FIX value_counts should skip NaT

doc/source/v0.14.1.txt

@@ -75,7 +75,7 @@ Enhancements
 
 
 
-
+- Add ``dropna`` argument to ``value_counts`` and ``nunique`` (:issue:`5569`).
 
 
 
@@ -159,7 +159,7 @@ Bug Fixes
 
 
 
-
+- Bug in ``value_counts`` where ``NaT`` did not qualify as missing (``NaN``) (:issue:`7423`) 
 
 
 

pandas/core/algorithms.py

@@ -168,7 +168,7 @@ def factorize(values, sort=False, order=None, na_sentinel=-1):
 
 
 def value_counts(values, sort=True, ascending=False, normalize=False,
-                 bins=None):
+                 bins=None, dropna=True):
     """
     Compute a histogram of the counts of non-null values
 
@@ -184,6 +184,8 @@ def value_counts(values, sort=True, ascending=False, normalize=False,
     bins : integer, optional
         Rather than count values, group them into half-open bins,
         convenience for pd.cut, only works with numeric data
+    dropna : boolean, default False
+        Don't include counts of NaN
 
     Returns
     -------
@@ -202,25 +204,31 @@ def value_counts(values, sort=True, ascending=False, normalize=False,
             raise TypeError("bins argument only works with numeric data.")
         values = cat.labels
 
-    if com.is_integer_dtype(values.dtype):
+    dtype = values.dtype
+    if com.is_integer_dtype(dtype):
         values = com._ensure_int64(values)
         keys, counts = htable.value_count_int64(values)
 
     elif issubclass(values.dtype.type, (np.datetime64, np.timedelta64)):
-        dtype = values.dtype
         values = values.view(np.int64)
         keys, counts = htable.value_count_int64(values)
 
+        if dropna:
+            from pandas.tslib import iNaT
+            msk = keys != iNaT
+            keys, counts = keys[msk], counts[msk]
         # convert the keys back to the dtype we came in
-        keys = Series(keys, dtype=dtype)
+        keys = keys.astype(dtype)
 
     else:
-        mask = com.isnull(values)
         values = com._ensure_object(values)
+        mask = com.isnull(values)
         keys, counts = htable.value_count_object(values, mask)
+        if not dropna:
+            keys = np.insert(keys, 0, np.NaN)
+            counts = np.insert(counts, 0, mask.sum())
 
     result = Series(counts, index=com._values_from_object(keys))
-
     if bins is not None:
         # TODO: This next line should be more efficient
         result = result.reindex(np.arange(len(cat.levels)), fill_value=0)

pandas/core/base.py

@@ -245,7 +245,7 @@ def min(self):
         return pandas.core.nanops.nanmin(self.values)
 
     def value_counts(self, normalize=False, sort=True, ascending=False,
-                     bins=None):
+                     bins=None, dropna=True):
         """
         Returns object containing counts of unique values. The resulting object
         will be in descending order so that the first element is the most
@@ -263,14 +263,16 @@ def value_counts(self, normalize=False, sort=True, ascending=False,
         bins : integer, optional
             Rather than count values, group them into half-open bins,
             a convenience for pd.cut, only works with numeric data
+        dropna : boolean, default False
+            Don't include counts of NaN
 
         Returns
         -------
         counts : Series
         """
         from pandas.core.algorithms import value_counts
         return value_counts(self.values, sort=sort, ascending=ascending,
-                            normalize=normalize, bins=bins)
+                            normalize=normalize, bins=bins, dropna=dropna)
 
     def unique(self):
         """
@@ -284,15 +286,15 @@ def unique(self):
         from pandas.core.nanops import unique1d
         return unique1d(self.values)
 
-    def nunique(self):
+    def nunique(self, dropna=True):
         """
         Return count of unique elements in the object. Excludes NA values.
 
