A Design Specification for nan_policy#

Many functions in scipy.stats have a parameter called nan_policy that determines how the function handles data that contains nan. In this section, we provide SciPy developer guidelines for how nan_policy is intended to be used, to ensure that as this parameter is added to new functions, we maintain a consistent API.

The basic API#

The parameter nan_policy accepts three possible strings: 'omit', 'raise' and 'propagate'. The meanings are:

  • nan_policy='omit': Ignore occurrences of nan in the input. Do not generate a warning if the input contains nan (unless the equivalent input with the nan values removed would generate a warning). For example, for the simple case of a function that accepts a single array and returns a scalar (and ignoring the possible use of axis for the moment):

    func([1.0, 3.0, np.nan, 5.0], nan_policy='omit')

    should behave the same as:

    func([1.0, 3.0, 5.0])

    More generally, for functions that return a scalar, func(a, nan_policy='omit') should behave the same as func(a[~np.isnan(a)]).

    For functions that transform a vector to a new vector of the same size and for which each entry in the output array depends on more than just the corresponding value in the input array [1] (e.g. scipy.stats.zscore, scipy.stats.boxcox when lmbda is None),:

    y = func(a, nan_policy='omit')

    should behave the same as:

    nan_mask = np.isnan(a)
y = np.empty(a.shape, dtype=np.float64)
y[~nan_mask] = func(a[~nan_mask])
y[nan_mask] = np.nan

    (In general, the dtype of y might depend on a and on the expected behavior of func). In other words, a nan in the input gives a corresponding nan in the output, but the presence of that nan does not affect the calculation of the non-nan values.

    Unit tests for this property should be used to test functions that handle nan_policy.

    For functions that return a scalar and that accept two or more arguments but whose values are not related (e.g. scipy.stats.ansari, scipy.stats.f_oneway), the same idea applies to each input array. So:

    func(a, b, nan_policy='omit')

    should behave the same as:

    func(a[~np.isnan(a)], b[~np.isnan(b)])

    For inputs with related or paired values (e.g. scipy.stats.pearsonr, scipy.stats.ttest_rel) the recommended behavior is to omit all the values for which any of the related values are nan. For a function with two related array inputs, this means:

    y = func(a, b, nan_policy='omit')

    should behave the same as:

    hasnan = np.isnan(a) | np.isnan(b)  # Union of the isnan masks.
y = func(a[~hasnan], b[~hasnan])

    The docstring for such a function should clearly state this behavior.

  • nan_policy='raise': Raise a ValueError.

  • nan_policy='propagate': Propagate the nan value to the output. Typically, this means just execute the function without checking for nan, but see

    for an example where that might lead to unexpected output.

nan_policy combined with an axis parameter#

There is nothing surprising here–the principle mentioned above still applies when the function has an axis parameter. Suppose, for example, func reduces a 1-d array to a scalar, and handles n-d arrays as a collection of 1-d arrays, with the axis parameter specifying the axis along which the reduction is to be applied. If, say:

func([1, 3, 4])     -> 10.0
func([2, -3, 8, 2]) ->  4.2
func([7, 8])        ->  9.5
func([])            -> -inf

then:

func([[  1, nan,   3,   4],
      [  2,  -3,   8,   2],
      [nan,   7, nan,   8],
      [nan, nan, nan, nan]], nan_policy='omit', axis=-1)

must give the result:

np.array([10.0, 4.2, 9.5, -inf])

Edge cases#

A function that implements the nan_policy parameter should gracefully handle the case where all the values in the input array(s) are nan. The basic principle described above still applies:

func([nan, nan, nan], nan_policy='omit')

should behave the same as:

func([])

In practice, when adding nan_policy to an existing function, it is not unusual to find that the function doesn’t already handle this case in a well-defined manner, and some thought and design may have to be applied to ensure that it works. The correct behavior (whether that be to return nan, return some other value, raise an exception, or something else) will be determined on a case-by-case basis.

Why doesn’t nan_policy also apply to inf?#

Although we learn in grade school that “infinity is not a number”, the floating point values nan and inf are qualitatively different. The values inf and -inf act much more like regular floating point values than nan.

  • One can compare inf to other floating point values and it behaves as expected, e.g. 3 < inf is True.

  • For the most part, arithmetic works “as expected” with inf, e.g. inf + inf = inf, -2*inf = -inf, 1/inf = 0, etc.

  • Many existing functions work “as expected” with inf: np.log(inf) = inf, np.exp(-inf) = 0, np.array([1.0, -1.0, np.inf]).min() = -1.0, etc.

So while nan almost always means “something went wrong” or “something is missing”, inf can in many cases be treated as a useful floating point value.

It is also consistent with the NumPy nan functions to not ignore inf:

>>> np.nanmax([1, 2, 3, np.inf, np.nan])
inf
>>> np.nansum([1, 2, 3, np.inf, np.nan])
inf
>>> np.nanmean([8, -np.inf, 9, 1, np.nan])
-inf

How not to implement nan_policy#

In the past (and possibly currently), some stats functions handled nan_policy by using a masked array to mask the nan values, and then computing the result using the functions in the mstats subpackage. The problem with this approach is that the masked array code might convert inf to a masked value, which we don’t want to do (see above). It also means that, if care is not taken, the return value will be a masked array, which will likely be a surprise to the user if they passed in regular arrays.

Footnotes

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