Pandas count NAs with a groupby for all columns [duplicate]

Question

This question shows how to count NAs in a dataframe for a particular column C. How do I count NAs for all columns (that aren't the groupby column)?

Here is some test code that doesn't work:

#!/usr/bin/env python3

import pandas as pd
import numpy as np

df = pd.DataFrame({'a':[1,1,2,2], 
                   'b':[1,np.nan,2,np.nan],
                   'c':[1,np.nan,2,3]})

# result = df.groupby('a').isna().sum()
# AttributeError: Cannot access callable attribute 'isna' of 'DataFrameGroupBy' objects, try using the 'apply' method

# result = df.groupby('a').transform('isna').sum()
# AttributeError: Cannot access callable attribute 'isna' of 'DataFrameGroupBy' objects, try using the 'apply' method

result = df.isna().groupby('a').sum()
print(result)
# result:
#          b    c
# a
# False  2.0  1.0

result = df.groupby('a').apply(lambda _df: df.isna().sum())
print(result)
# result:
#    a  b  c
# a
# 1  0  2  1
# 2  0  2  1

Desired output:

     b    c
a
1    1    1
2    1    0

Answer 1

It's always best to avoid groupby.apply in favor of the basic functions which are cythonized, as this scales better with many groups. This will lead to a great increase in performance. In this case first check isnull() on the entire DataFrame then groupby + sum.

df[df.columns.difference(['a'])].isnull().groupby(df.a).sum().astype(int)
#   b  c
#a      
#1  1  1
#2  1  0

---

To illustrate the performance gain:

import pandas as pd
import numpy as np

N = 50000
df = pd.DataFrame({'a': [*range(N//2)]*2,
                   'b': np.random.choice([1, np.nan], N),
                   'c': np.random.choice([1, np.nan], N)})

%timeit df[df.columns.difference(['a'])].isnull().groupby(df.a).sum().astype(int)
#7.89 ms ± 187 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

%timeit df.groupby('a')[['b', 'c']].apply(lambda x: x.isna().sum())
#9.47 s ± 111 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

Answer 2

Your question has the answer (You mistyped _df as df):

result = df.groupby('a')['b', 'c'].apply(lambda _df: _df.isna().sum())
result
   b  c
a      
1  1  1
2  1  0