.. currentmodule:: pandas .. _gotchas: .. ipython:: python :suppress: import os import numpy as np from pandas import * randn = np.random.randn np.set_printoptions(precision=4, suppress=True) ******************* Caveats and Gotchas ******************* ``NaN``, Integer ``NA`` values and ``NA`` type promotions --------------------------------------------------------- Choice of ``NA`` representation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For lack of ``NA`` (missing) support from the ground up in NumPy and Python in general, we were given the difficult choice between either - A *masked array* solution: an array of data and an array of boolean values indicating whether a value - Using a special sentinel value, bit pattern, or set of sentinel values to denote ``NA`` across the dtypes For many reasons we chose the latter. After years of production use it has proven, at least in my opinion, to be the best decision given the state of affairs in NumPy and Python in general. The special value ``NaN`` (Not-A-Number) is used everywhere as the ``NA`` value, and there are API functions ``isnull`` and ``notnull`` which can be used across the dtypes to detect NA values. However, it comes with it a couple of trade-offs which I most certainly have not ignored. Support for integer ``NA`` ~~~~~~~~~~~~~~~~~~~~~~~~~~ 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. For example: .. ipython:: python s = Series([1, 2, 3, 4, 5], index=list('abcde')) s s.dtype s2 = s.reindex(['a', 'b', 'c', 'f', 'u']) s2 s2.dtype This trade-off is made largely for memory and performance reasons, and also so that the resulting Series continues to be "numeric". One possibility is to use ``dtype=object`` arrays instead. ``NA`` type promotions ~~~~~~~~~~~~~~~~~~~~~~ When introducing NAs into an existing Series or DataFrame via ``reindex`` or some other means, boolean and integer types will be promoted to a different dtype in order to store the NAs. These are summarized by this table: .. csv-table:: :header: "Typeclass","Promotion dtype for storing NAs" :widths: 40,60 ``floating``, no change ``object``, no change ``integer``, cast to ``float64`` ``boolean``, cast to ``object`` While this may seem like a heavy trade-off, in practice I have found very few cases where this is an issue in practice. Some explanation for the motivation here in the next section. Why not make NumPy like R? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Many people have suggested that NumPy should simply emulate the ``NA`` support present in the more domain-specific statistical programming langauge `R `__. Part of the reason is the NumPy type hierarchy: .. csv-table:: :header: "Typeclass","Dtypes" :widths: 30,70 :delim: | ``numpy.floating`` | ``float16, float32, float64, float128`` ``numpy.integer`` | ``int8, int16, int32, int64`` ``numpy.unsignedinteger`` | ``uint8, uint16, uint32, uint64`` ``numpy.object_`` | ``object_`` ``numpy.bool_`` | ``bool_`` ``numpy.character`` | ``string_, unicode_`` The R language, by contrast, only has a handful of built-in data types: ``integer``, ``numeric`` (floating-point), ``character``, and ``boolean``. ``NA`` types are implemented by reserving special bit patterns for each type to be used as the missing value. While doing this with the full NumPy type hierarchy would be possible, it would be a more substantial trade-off (especially for the 8- and 16-bit data types) and implementation undertaking. An alternate approach is that of using masked arrays. A masked array is an array of data with an associated boolean *mask* denoting whether each value should be considered ``NA`` or not. I am personally not in love with this approach as I feel that overall it places a fairly heavy burden on the user and the library implementer. Additionally, it exacts a fairly high performance cost when working with numerical data compared with the simple approach of using ``NaN``. Thus, I have chosen the Pythonic "practicality beats purity" approach and traded integer ``NA`` capability for a much simpler approach of using a special value in float and object arrays to denote ``NA``, and promoting integer arrays to floating when NAs must be introduced. Integer indexing ---------------- Label-based indexing with integer axis labels is a thorny topic. It has been discussed heavily on mailing lists and among various members of the scientific Python community. In pandas, our general viewpoint is that labels matter more than integer locations. Therefore, with an integer axis index *only* label-based indexing is possible with the standard tools like ``.ix``. The following code will generate exceptions: .. code-block:: python s = Series(range(5)) s[-1] df = DataFrame(np.random.randn(5, 4)) df df.ix[-2:] This deliberate decision was made to prevent ambiguities and subtle bugs (many users reported finding bugs when the API