         Returns
         -------
         nunique : int
         """
-        return len(self.value_counts())
+        return len(self.value_counts(dropna=dropna))
 
     def factorize(self, sort=False, na_sentinel=-1):
         """

pandas/tests/test_algos.py

@@ -237,6 +237,19 @@ def test_value_counts_dtypes(self):
 
         self.assertRaises(TypeError, lambda s: algos.value_counts(s, bins=1), ['1', 1])
 
+    def test_value_counts_nat(self):
+        td = Series([np.timedelta64(10000), pd.NaT], dtype='timedelta64[ns]')
+        dt = pd.to_datetime(['NaT', '2014-01-01'])
+
+        for s in [td, dt]:
+            vc = algos.value_counts(s)
+            vc_with_na = algos.value_counts(s, dropna=False)
+            self.assertEqual(len(vc), 1)
+            self.assertEqual(len(vc_with_na), 2)
+
+        exp_dt = pd.Series({pd.Timestamp('2014-01-01 00:00:00'): 1})
+        tm.assert_series_equal(algos.value_counts(dt), exp_dt)
+        # TODO same for (timedelta)
 
 def test_quantile():
     s = Series(np.random.randn(100))

pandas/tests/test_base.py

@@ -292,12 +292,13 @@ def test_value_counts_unique_nunique(self):
                     o = klass(np.repeat(values, range(1, len(o) + 1)))
 
                 if isinstance(o, DatetimeIndex):
-                    # DatetimeIndex: nan is casted to Nat and included
-                    expected_s = Series(list(range(10, 2, -1)) + [3], index=values[9:0:-1])
+                    expected_s_na = Series(list(range(10, 2, -1)) + [3], index=values[9:0:-1])
+                    expected_s = Series(list(range(10, 2, -1)), index=values[9:1:-1])
                 else:
-                    # nan is excluded
-                    expected_s = Series(range(10, 2, -1), index=values[9:1:-1], dtype='int64')
+                    expected_s_na = Series(list(range(10, 2, -1)) +[3], index=values[9:0:-1], dtype='int64')
+                    expected_s = Series(list(range(10, 2, -1)), index=values[9:1:-1], dtype='int64')
 
+                tm.assert_series_equal(o.value_counts(dropna=False), expected_s_na)
                 tm.assert_series_equal(o.value_counts(), expected_s)
 
                 # numpy_array_equal cannot compare arrays includes nan
@@ -309,10 +310,8 @@ def test_value_counts_unique_nunique(self):
                 else:
                     self.assertTrue(pd.isnull(result[0]))
 
-                if isinstance(o, DatetimeIndex):
-                    self.assertEqual(o.nunique(), 9)
-                else:
-                    self.assertEqual(o.nunique(), 8)
+                self.assertEqual(o.nunique(), 8)
+                self.assertEqual(o.nunique(dropna=False), 9)
 
     def test_value_counts_inferred(self):
         klasses = [Index, Series]
@@ -406,6 +405,9 @@ def test_value_counts_inferred(self):
 
             result = s.value_counts()
             self.assertEqual(result.index.dtype, 'datetime64[ns]')
+            tm.assert_series_equal(result, expected_s)
+
+            result = s.value_counts(dropna=False)
             expected_s[pd.NaT] = 1
             tm.assert_series_equal(result, expected_s)
 
@@ -415,7 +417,8 @@ def test_value_counts_inferred(self):
             self.assert_numpy_array_equal(unique[:3], expected)
             self.assertTrue(unique[3] is pd.NaT or unique[3].astype('int64') == pd.tslib.iNaT)
 
-            self.assertEqual(s.nunique(), 4)
+            self.assertEqual(s.nunique(), 3)
+            self.assertEqual(s.nunique(dropna=False), 4)
 
             # timedelta64[ns]
             td = df.dt - df.dt + timedelta(1)

pandas/tseries/tests/test_timeseries.py

@@ -106,16 +106,19 @@ def test_index_unique(self):
         self.assertEqual(result.name, 'foo')
         self.assertTrue(result.equals(expected))
 
-        # NaT
+        # NaT, note this is excluded
         arr = [ 1370745748 + t for t in range(20) ] + [iNaT]
         idx = DatetimeIndex(arr * 3)
         self.assertTrue(idx.unique().equals(DatetimeIndex(arr)))
-        self.assertEqual(idx.nunique(), 21)
+        self.assertEqual(idx.nunique(), 20)
+        self.assertEqual(idx.nunique(dropna=False), 21)
 
         arr = [ Timestamp('2013-06-09 02:42:28') + timedelta(seconds=t) for t in range(20) ] + [NaT]
         idx = DatetimeIndex(arr * 3)
         self.assertTrue(idx.unique().equals(DatetimeIndex(arr)))
-        self.assertEqual(idx.nunique(), 21)
+        self.assertEqual(idx.nunique(), 20)
+        self.assertEqual(idx.nunique(dropna=False), 21)
+
 
     def test_index_dupes_contains(self):
         d = datetime(2011, 12, 5, 20, 30)