Pandas Merging 101 | Python pandas [Answered]

In this post we’ll be sharing the top best answers for the following queries:

  • How can I perform a (INNER| (LEFT|RIGHT|FULLOUTERJOIN with pandas?
  • How do I add NaNs for missing rows after a merge?
  • How do I get rid of NaNs after merging?
  • Can I merge on the index?
  • How do I merge multiple DataFrames?
  • Cross join with pandas
  • mergejoinconcatupdate? Who? What? Why?!

… and more. I’ve seen these recurring questions asking about various facets of the pandas merge functionality. Most of the information regarding merge and its various use cases today is fragmented across dozens of badly worded, unsearchable posts. The aim here is to collate some of the more important points for posterity.

Pandas merging 101- Answer #1:

This post aims to give readers a primer on SQL-flavored merging with Pandas, how to use it, and when not to use it.

In particular, here’s what this post will go through:

  • The basics – types of joins (LEFT, RIGHT, OUTER, INNER)
    • merging with different column names
    • merging with multiple columns
    • avoiding duplicate merge key column in output

What this post (and other posts by me on this thread) will not go through:

  • Performance-related discussions and timings (for now). Mostly notable mentions of better alternatives, wherever appropriate.
  • Handling suffixes, removing extra columns, renaming outputs, and other specific use cases. There are other (read: better) posts that deal with that, so figure it out!

Note Most examples default to INNER JOIN operations while demonstrating various features, unless otherwise specified.

Furthermore, all the DataFrames here can be copied and replicated so you can play with them. Also, see this post on how to read DataFrames from your clipboard.

Lastly, all visual representation of JOIN operations have been hand-drawn using Google Drawings. Inspiration from here.

Enough talk – just show me how to use merge!

Setup & Basics

left = pd.DataFrame({'key': ['A', 'B', 'C', 'D'], 'value': np.random.randn(4)})
right = pd.DataFrame({'key': ['B', 'D', 'E', 'F'], 'value': np.random.randn(4)})


  key     value
0   A  1.764052
1   B  0.400157
2   C  0.978738
3   D  2.240893


  key     value
0   B  1.867558
1   D -0.977278
2   E  0.950088
3   F -0.151357

For the sake of simplicity, the key column has the same name (for now).

An INNER JOIN is represented by

Note This, along with the forthcoming figures all follow this convention:

  • blue indicates rows that are present in the merge result
  • red indicates rows that are excluded from the result (i.e., removed)
  • green indicates missing values that are replaced with NaNs in the result

To perform an INNER JOIN, call merge on the left DataFrame, specifying the right DataFrame and the join key (at the very least) as arguments.

left.merge(right, on='key')
# Or, if you want to be explicit
# left.merge(right, on='key', how='inner')

  key   value_x   value_y
0   B  0.400157  1.867558
1   D  2.240893 -0.977278

This returns only rows from left and right which share a common key (in this example, “B” and “D).

LEFT OUTER JOIN, or LEFT JOIN is represented by

This can be performed by specifying how='left'.

left.merge(right, on='key', how='left')

  key   value_x   value_y
0   A  1.764052       NaN
1   B  0.400157  1.867558
2   C  0.978738       NaN
3   D  2.240893 -0.977278

Carefully note the placement of NaNs here. If you specify how='left', then only keys from left are used, and missing data from right is replaced by NaN.

And similarly, for a RIGHT OUTER JOIN, or RIGHT JOIN which is…

…specify how='right':

left.merge(right, on='key', how='right')

  key   value_x   value_y
0   B  0.400157  1.867558
1   D  2.240893 -0.977278
2   E       NaN  0.950088
3   F       NaN -0.151357

Here, keys from right are used, and missing data from left is replaced by NaN.

Finally, for the FULL OUTER JOIN, given by

specify how='outer'.

left.merge(right, on='key', how='outer')

  key   value_x   value_y
0   A  1.764052       NaN
1   B  0.400157  1.867558
2   C  0.978738       NaN
3   D  2.240893 -0.977278
4   E       NaN  0.950088
5   F       NaN -0.151357

This uses the keys from both frames, and NaNs are inserted for missing rows in both.

