Combining DataFrames with pandas
Last updated on 2024-02-13 | Edit this page
Estimated time: 45 minutes
Overview
Questions
- Can I work with data from multiple sources?
- How can I combine data from different data sets?
Objectives
- Combine data from multiple files into a single DataFrame using merge and concat.
- Combine two DataFrames using a unique ID found in both DataFrames.
- Employ
to_csvto export a DataFrame in CSV format. - Join DataFrames using common fields (join keys).
In many “real world” situations, the data that we want to use come in
multiple files. We often need to combine these files into a single
DataFrame to analyze the data. The pandas package provides various
methods for combining DataFrames including merge and
concat.
To work through the examples below, we first need to load the species and surveys files into pandas DataFrames. The authors.csv and places.csv data can be found in the data folder.
PYTHON
import pandas as pd
authors_df = pd.read_csv("authors.csv",
keep_default_na=False, na_values=[""])
authors_df
TCP Author
0 A00002 Aylett, Robert, 1583-1655?
1 A00005 Higden, Ranulf, d. 1364. Polycronicon. English...
2 A00007 Higden, Ranulf, d. 1364. Polycronicon.
3 A00008 Wood, William, fl. 1623, attributed name.
4 A00011
places_df = pd.read_csv("places.csv",
keep_default_na=False, na_values=[""])
places_df
A00002 London
0 A00005 London
1 A00007 London
2 A00008 The Netherlands?
3 A00011 Amsterdam
4 A00012 London
5 A00014 LondonTake note that the read_csv method we used can take some
additional options which we didn’t use previously. Many functions in
python have a set of options that can be set by the user if needed. In
this case, we have told Pandas to assign empty values in our CSV to NaN
keep_default_na=False, na_values=[""]. More
about all of the read_csv options here.
Concatenating DataFrames
We can use the concat function in Pandas to append
either columns or rows from one DataFrame to another. Let’s grab two
subsets of our data to see how this works.
PYTHON
# read in first 10 lines of the places table
place_sub = places_df.head(10)
# grab the last 20 rows
place_sub_last10 = places_df.tail(20)
#reset the index values to the second dataframe appends properly
place_sub_last10 = place_sub_last10.reset_index(drop=True)
# drop=True option avoids adding new index column with old index valuesWhen we concatenate DataFrames, we need to specify the axis.
axis=0 tells Pandas to stack the second DataFrame under the
first one. It will automatically detect whether the column names are the
same and will stack accordingly. axis=1 will stack the
columns in the second DataFrame to the RIGHT of the first DataFrame. To
stack the data vertically, we need to make sure we have the same columns
and associated column format in both datasets. When we stack
horizonally, we want to make sure what we are doing makes sense (ie the
data are related in some way).
PYTHON
# stack the DataFrames on top of each other
vertical_stack = pd.concat([place_sub, place_sub_last10], axis=0)
# place the DataFrames side by side
horizontal_stack = pd.concat([place_sub, place_sub_last10], axis=1)Row Index Values and Concat
Have a look at the vertical_stack dataframe? Notice
anything unusual? The row indexes for the two data frames
place_sub and place_sub_last10 have been
repeated. We can reindex the new dataframe using the
reset_index() method.
Writing Out Data to CSV
We can use the to_csv command to do export a DataFrame
in CSV format. Note that the code below will by default save the data
into the current working directory. We can save it to a different folder
by adding the foldername and a slash to the file
vertical_stack.to_csv('foldername/out.csv'). We use the
‘index=False’ so that pandas doesn’t include the index number for each
line.
Check out your working directory to make sure the CSV wrote out properly, and that you can open it! If you want, try to bring it back into python to make sure it imports properly.
PYTHON
# for kicks read our output back into python and make sure all looks good
new_output = pd.read_csv('out.csv', keep_default_na=False, na_values=[""])Challenge - Combine Data
In the data folder, there are two catalogue data files:
1635.csv and 1640.csv. Read the data into
python and combine the files to make one new data frame.
Joining DataFrames
When we concatenated our DataFrames we simply added them to each other - stacking them either vertically or side by side. Another way to combine DataFrames is to use columns in each dataset that contain common values (a common unique id). Combining DataFrames using a common field is called “joining”. The columns containing the common values are called “join key(s)”. Joining DataFrames in this way is often useful when one DataFrame is a “lookup table” containing additional data that we want to include in the other.
NOTE: This process of joining tables is similar to what we do with tables in an SQL database.
The places.csv file is table that contains the place and
EEBO id for some titles. When we want to access that information, we can
create a query that joins the additional columns of information to the
author data.
Storing data in this way has many benefits including:
Identifying join keys
To identify appropriate join keys we first need to know which field(s) are shared between the files (DataFrames). We might inspect both DataFrames to identify these columns. If we are lucky, both DataFrames will have columns with the same name that also contain the same data. If we are less lucky, we need to identify a (differently-named) column in each DataFrame that contains the same information.
PYTHON
>>> authors_df.columns
Index(['TCP', 'Author'], dtype='object')
>>> places_df.columns
Index(['TCP', 'Place'], dtype='object')In our example, the join key is the column containing the identifier,
which is called TCP.
Now that we know the fields with the common TCP ID attributes in each DataFrame, we are almost ready to join our data. However, since there are different types of joins, we also need to decide which type of join makes sense for our analysis.
Inner joins
The most common type of join is called an inner join. An inner join combines two DataFrames based on a join key and returns a new DataFrame that contains only those rows that have matching values in both of the original DataFrames.
