Question
- How can I perform a (
INNER
| (LEFT
|RIGHT
|FULL
)OUTER
)JOIN
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
merge
?join
?concat
?update
? 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.
This Q&A is meant to be the next installment in a series of helpful user guides on common pandas idioms (see [this post on pivoting](https://stackoverflow.com/questions/47152691/how-to-pivot-a- dataframe), and [this post on concatenation](https://stackoverflow.com/questions/49620538/what-are-the- levels-keys-and-names-arguments-for-in-pandas-concat-functio), which I will be touching on, later).
Please note that this post is not meant to be a replacement for [the documentation](https://pandas.pydata.org/pandas- docs/stable/user_guide/merging.html), so please read that as well! Some of the examples are taken from there.
Table of Contents
For ease of access.
-
Merging basics - basic types of joins (read this first)
Answer
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](https://stackoverflow.com/questions/31610889/how-to-copy-paste- dataframe-from-stackoverflow-into-python) 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
np.random.seed(0)
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)})
left
key value
0 A 1.764052
1 B 0.400157
2 C 0.978738
3 D 2.240893
right
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
NaN
s in the result
To perform an INNER JOIN, call [merge
](https://pandas.pydata.org/pandas-
docs/stable/generated/pandas.DataFrame.merge.html) 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).
A 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:
**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 to rows coming from
left
only (excluding everything from the right),
(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
Where,
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)
left2
keyLeft value
0 A 1.764052
1 B 0.400157
2 C 0.978738
3 D 2.240893
right2
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 theDataFrames
For example, consider
right3 = right.assign(newcol=np.arange(len(right)))
right3
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 "newcol" (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']))
left.assign(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 usefulmerge*
operations and functions
-
Merging a DataFrame with Series on index: See this answer.
-
Besides
merge
,DataFrame.update
andDataFrame.combine_first
are also used in certain cases to update one DataFrame with another. -
pd.merge_ordered
is a useful function for ordered JOINs. -
pd.merge_asof
(read: merge_asOf) is useful for approximate joins.
This section only covers the very basics, and is designed to only whet your
appetite. For more examples and cases, see the[documentation on merge
,
join
, and concat
](https://pandas.pydata.org/pandas-
docs/stable/merging.html) as well as the links to the function
specifications.
Continue Reading
Jump to other topics in Pandas Merging 101 to continue learning:
*You are here.