The documentation summarizes these various merges nicely:

Enter image description here

Other JOINs – LEFT-Excluding, RIGHT-Excluding, and FULL-Excluding/ANTI JOINs

If you need LEFT-Excluding JOINs and RIGHT-Excluding JOINs in two steps.

For LEFT-Excluding JOIN, represented as

Start by performing a LEFT OUTER JOIN and then filtering (excluding!) rows coming from left only,

(left.merge(right, on='key', how='left', indicator=True)
     .query('_merge == "left_only"')
     .drop('_merge', 1))

  key   value_x  value_y
0   A  1.764052      NaN
2   C  0.978738      NaN


left.merge(right, on='key', how='left', indicator=True)

  key   value_x   value_y     _merge
0   A  1.764052       NaN  left_only
1   B  0.400157  1.867558       both
2   C  0.978738       NaN  left_only
3   D  2.240893 -0.977278       both

And similarly, for a RIGHT-Excluding JOIN,

(left.merge(right, on='key', how='right', indicator=True)
     .query('_merge == "right_only"')
     .drop('_merge', 1))

  key  value_x   value_y
2   E      NaN  0.950088
3   F      NaN -0.151357

Lastly, if you are required to do a merge that only retains keys from the left or right, but not both (IOW, performing an ANTI-JOIN),

You can do this in similar fashion—

(left.merge(right, on='key', how='outer', indicator=True)
     .query('_merge != "both"')
     .drop('_merge', 1))

  key   value_x   value_y
0   A  1.764052       NaN
2   C  0.978738       NaN
4   E       NaN  0.950088
5   F       NaN -0.151357

Different names for key columns

If the key columns are named differently—for example, left has keyLeft, and right has keyRight instead of key—then you will have to specify left_on and right_on as arguments instead of on:

left2 = left.rename({'key':'keyLeft'}, axis=1)
right2 = right.rename({'key':'keyRight'}, axis=1)


  keyLeft     value
0       A  1.764052
1       B  0.400157
2       C  0.978738
3       D  2.240893


  keyRight     value
0        B  1.867558
1        D -0.977278
2        E  0.950088
3        F -0.151357
left2.merge(right2, left_on='keyLeft', right_on='keyRight', how='inner')

  keyLeft   value_x keyRight   value_y
0       B  0.400157        B  1.867558
1       D  2.240893        D -0.977278

Avoiding duplicate key column in output

When merging on keyLeft from left and keyRight from right, if you only want either of the keyLeft or keyRight (but not both) in the output, you can start by setting the index as a preliminary step.

left3 = left2.set_index('keyLeft')
left3.merge(right2, left_index=True, right_on='keyRight')

    value_x keyRight   value_y
0  0.400157        B  1.867558
1  2.240893        D -0.977278

Contrast this with the output of the command just before (that is, the output of left2.merge(right2, left_on='keyLeft', right_on='keyRight', how='inner')), you’ll notice keyLeft is missing. You can figure out what column to keep based on which frame’s index is set as the key. This may matter when, say, performing some OUTER JOIN operation.

Merging only a single column from one of the DataFrames

For example, consider

right3 = right.assign(newcol=np.arange(len(right)))
  key     value  newcol
0   B  1.867558       0
1   D -0.977278       1
2   E  0.950088       2
3   F -0.151357       3

If you are required to merge only “new_val” (without any of the other columns), you can usually just subset columns before merging:

left.merge(right3[['key', 'newcol']], on='key')

  key     value  newcol
0   B  0.400157       0
1   D  2.240893       1

If you’re doing a LEFT OUTER JOIN, a more performant solution would involve map:

# left['newcol'] = left['key'].map(right3.set_index('key')['newcol']))

  key     value  newcol
0   A  1.764052     NaN
1   B  0.400157     0.0
2   C  0.978738     NaN
3   D  2.240893     1.0

As mentioned, this is similar to, but faster than

left.merge(right3[['key', 'newcol']], on='key', how='left')

  key     value  newcol
0   A  1.764052     NaN
1   B  0.400157     0.0
2   C  0.978738     NaN
3   D  2.240893     1.0

Merging on multiple columns

To join on more than one column, specify a list for on (or left_on and right_on, as appropriate).

left.merge(right, on=['key1', 'key2'] ...)

