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Python Pandas Groupby Tutorial

In this Pandas groupby tutorial, we are going to learn how to organize Pandas dataframes by groups. More specifically, we are going to learn how to group by one and multiple columns.

Furthermore, we are going to learn how calculate some basics summary statistics (e.g., mean, median), convert Pandas groupby to dataframe, calculate the percentage of observations in each group, and many more useful things.

First of all we are going to import pandas as pd, and read a CSV file, using the read_csv method, to a dataframe. In the example below, we use index_col=0 because the first row in the dataset is the index column.

import pandas as pd

data_url = 'http://vincentarelbundock.github.io/Rdatasets/csv/carData/Salaries.csv'
df = pd.read_csv(data_url, index_col=0)

df.head()

We used Pandas head to see the first 5 rows of our dataframe. In the image above we can see that we have, at least, three variables that we can group our data by. That is, we can group our data by “rank”, “discipline”, and “sex”.

Of course, we could also group it by yrs.since.phd or yrs.service but it may be a lot of groups.  As previously mentioned we are going to use Pandas groupby to group a dataframe based on one, two, three, or more columns.

Data can be loaded from other file formats as well (e.g., Excel, HTML, JSON):

What is Groupby in Pandas?

In this section, we are briefly answer the question what is groupby in Pandas? Pandas groupby() method is what we use to split the data into groups based on criteria we specify.

Python Pandas Groupby Example

Now we are going to learn how to use Pandas groupby. In this tutorial, we are starting with the simplest example; grouping by one column. Specifically, in the Pandas groupby example below we are going to group by the column “rank”.

There are many different methods that we can use on Pandas groupby objects (and Pandas dataframe objects). All available methods on a Python object can be found using this code:

import IPython

# Grouping by one factor
df_rank = df.groupby('rank')

# Getting all methods from the groupby object:
meth = [method_name for method_name in dir(df_rank)
     if callable(getattr(df_rank, method_name)) & ~method_name.startswith('_')]

# Printing the result
print(IPython.utils.text.columnize(meth))

Note, that in the code example above we also import IPython to print the list in columns. In the following examples we are going to use some of these methods.

How to Display Pandas groupby Objects

In this subsection, we are going to learn how to print a Pandas groupby object. First, we can print out the groups by using the groups method to get a dictionary of groups:

df_rank.groups

We can also use the groupby method get_group to filter the grouped data. In the next code example we are going to select the Assistant Professor group (i.e., “AsstProf”).

# Get group
df_rank.get_group('AsstProf').head()

If we want print some parts of the groupby object we can use the the head method:

df_rank.head()

Pandas Groupby Count

If we want to find out how big each group is (e.g., how many observations in each group), we can use use .size() to count the number of rows in each group:

df_rank.size()

# Output:
#
# rank
# AssocProf     64
# AsstProf      67
# Prof         266
# dtype: int64

Additionally, we can also use Pandas groupby count method to count by group(s) and get the entire dataframe. If we don’t have any missing values the number should be the same for each column and group. Thus, this by using Pandas group, like in the example here, we can explore the dataset and see if there are any missing values in any column.

df_rank.count()

That was how to use Pandas size to count the number of rows in each group. We will return to this, later, when we are grouping by multiple columns.  In some cases we may want to find out the number of unique values in each group. This can be done using the groupby method nunique:

df_rank.nunique()

As can be seen in the the last column (salary) there are 63 Associate Professors, 53 Assistant Professors, and 261 Professors in the dataset.

In this example we have a complete dataset and we can see that some have the same salary (e.g., there are 261 unique values in the column salary for Professors). If we have missing values in the dataframe we would get a different result. In the next example we are using Pandas mask method together with NumPy’s random.random to insert missing values (i.e., np.NaN) in 10% of the dataframe:

df_null = df.mask(np.random.random(df.shape) < .1)
df_null.isnull().sum().reset_index(name='N Missing Values')

Note, we used the reset_index method above to get the multi-level indexed grouped dataframe to become a single indexed. In the particular example, above, we used the parameter name to name the count column (“N Missing Values”). This parameter, however, can only be used on Pandas series objects and not dataframe objects.

That said, let’s return to the example; if we run the same code as above (counting unique values by group) we can see that it will not count missing values:

df_null.groupby('rank').nunique()

That is, we don’t get the same numbers in the two tables because of the missing values. In the following examples we are going to work with Pandas groupby to calculate the mean, median, and standard deviation by one group.

Pandas Groupby Mean

If we want to calculate the mean salary grouped by one column (rank, in this case) it’s simple. We just use Pandas mean method on the grouped dataframe:

df_rank['salary'].mean().reset_index()

Having a column named salary may not be useful. For instance, if someone else are going to see the table they may not know that it’s the mean salary for each group. Luckily, we can add the rename method to the above code to rename the columns of the grouped data:

df_rank['salary'].mean().reset_index().rename(
    columns={'rank':'Rank','salary' : 'Mean Salary'})

Median Score of a Group Using the groupby Method in Pandas

Now lets group by discipline of the academic and find the median salary in the next Pandas groupby example

df.groupby('rank')['salary'].median().reset_index().rename(
    columns={'rank':'Rank','salary' : 'MedianSalary'})

Aggregate Data by Group using Pandas Groupby

Most of the time we want to have our summary statistics in the same table. We can calculate the mean and median salary, by groups, using the agg method. In this next Pandas groupby example we are also adding the minimum and maximum salary by group (rank):

df_rank['salary'].agg(['mean', 'median', 
                                  'std', 'min', 'max']).reset_index()

