensures that the final dataframe has the union of indexes from both original dataframes and introduces NaN where values are missing.

Bonus One-Liner Method 5: combine_first()

For a quick one-liner, pd.DataFrame.combine_first() allows you to stack two dataframes and automatically fill in NaN values from one dataframe with corresponding values from another. It’s handy when you need to complement the missing data in one dataframe with another’s data without explicitly joining on a key.

Here’s an example:

import pandas as pd

# DataFrames with overlapping, but incomplete data
df1 = pd.DataFrame({'A': [1, np.nan]})
df2 = pd.DataFrame({'A': [np.nan, 2]})

# Use df2 to fill in missing values in df1
result = df1.combine_first(df2)


0  1.0
1  2.0

This one-liner df1.combine_first(df2) is used to fill in the missing values in df1 with data from df2. Its conciseness makes it appealing when merging two dataframes of varying lengths to complement each other.


  • Method 1: Concatenation with pd.concat(). Best for simply stacking datasets vertically or horizontally. Not key-based, meaning it won’t match rows on a specific column.
  • Method 2: Merge with pd.merge(). Ideal for key-based joins and complex mergers, similar to SQL JOIN operations. It can handle different join types but is more complex than other methods.
  • Method 3: Custom merge with pd.DataFrame.append(). Good for quick row additions. It won’t match data and is less efficient with large dataframes.
  • Method 4: Use of pd.DataFrame.join(). Useful when dataframes share the same index. Provides an easy interface for combining dataframes but is limited to index-based joins.
  • Bonus Method 5: One-liner combine_first(). Quick fix to fill missing data by leveraging another dataframe. Simple to use but provides less control over the merge logic.