[Scipy-svn] r5396 - in trunk/scipy/stats: . tests

[scipy-svn at scipy.org]

Author: cdavid
Date: 2009-01-08 06:38:03 -0600 (Thu, 08 Jan 2009)
New Revision: 5396

Modified:
   trunk/scipy/stats/morestats.py
   trunk/scipy/stats/stats.py
   trunk/scipy/stats/tests/test_stats.py
Log:
Do not use scipy.stats.std anymore.

Modified: trunk/scipy/stats/morestats.py
===================================================================
--- trunk/scipy/stats/morestats.py	2009-01-08 12:37:43 UTC (rev 5395)
+++ trunk/scipy/stats/morestats.py	2009-01-08 12:38:03 UTC (rev 5396)
@@ -502,7 +502,7 @@
     xbar = np.mean(x, axis=0)
     N = len(y)
     if dist == 'norm':
-        s = stats.std(x)
+        s = np.std(x, ddof=1, axis=0)
         w = (y-xbar)/s
         z = distributions.norm.cdf(w)
         sig = array([15,10,5,2.5,1])
@@ -520,7 +520,7 @@
             val = [sum(1.0/(1+tmp2),axis=0)-0.5*N,
                    sum(tmp*(1.0-tmp2)/(1+tmp2),axis=0)+N]
             return array(val)
-        sol0=array([xbar,stats.std(x)])
+        sol0=array([xbar,np.std(x, ddof=1, axis=0)])
         sol = optimize.fsolve(rootfunc,sol0,args=(x,N),xtol=1e-5)
         w = (y-sol[0])/sol[1]
         z = distributions.logistic.cdf(w)

Modified: trunk/scipy/stats/stats.py
===================================================================
--- trunk/scipy/stats/stats.py	2009-01-08 12:37:43 UTC (rev 5395)
+++ trunk/scipy/stats/stats.py	2009-01-08 12:38:03 UTC (rev 5396)
@@ -1304,7 +1304,7 @@
 the passed array (i.e., N-1).  Axis can equal None (ravel array
 first), or an integer (the axis over which to operate).
 """
-    warnings.warn("""\
+    raise DeprecationWarning("""\
 scipy.stats.std is deprecated; please update your code to use numpy.std.
 Please note that:
     - numpy.std axis argument defaults to None, not 0
@@ -1321,7 +1321,7 @@
 first), or an integer (the axis over which to operate).
 """
     a, axis = _chk_asarray(a, axis)
-    return std(a,axis) / float(np.sqrt(a.shape[axis]))
+    return np.std(a,axis,ddof=1) / float(np.sqrt(a.shape[axis]))
 
 
 def sem(a, axis=0):

Modified: trunk/scipy/stats/tests/test_stats.py
===================================================================
--- trunk/scipy/stats/tests/test_stats.py	2009-01-08 12:37:43 UTC (rev 5395)
+++ trunk/scipy/stats/tests/test_stats.py	2009-01-08 12:38:03 UTC (rev 5396)
@@ -109,7 +109,7 @@
         assert_almost_equal(y, 5.0)
 
     def test_stdX(self):
-        y = stats.std(X)
+        y = np.std(X, ddof=1)
         assert_almost_equal(y, 2.738612788)
 
     def test_tmeanX(self):
@@ -129,7 +129,7 @@
         assert_almost_equal(y, 0.0)
 
     def test_stdZERO(self):
-        y = stats.std(ZERO)
+        y = np.std(ZERO, ddof=1)
         assert_almost_equal(y, 0.0)
 
 ##    Really need to write these tests to handle missing values properly
@@ -147,7 +147,7 @@
         assert_almost_equal(y, 99999995.00)
 
     def test_stdBIG(self):
-        y = stats.std(BIG)
+        y = np.std(BIG, ddof=1)
         assert_almost_equal(y, 2.738612788)
 
     def test_meanLITTLE(self):
@@ -155,7 +155,7 @@
         assert_approx_equal(y, 0.999999950)
 
     def test_stdLITTLE(self):
-        y = stats.std(LITTLE)
+        y = np.std(LITTLE, ddof=1)
         assert_approx_equal(y, 2.738612788e-8)
 
     def test_meanHUGE(self):
@@ -163,7 +163,7 @@
         assert_approx_equal(y, 5.00000e+12)
 
     def test_stdHUGE(self):
-        y = stats.std(HUGE)
+        y = np.std(HUGE, ddof=1)
         assert_approx_equal(y, 2.738612788e12)
 
     def test_meanTINY(self):
@@ -171,7 +171,7 @@
         assert_almost_equal(y, 0.0)
 
     def test_stdTINY(self):
-        y = stats.std(TINY)
+        y = np.std(TINY, ddof=1)
         assert_almost_equal(y, 0.0)
 
     def test_meanROUND(self):
@@ -179,7 +179,7 @@
         assert_approx_equal(y, 4.500000000)
 
     def test_stdROUND(self):
-        y = stats.std(ROUND)
+        y = np.std(ROUND, ddof=1)
         assert_approx_equal(y, 2.738612788)
 
 class TestNanFunc(TestCase):
@@ -213,12 +213,12 @@
     def test_nanstd_none(self):
         """Check nanstd when no values are nan."""
         s = stats.nanstd(self.X)
-        assert_approx_equal(s, stats.std(self.X))
+        assert_approx_equal(s, np.std(self.X, ddof=1))
 
     def test_nanstd_some(self):
         """Check nanstd when some values only are nan."""
         s = stats.nanstd(self.Xsome)
-        assert_approx_equal(s, stats.std(self.Xsomet))
+        assert_approx_equal(s, np.std(self.Xsomet, ddof=1))
 
     def test_nanstd_all(self):
         """Check nanstd when all values are nan."""
@@ -655,8 +655,8 @@
     def test_basic(self):
         a = [3,4,5,10,-3,-5,6]
         b = [3,4,5,10,-3,-5,-6]
-        assert_almost_equal(stats.std(a),5.2098807225172772,11)
-        assert_almost_equal(stats.std(b),5.9281411203561225,11)
+        assert_almost_equal(np.std(a, ddof=1),5.2098807225172772,11)
+        assert_almost_equal(np.std(b, ddof=1),5.9281411203561225,11)
 
     def test_2d(self):
         a = [[1.0, 2.0, 3.0],
@@ -665,9 +665,8 @@
         b1 = array((3.7859388972001824, 5.2915026221291814,
                     2.0816659994661335))
         b2 = array((1.0,2.0,2.64575131106))
-        assert_array_almost_equal(stats.std(a),b1,11)
-        assert_array_almost_equal(stats.std(a,axis=0),b1,11)
-        assert_array_almost_equal(stats.std(a,axis=1),b2,11)
+        assert_array_almost_equal(np.std(a,ddof=1,axis=0),b1,11)
+        assert_array_almost_equal(np.std(a,ddof=1,axis=1),b2,11)
 
 
 class TestCMedian(TestCase):
@@ -713,7 +712,7 @@
     """
     testcase = [1,2,3,4]
     def test_std(self):
-        y = stats.std(self.testcase)
+        y = np.std(self.testcase, ddof=1)
         assert_approx_equal(y,1.290994449)
 
     def test_var(self):