change was made to stop "falling back" on position-based indexing). Label-based slicing conventions ------------------------------- Non-monotonic indexes require exact matches ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Endpoints are inclusive ~~~~~~~~~~~~~~~~~~~~~~~ Compared with standard Python sequence slicing in which the slice endpoint is not inclusive, label-based slicing in pandas **is inclusive**. The primary reason for this is that it is often not possible to easily determine the "successor" or next element after a particular label in an index. For example, consider the following Series: .. ipython:: python s = Series(randn(6), index=list('abcdef')) s Suppose we wished to slice from ``c`` to ``e``, using integers this would be .. ipython:: python s[2:5] However, if you only had ``c`` and ``e``, determining the next element in the index can be somewhat complicated. For example, the following does not work: :: s.ix['c':'e'+1] A very common use case is to limit a time series to start and end at two specific dates. To enable this, we made the design design to make label-based slicing include both endpoints: .. ipython:: python s.ix['c':'e'] This is most definitely a "practicality beats purity" sort of thing, but it is something to watch out for if you expect label-based slicing to behave exactly in the way that standard Python integer slicing works. Miscellaneous indexing gotchas ------------------------------ Reindex versus ix gotchas ~~~~~~~~~~~~~~~~~~~~~~~~~ Many users will find themselves using the ``ix`` indexing capabilities as a concise means of selecting data from a pandas object: .. ipython:: python df = DataFrame(randn(6, 4), columns=['one', 'two', 'three', 'four'], index=list('abcdef')) df df.ix[['b', 'c', 'e']] This is, of course, completely equivalent *in this case* to using th ``reindex`` method: .. ipython:: python df.reindex(['b', 'c', 'e']) Some might conclude that ``ix`` and ``reindex`` are 100% equivalent based on this. This is indeed true **except in the case of integer indexing**. For example, the above operation could alternately have been expressed as: .. ipython:: python df.ix[[1, 2, 4]] If you pass ``[1, 2, 4]`` to ``reindex`` you will get another thing entirely: .. ipython:: python df.reindex([1, 2, 4]) So it's important to remember that ``reindex`` is **strict label indexing only**. This can lead to some potentially surprising results in pathological cases where an index contains, say, both integers and strings: .. ipython:: python s = Series([1, 2, 3], index=['a', 0, 1]) s s.ix[[0, 1]] s.reindex([0, 1]) Because the index in this case does not contain solely integers, ``ix`` falls back on integer indexing. By contrast, ``reindex`` only looks for the values passed in the index, thus finding the integers ``0`` and ``1``. While it would be possible to insert some logic to check whether a passed sequence is all contained in the index, that logic would exact a very high cost in large data sets. Timestamp limitations --------------------- Minimum and maximum timestamps ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Since pandas represents timestamps in nanosecond resolution, the timespan that can be represented using a 64-bit integer is limited to approximately 584 years: .. ipython:: python begin = Timestamp(-9223285636854775809L) begin end = Timestamp(np.iinfo(np.int64).max) end If you need to represent time series data outside the nanosecond timespan, use PeriodIndex: .. ipython:: python span = period_range('1215-01-01', '1381-01-01', freq='D') span Parsing Dates from Text Files ----------------------------- When parsing multiple text file columns into a single date column, the new date column is prepended to the data and then `index_col` specification is indexed off of the new set of columns rather than the original ones: .. ipython:: python :suppress: data = ("KORD,19990127, 19:00:00, 18:56:00, 0.8100\n" "KORD,19990127, 20:00:00, 19:56:00, 0.0100\n" "KORD,19990127, 21:00:00, 20:56:00, -0.5900\n" "KORD,19990127, 21:00:00, 21:18:00, -0.9900\n" "KORD,19990127, 22:00:00, 21:56:00, -0.5900\n" "KORD,19990127, 23:00:00, 22:56:00, -0.5900") with open('tmp.csv', 'w') as fh: fh.write(data) .. ipython:: python print open('tmp.csv').read() date_spec = {'nominal': [1, 2], 'actual': [1, 3]} df = read_csv('tmp.csv', header=None, parse_dates=date_spec, keep_date_col=True, index_col=0) # index_col=0 refers to the combined column "nominal" and not the original # first column of 'KORD' strings df .. ipython:: python :suppress: os.remove('tmp.csv') Differences with NumPy ---------------------- For Series and DataFrame objects, ``var`` normalizes by ``N-1`` to produce unbiased estimates of the sample variance, while NumPy's ``var`` normalizes by N, which measures the variance of the sample. Note that ``cov`` normalizes by ``N-1`` in both pandas and NumPy.