Wrong percentage calculated when categorical column includes missing values.

[rherman9]

When your categorical variables include missing values, a wrong percentage gets calculated.

See Parameter1:

Currently percentages for categorical variables get calculated with the total being the amount of non-missing values for that variable.

In my opinion the percentage, in cell E3 for example should be 17.1, because you're interested in how many times Parameter1 Category 1.0 occured in the validation_set: 104/609

A quick workaround is to replace all nan values in categorical variables to some number and then dropping the rows with that number:

df[categorical] = df[categorical].replace(np.nan, 199848) mytable = mytable.tableone[mytable.tableone.index.get_level_values(1) != "199848.0"]

Great library though!

[tompollard]

@rherman9 thanks for picking this up. we'll take a look!

[tompollard]

To reproduce this issue:

import pandas as pd
from tableone import tableone

df = pd.DataFrame(
    {'cats': ["1", "2", "3", "4", None, None],
    'set': ["train","train", "val", "val", "val", "val"]}
    )

t = tableone(df, groupby = "set")
print(t.tabulate(headers=None, tablefmt="github"))

Output:

		Missing	Overall	train	val
n			6	2	4
cats, n (%)	1	2	1 (25.0)	1 (50.0)
	2		1 (25.0)	1 (50.0)
	3		1 (25.0)		1 (50.0)
	4		1 (25.0)		1 (50.0)

Expected output:

		Missing	Overall	train	val
n			6	2	4
cats, n (%)	1	2	1 (25.0)	1 (50.0)
	2		1 (25.0)	1 (50.0)
	3		1 (25.0)		1 (25.0)
	4		1 (25.0)		1 (25.0)

The best fix for this might be to treat NaN/None etc as a category? @lbulgarelli any thoughts?

[lbulgarelli]

It is a good idea to add missing as a category itself, especially because it will allow to easily compare missing values between groups.

That said, the number of missing alone is not very informative for non-categorical variables, so I'd also probably hide that information by default, with the option to display it.

[tompollard]

That said, the number of missing alone is not very informative for non-categorical variables, so I'd also probably hide that information by default, with the option to display it.

I feel like it's pretty important to know how many data points are missing, even for continuous variables. If you're reporting a summary statistic and it is based on a small proportion of your overall data, it feels like it would be good to know.

@jraffa any thoughts on this conversation? (how to handle missing values for categorical and continuous variables).

[tompollard]

Should be fixed in https://github.com/tompollard/tableone/pull/175, which adds an include_null argument. When include_null=True (the default), missing values are treated as a level of the categorical variable.

! pip install git+https://github.com/tompollard/tableone.git@main

df = pd.DataFrame(
    {'cats': ["1", "2", "3", "4", None, None],
    'set': ["train","train", "val", "val", "val", "val"]}
    )

t = tableone(df, groupby = "set")
print(t.tabulate(headers=None, tablefmt="github"))

Outputs:

		Missing	Overall	train	val
n			6	2	4
cats, n (%)	1		1 (16.7)	1 (50.0)
	2		1 (16.7)	1 (50.0)
	3		1 (16.7)		1 (25.0)
	4		1 (16.7)		1 (25.0)
	None		2 (33.3)		2 (50.0)