Inner joins yield a DataFrame that contains only rows where the value being joins exists in BOTH tables. An example of an inner join, adapted from this page is below:
The pandas function for performing joins is called merge
and an Inner join is the default option:
PYTHON
merged_inner = pd.merge(left=authors_df,right=places_df, left_on='TCP', right_on='TCP')
# in this case `species_id` is the only column name in both dataframes, so if we skippd `left_on`
# and `right_on` arguments we would still get the same result
# what's the size of the output data?
merged_inner.shape
merged_innerOUTPUT:
TCP Author Place
0 A00002 Aylett, Robert, 1583-1655? London
1 A00005 Higden, Ranulf, d. 1364. Polycronicon. English... London
2 A00007 Higden, Ranulf, d. 1364. Polycronicon. London
3 A00008 Wood, William, fl. 1623, attributed name. The Netherlands?
4 A00011 NaN AmsterdamThe result of an inner join of authors_df and
places_df is a new DataFrame that contains the combined set
of columns from those tables. It only contains rows that have
two-letter species codes that are the same in both the
authos_df and place_df DataFrames. In other
words, if a row in authors_df has a value of
TCP that does not appear in the TCP
column of TCP, it will not be included in the DataFrame
returned by an inner join. Similarly, if a row in places_df
has a value of TCP that does not appear in the
TCP column of places_df, that row will not be
included in the DataFrame returned by an inner join.
The two DataFrames that we want to join are passed to the
merge function using the left and
right argument. The left_on='TCP' argument
tells merge to use the TCP column as the join
key from places_df (the left DataFrame).
Similarly , the right_on='TCP' argument tells
merge to use the TCP column as the join key
from authors_df (the right DataFrame). For
inner joins, the order of the left and right
arguments does not matter.
The result merged_inner DataFrame contains all of the
columns from authors (TCP, Person) as well as all the
columns from places_df (TCP, Place).
Notice that merged_inner has fewer rows than
place_sub. This is an indication that there were rows in
place_df with value(s) for EEBO that do not
exist as value(s) for EEBO in authors_df.
Left joins
What if we want to add information from cat_sub to
survey_sub without losing any of the information from
survey_sub? In this case, we use a different type of join
called a “left outer join”, or a “left join”.
Like an inner join, a left join uses join keys to combine two
DataFrames. Unlike an inner join, a left join will return all
of the rows from the left DataFrame, even those rows whose
join key(s) do not have values in the right DataFrame. Rows
in the left DataFrame that are missing values for the join
key(s) in the right DataFrame will simply have null (i.e.,
NaN or None) values for those columns in the resulting joined
DataFrame.
Note: a left join will still discard rows from the right
DataFrame that do not have values for the join key(s) in the
left DataFrame.
A left join is performed in pandas by calling the same
merge function used for inner join, but using the
how='left' argument:
PYTHON
merged_left = pd.merge(left=places_df,right=authors_df, how='left', left_on='TCP', right_on='TCP')
merged_left
**OUTPUT:**
TCP Place Author
0 A00002 London Aylett, Robert, 1583-1655?
1 A00005 London Higden, Ranulf, d. 1364. Polycronicon. English...
2 A00007 London Higden, Ranulf, d. 1364. Polycronicon.
3 A00008 The Netherlands? Wood, William, fl. 1623, attributed name.
4 A00011 Amsterdam NaNThe result DataFrame from a left join (merged_left)
looks very much like the result DataFrame from an inner join
(merged_inner) in terms of the columns it contains.
However, unlike merged_inner, merged_left
contains the same number of rows as the original
place_sub DataFrame. When we inspect
merged_left, we find there are rows where the information
that should have come from authors_df (i.e.,
Author) is missing (they contain NaN values):
PYTHON
merged_inner[ pd.isnull(merged_inner.Author) ]
**OUTPUT:**
TCP Author Place
4 A00011 NaN Amsterdam
6 A00014 NaN London
8 A00018 NaN Germany?These rows are the ones where the value of Author from
authors_df does not occur in places_df.
Other join types
The pandas merge function supports two other join
types:
- Right (outer) join: Invoked by passing
how='right'as an argument. Similar to a left join, except all rows from therightDataFrame are kept, while rows from theleftDataFrame without matching join key(s) values are discarded. - Full (outer) join: Invoked by passing
how='outer'as an argument. This join type returns the all pairwise combinations of rows from both DataFrames; i.e., the result DataFrame willNaNwhere data is missing in one of the dataframes. This join type is very rarely used.
Final Challenges
Challenge - Distributions
Create a new DataFrame by joining the contents of the
authors.csv and places.csv tables. Calculate
the:
- Number of unique places
- Number of books that do not have a known place
- Number of books that do not have either a known place or author
PYTHON
merged = pd.merge(
left=pd.read_csv("authors.csv"),
right=pd.read_csv("places.csv"),
left_on="TCP",
right_on="TCP"
)
# Part 1: number of unique places - we can use the .nunique() method
num_unique_places = merged["Place"].nunique()
# Part 2: we can take advantage of the behaviour that the .count() method
# excludes NaN values. So .count() gives us the number that have place
# values
num_no_place = len(merged) - merged["Place"].count()
# Part 3: This needs us to check both columns and combine the resulting masks
# Then we can use the trick of converting boolean to int, and summing,
# to convert the combined mask to a number of True values
no_author = pd.isnull(merged["Author"]) # True where is null
no_place = pd.isnull(merged["Place"])
neither = no_author & no_place
num_neither = sum(neither)