Or, in the event the names are different,

left.merge(right, left_on=['lkey1', 'lkey2'], right_on=['rkey1', 'rkey2'])

Other useful merge* operations and functions

This section only covers the very basics, and is designed to only whet your appetite. For more examples and cases, see the documentation on mergejoin, and concat as well as the links to the function specifications.

Follow the other answers of the post to continue learning.

Pandas merging 101- Answer #2:

This answer will go through the following topics:

  • Merging with index under different conditions
    • options for index-based joins: mergejoinconcat
    • merging on indexes
    • merging on index of one, column of other
  • effectively using named indexes to simplify merging syntax

Index-based joins


There are a few options, some simpler than others depending on the use case.

  1. DataFrame.merge with left_index and right_index (or left_on and right_on using names indexes)
    • supports inner/left/right/full
    • can only join two at a time
    • supports column-column, index-column, index-index joins
  2. DataFrame.join (join on index)
    • supports inner/left (default)/right/full
    • can join multiple DataFrames at a time
    • supports index-index joins
  3. pd.concat (joins on index)
    • supports inner/full (default)
    • can join multiple DataFrames at a time
    • supports index-index joins

Index to index joins

Setup & Basics

import pandas as pd
import numpy as np

np.random.seed([3, 14])
left = pd.DataFrame(data={'value': np.random.randn(4)}, 
                    index=['A', 'B', 'C', 'D'])    
right = pd.DataFrame(data={'value': np.random.randn(4)},  
                     index=['B', 'D', 'E', 'F']) = = 'idxkey'

A      -0.602923
B      -0.402655
C       0.302329
D      -0.524349

B       0.543843
D       0.013135
E      -0.326498
F       1.385076

Typically, an inner join on index would look like this:

left.merge(right, left_index=True, right_index=True)

         value_x   value_y
B      -0.402655  0.543843
D      -0.524349  0.013135

Other joins follow similar syntax.

Notable Alternatives

  1. DataFrame.join defaults to joins on the index. DataFrame.join does a LEFT OUTER JOIN by default, so how='inner' is necessary here. left.join(right, how='inner', lsuffix='_x', rsuffix='_y') value_x value_y idxkey B -0.402655 0.543843 D -0.524349 0.013135 Note that I needed to specify the lsuffix and rsuffix arguments since join would otherwise error out: left.join(right) ValueError: columns overlap but no suffix specified: Index(['value'], dtype='object') Since the column names are the same. This would not be a problem if they were differently named. left.rename(columns={'value':'leftvalue'}).join(right, how='inner') leftvalue value idxkey B -0.402655 0.543843 D -0.524349 0.013135
  2. pd.concat joins on the index and can join two or more DataFrames at once. It does a full outer join by default, so how='inner' is required here.. pd.concat([left, right], axis=1, sort=False, join='inner') value value idxkey B -0.402655 0.543843 D -0.524349 0.013135 For more information on concat, see this post.

Index to Column joins

To perform an inner join using index of left, column of right, you will use DataFrame.merge a combination of left_index=True and right_on=....

right2 = right.reset_index().rename({'idxkey' : 'colkey'}, axis=1)
  colkey     value
0      B  0.543843
1      D  0.013135
2      E -0.326498
3      F  1.385076

left.merge(right2, left_index=True, right_on='colkey')

    value_x colkey   value_y
0 -0.402655      B  0.543843
1 -0.524349      D  0.013135

Other joins follow a similar structure. Note that only merge can perform index to column joins. You can join on multiple columns, provided the number of index levels on the left equals the number of columns on the right.

join and concat are not capable of mixed merges. You will need to set the index as a pre-step using DataFrame.set_index.

Effectively using Named Index [pandas >= 0.23]

If your index is named, then from pandas >= 0.23, DataFrame.merge allows you to specify the index name to on (or left_on and right_on as necessary).

left.merge(right, on='idxkey')

         value_x   value_y
B      -0.402655  0.543843
D      -0.524349  0.013135

For the previous example of merging with the index of left, column of right, you can use left_on with the index name of left:

left.merge(right2, left_on='idxkey', right_on='colkey')

    value_x colkey   value_y
0 -0.402655      B  0.543843
1 -0.524349      D  0.013135

Follow the next answer to continue learning.