A very neat thing with Pandas agg method is that we can write custom functions and pass them along. Let’s say that we wanted, instead of having one column for min salary and one column for max salary, to have a column with the salary range:

def salary_range(df):
    mini = df.min()
    maxi = df.max()
    rang = '%s - %s' % (mini, maxi)
    
    return rang

df_descriptive = df_rank['salary'].agg(['mean', 'median', 'std', salary_range]).reset_index()

Here, however, the output will have the name of the methods/functions used. That is, we will have a column named ‘salary_range’ and we are going to rename this column:

# Renaming Pandas Dataframe Columns
df_descriptive.rename(columns={'rank':'Rank', 'mean':'Mean', 'median':'Median', 
                               'std':'Standard Deviation', 'salary_range':'Range'})

Furthermore, it’s possible to use methods from other Python packages such as SciPy and NumPy. For instance, if we wanted to calculate the harmonic and geometric mean we can use SciPy:

from scipy.stats.mstats import gmean, hmean

df_descriptive = df_rank['salary'].agg(['mean', 'median', hmean, gmean]).reset_index()
df_descriptive

More about doing descriptive statistics using Python:

Pandas Groupby Multiple Columns

In this section we are going to continue using Pandas groupby but grouping by many columns. In the first example we are going to group by two columns and the we will continue with grouping by two columns, ‘discipline’ and ‘rank’. To use Pandas groupby with multiple columns we add a list containing the column names. In the example below we also count the number of observations in each group:

df_grp = df.groupby(['rank', 'discipline'])
df_grp.size().reset_index(name='count')

Again, we can use the get_group method to select groups. However, in this case we have to input a tuple and select two groups:

# Get two groups
df_grp.get_group(('AssocProf', 'A')).head()

Pandas Groupby Count Multiple Groups

In the next groupby example we are going to calculate the number of observations in three groups (i.e., “n”). We have to start by grouping by “rank”, “discipline” and “sex” using groupby. As with the previous example (groupby one column) we use the method size to calculate the n and reset_index, with the parameter name=”n”, to get the series to a dataframe:

df_3grps = df.groupby(['rank', 'discipline', 'sex'])
df_n_per_group = df_3grps.size().reset_index(name='n')

Now we can continue and calculate the percentage of men and women in each rank and discipline. In this, and the next, Pandas groupby example we are going to use the apply method together with the lambdafunction.

perc = df.groupby(['rank', 'discipline', 'sex'])['salary'].size()

# Give the percentage on the level of Rank:
percbyrank = perc.groupby(level=0).apply(lambda x: 100 * x / float(x.sum()))

print(percbyrank)
print('Total percentage in group AssocProf. ',
      percbyrank.reset_index().query('rank == "AssocProf"')['salary'].sum())

Note, in the last line of code above we calculated the total of % for the group AssocProf and it’s 100, which is good. We are going to continue with calculating the percentage of men and women in each group (i.e., rank and discipline). In the next code we have to summarize the total (n=397). We can, for instance, see that there are more male professors regardless of discipline.

n = perc.reset_index()['salary'].sum()
totalperc =  perc.groupby(level=0).apply(lambda x:100*x/n).reset_index(name='% of total n')
totalperc.reset_index()
df_rn = df.groupby(['rank', 'discipline']).mean()

Furthermore, if we use the index method we can see that it is MultiIndex:

df_rn.index

It’s easy to convert the Pandas groupby to dataframe; we have actually already done it. In this example, however, we are going to calculate the mean values per the three groups. Furthermore, we are going to add a suffix to each column and use reset_index to get a dataframe.

df_rn = df_rn.add_suffix('_Mean').reset_index()
type(df_rn)

# Output: pandas.core.frame.DataFrame

Pandas groupby agg with Multiple Groups

In this last section we are going use agg, again. We are not going into detail on how to use mean, median, and other methods to get summary statistics, however. This is because it’s basically the same as for grouping by n groups and it’s better to get all the summary statistics in one table.

That is, we are going to calculate mean, median, and standard deviation using the agg method. In this groupby example we are also adding the summary statistics (i.e., “mean”, “median”, and “std”) to each column. Otherwise we will get a multi-level indexed result like the image below:

If we use Pandas columns and the method ravel together with list comprehension we can add the suffixes to our column name and get another table. Note, in the example code below we only print the first 7 columns. In fact, with many columns it may be better to keep the result multi-level indexed.

df_stats = df.groupby(['rank', 'discipline', 'sex']).agg(['mean', 'median', 'std'])
df_stats.columns = ["_".join(x) for x in df_stats.columns.ravel()]

df_stats.iloc[:,0:6].reset_index()
  • Learn more about working with Pandas iloc in this post.

Note, if we wanted an output as the first image we just remove the second line above (“df_stats.columns = …”). Additionally, as previously mentioned, we can also use custom functions, NumPy and SciPy methods when working with groupby agg. Just scroll back up and look at those examples, for grouping by one column, and apply them to the data grouped by multiple columns. More information about the different methods and objects used here can be found in the Pandas documentation.

If you want a runnable Jupyter notebook of the code used in this Pandas groupby tutorial click here.

Conclusion:

In this Pandas groupby tutorial, we have learned how to use Pandas groupby to:

  • group one or many columns
  • count observations using Pandas groupby count and size
  • calculate simple summary statistics using:
    • groupby mean, median, std
    • groupby agg (aggregate)
    • agg with our own function
  • Calculate the percentage of observations in different groups

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