python - NumPy or Pandas: Keeping array type as integer while having a NaN value

NaN can't be stored in an integer array. This is a known limitation of pandas at the moment; I have been waiting for progress to be made with NA values in NumPy (similar to NAs in R), but it will be at least 6 months to a year before NumPy gets these features, it seems:

http://pandas.pydata.org/pandas-docs/stable/gotchas.html#support-for-integer-na

(This feature has been added beginning with version 0.24 of pandas, but note it requires the use of extension dtype Int64 (capitalized), rather than the default dtype int64 (lower case): https://pandas.pydata.org/pandas-docs/version/0.24/whatsnew/v0.24.0.html#optional-integer-na-support )

This capability has been added to pandas (beginning with version 0.24): https://pandas.pydata.org/pandas-docs/version/0.24/whatsnew/v0.24.0.html#optional-integer-na-support

At this point, it requires the use of extension dtype Int64 (capitalized), rather than the default dtype int64 (lowercase).

If performance is not the main issue, you can store strings instead.

df.col = df.col.dropna().apply(lambda x: str(int(x)) ) 

Then you can mix then with NaN as much as you want. If you really want to have integers, depending on your application, you can use -1, or 0, or 1234567890, or some other dedicated value to represent NaN.

You can also temporarily duplicate the columns: one as you have, with floats; the other one experimental, with ints or strings. Then inserts asserts in every reasonable place checking that the two are in sync. After enough testing you can let go of the floats.

This is not a solution for all cases, but mine (genomic coordinates) I've resorted to using 0 as NaN

a3['MapInfo'] = a3['MapInfo'].fillna(0).astype(int) 

This at least allows for the proper 'native' column type to be used, operations like subtraction, comparison etc work as expected

Pandas v0.24+

Functionality to support NaN in integer series will be available in v0.24 upwards. There's information on this in the v0.24 "What's New" section, and more details under Nullable Integer Data Type.

Pandas v0.23 and earlier

In general, it's best to work with float series where possible, even when the series is upcast from int to float due to inclusion of NaN values. This enables vectorised NumPy-based calculations where, otherwise, Python-level loops would be processed.

The docs do suggest : "One possibility is to use dtype=object arrays instead." For example:

s = pd.Series([1, 2, 3, np.nan])  print(s.astype(object))  0      1 1      2 2      3 3    NaN dtype: object 

For cosmetic reasons, e.g. output to a file, this may be preferable.

Pandas v0.23 and earlier: background

NaN is considered a float. The docs currently (as of v0.23) specify the reason why integer series are upcasted to float:

In the absence of high performance NA support being built into NumPy from the ground up, the primary casualty is the ability to represent NAs in integer arrays.

This trade-off is made largely for memory and performance reasons, and also so that the resulting Series continues to be “numeric”.

The docs also provide rules for upcasting due to NaN inclusion:

Typeclass   Promotion dtype for storing NAs floating    no change object      no change integer     cast to float64 boolean     cast to object