Pandas merging 101- Answer #3:

This answer will go through the following topics:

  • how to correctly generalize to multiple DataFrames (and why merge has shortcomings here)
  • merging on unique keys
  • merging on non-unqiue keys

Generalizing to multiple DataFrames

Oftentimes, the situation arises when multiple DataFrames are to be merged together. Naively, this can be done by chaining merge calls:

df1.merge(df2, ...).merge(df3, ...)

However, this quickly gets out of hand for many DataFrames. Furthermore, it may be necessary to generalise for an unknown number of DataFrames.

Here I introduce pd.concat for multi-way joins on unique keys, and DataFrame.join for multi-way joins on non-unique keys. First, the setup.

# Setup.
A = pd.DataFrame({'key': ['A', 'B', 'C', 'D'], 'valueA': np.random.randn(4)})    
B = pd.DataFrame({'key': ['B', 'D', 'E', 'F'], 'valueB': np.random.randn(4)})
C = pd.DataFrame({'key': ['D', 'E', 'J', 'C'], 'valueC': np.ones(4)})
dfs = [A, B, C] 

# Note, the "key" column values are unique, so the index is unique.
A2 = A.set_index('key')
B2 = B.set_index('key')
C2 = C.set_index('key')

dfs2 = [A2, B2, C2]

Multiway merge on unique keys

If your keys (here, the key could either be a column or an index) are unique, then you can use pd.concat. Note that pd.concat joins DataFrames on the index.

# merge on `key` column, you'll need to set the index before concatenating
    df.set_index('key') for df in dfs], axis=1, join='inner'

  key    valueA    valueB  valueC
0   D  2.240893 -0.977278     1.0

# merge on `key` index
pd.concat(dfs2, axis=1, sort=False, join='inner')

       valueA    valueB  valueC
D    2.240893 -0.977278     1.0

Omit join='inner' for a FULL OUTER JOIN. Note that you cannot specify LEFT or RIGHT OUTER joins (if you need these, use join, described below).

Multiway merge on keys with duplicates

concat is fast, but has its shortcomings. It cannot handle duplicates.

A3 = pd.DataFrame({'key': ['A', 'B', 'C', 'D', 'D'], 'valueA': np.random.randn(5)})
pd.concat([df.set_index('key') for df in [A3, B, C]], axis=1, join='inner')
ValueError: Shape of passed values is (3, 4), indices imply (3, 2)

In this situation, we can use join since it can handle non-unique keys (note that join joins DataFrames on their index; it calls merge under the hood and does a LEFT OUTER JOIN unless otherwise specified).

# join on `key` column, set as the index first
# For inner join. For left join, omit the "how" argument.
    [df.set_index('key') for df in (B, C)], how='inner').reset_index()

  key    valueA    valueB  valueC
0   D  2.240893 -0.977278     1.0

# join on `key` index
A3.set_index('key').join([B2, C2], how='inner')

       valueA    valueB  valueC
D    1.454274 -0.977278     1.0
D    0.761038 -0.977278     1.0

Pandas merging 101- Answer #4:

Let’s start by establishing a benchmark. The easiest method for solving this is using a temporary “key” column:

# pandas <= 1.1.X
def cartesian_product_basic(left, right):
    return (
       left.assign(key=1).merge(right.assign(key=1), on='key').drop('key', 1))

cartesian_product_basic(left, right)
# pandas >= 1.2 (est)
left.merge(right, how="cross")
  col1_x  col2_x col1_y  col2_y
0      A       1      X      20
1      A       1      Y      30
2      A       1      Z      50
3      B       2      X      20
4      B       2      Y      30
5      B       2      Z      50
6      C       3      X      20
7      C       3      Y      30
8      C       3      Z      50

How this works is that both DataFrames are assigned a temporary “key” column with the same value (say, 1). merge then performs a many-to-many JOIN on “key”.

While the many-to-many JOIN trick works for reasonably sized DataFrames, you will see relatively lower performance on larger data.

