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BUG: margin for pivot_table is incorrect with NA column/index values #61509

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vtraag opened this issue May 28, 2025 · 2 comments · May be fixed by #61524
Open
3 tasks done

BUG: margin for pivot_table is incorrect with NA column/index values #61509

vtraag opened this issue May 28, 2025 · 2 comments · May be fixed by #61524
Labels
Bug Missing-data np.nan, pd.NaT, pd.NA, dropna, isnull, interpolate Reshaping Concat, Merge/Join, Stack/Unstack, Explode

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@vtraag
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vtraag commented May 28, 2025

Pandas version checks

  • I have checked that this issue has not already been reported.

  • I have confirmed this bug exists on the latest version of pandas.

  • I have confirmed this bug exists on the main branch of pandas.

Reproducible Example

#%%
import pandas as pd

df = pd.DataFrame({"i": [1, 2, 3],
                   "g1": ["a", "b", "b"],
                   "g2": ["x", None, None],
                   })

df.pivot_table(index="g1",
               columns="g2",
               values="i",
               aggfunc="count",
               dropna=False, margins=True)

Issue Description

The margins of a pivot_table are incorrect when the index or columns variables contains missing variables. In particular, for the variable with the missing value, the total is missing.

g1 x nan Total
a 1.0 1
b 2.0 2
All 1.0 3

Expected Behavior

Margins should also be included for columns/indices with missing values.

In particular, the table should look like this

g1 x nan Total
a 1.0 1
b 2.0 2
All 1.0 2.0 3

Installed Versions

INSTALLED VERSIONS

commit : f538741
python : 3.12.8.final.0
python-bits : 64
OS : Linux
OS-release : 6.11.0-26-generic
Version : #26~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 17 19:20:47 UTC 2
machine : x86_64
processor : x86_64
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8

pandas : 2.2.0
numpy : 1.26.4
pytz : 2025.1
dateutil : 2.9.0.post0
setuptools : 75.8.0
pip : 25.0
Cython : None
pytest : None
hypothesis : None
sphinx : 8.1.3
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.1.5
IPython : 8.22.0
pandas_datareader : None
adbc-driver-postgresql: None
adbc-driver-sqlite : None
bs4 : 4.13.0
bottleneck : None
dataframe-api-compat : None
fastparquet : None
fsspec : None
gcsfs : None
matplotlib : 3.9.4
numba : None
numexpr : None
odfpy : None
openpyxl : 3.1.4
pandas_gbq : None
pyarrow : 16.1.0
pyreadstat : None
python-calamine : None
pyxlsb : None
s3fs : None
scipy : 1.14.0
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
zstandard : 0.23.0
tzdata : 2025.1
qtpy : 2.4.2
pyqt5 : None
@vtraag vtraag added Bug Needs Triage Issue that has not been reviewed by a pandas team member labels May 28, 2025
@rhshadrach
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Thanks for the report. Confirmed on main, further investigations and a PR to fix is welcome!

Related: #53521

@rhshadrach rhshadrach added Reshaping Concat, Merge/Join, Stack/Unstack, Explode Missing-data np.nan, pd.NaT, pd.NA, dropna, isnull, interpolate and removed Needs Triage Issue that has not been reviewed by a pandas team member labels May 30, 2025
@iabhi4 iabhi4 linked a pull request May 31, 2025 that will close this issue
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@iabhi4
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iabhi4 commented May 31, 2025

Thanks for the report. Confirmed on main, further investigations and a PR to fix is welcome!

Hi @rhshadrach just raised a PR for this

It ensures pivot_table(..., margins=True, dropna=False) properly includes rows/columns with NA values in the margin computation. Let me know if there's anything you'd like adjusted!

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BUG: Fix pivot_table margins to include NaN groups when dropna=False iabhi4/pandas
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@vtraag @rhshadrach @iabhi4