A faster implementation will require NumPy. Here are some famous NumPy implementations of 1D cartesian product. We can build on some of these performant solutions to get our desired output. My favourite, however, is @senderle’s first implementation.

def cartesian_product(*arrays):
    la = len(arrays)
    dtype = np.result_type(*arrays)
    arr = np.empty([len(a) for a in arrays] + [la], dtype=dtype)
    for i, a in enumerate(np.ix_(*arrays)):
        arr[...,i] = a
    return arr.reshape(-1, la)  

Generalizing: CROSS JOIN on Unique or Non-Unique Indexed DataFrames

These solutions are optimised for DataFrames with non-mixed scalar dtypes. If dealing with mixed dtypes, use at your own risk!

This trick will work on any kind of DataFrame. We compute the cartesian product of the DataFrames’ numeric indices using the aforementioned cartesian_product, use this to reindex the DataFrames, and

def cartesian_product_generalized(left, right):
    la, lb = len(left), len(right)
    idx = cartesian_product(np.ogrid[:la], np.ogrid[:lb])
    return pd.DataFrame(
        np.column_stack([left.values[idx[:,0]], right.values[idx[:,1]]]))

cartesian_product_generalized(left, right)

   0  1  2   3
0  A  1  X  20
1  A  1  Y  30
2  A  1  Z  50
3  B  2  X  20
4  B  2  Y  30
5  B  2  Z  50
6  C  3  X  20
7  C  3  Y  30
8  C  3  Z  50

np.array_equal(cartesian_product_generalized(left, right),
               cartesian_product_basic(left, right))

And, along similar lines,

left2 = left.copy()
left2.index = ['s1', 's2', 's1']

right2 = right.copy()
right2.index = ['x', 'y', 'y']

   col1  col2
s1    A     1
s2    B     2
s1    C     3

  col1  col2
x    X    20
y    Y    30
y    Z    50

np.array_equal(cartesian_product_generalized(left, right),
               cartesian_product_basic(left2, right2))

This solution can generalise to multiple DataFrames. For example,

def cartesian_product_multi(*dfs):
    idx = cartesian_product(*[np.ogrid[:len(df)] for df in dfs])
    return pd.DataFrame(
        np.column_stack([df.values[idx[:,i]] for i,df in enumerate(dfs)]))

cartesian_product_multi(*[left, right, left]).head()

   0  1  2   3  4  5
0  A  1  X  20  A  1
1  A  1  X  20  B  2
2  A  1  X  20  C  3
3  A  1  X  20  D  4
4  A  1  Y  30  A  1

Further Simplification

A simpler solution not involving @senderle’s cartesian_product is possible when dealing with just two DataFrames. Using np.broadcast_arrays, we can achieve almost the same level of performance.

def cartesian_product_simplified(left, right):
    la, lb = len(left), len(right)
    ia2, ib2 = np.broadcast_arrays(*np.ogrid[:la,:lb])

    return pd.DataFrame(
        np.column_stack([left.values[ia2.ravel()], right.values[ib2.ravel()]]))

np.array_equal(cartesian_product_simplified(left, right),
               cartesian_product_basic(left2, right2))

Performance Comparison

Benchmarking these solutions on some contrived DataFrames with unique indices, we have

enter image description here

Do note that timings may vary based on your setup, data, and choice of cartesian_product helper function as applicable.

Performance Benchmarking Code
This is the timing script. All functions called here are defined above.

from timeit import timeit
import pandas as pd
import matplotlib.pyplot as plt

res = pd.DataFrame(
       index=['cartesian_product_basic', 'cartesian_product_generalized', 
              'cartesian_product_multi', 'cartesian_product_simplified'],
       columns=[1, 10, 50, 100, 200, 300, 400, 500, 600, 800, 1000, 2000],

for f in res.index: 
    for c in res.columns:
        # print(f,c)
        left2 = pd.concat([left] * c, ignore_index=True)
        right2 = pd.concat([right] * c, ignore_index=True)
        stmt = '{}(left2, right2)'.format(f)
        setp = 'from __main__ import left2, right2, {}'.format(f)[f, c] = timeit(stmt, setp, number=5)

ax = res.div(res.min()).T.plot(loglog=True) 
ax.set_ylabel("time (relative)");

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About ᴾᴿᴼᵍʳᵃᵐᵐᵉʳ

Linux and Python enthusiast, in love with open source since 2014, Writer at, India.

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