[Scipy-svn] r5564 - in trunk/scipy/stats: . tests

[scipy-svn at scipy.org]

Author: josef
Date: 2009-02-18 22:43:39 -0600 (Wed, 18 Feb 2009)
New Revision: 5564

Modified:
   trunk/scipy/stats/stats.py
   trunk/scipy/stats/tests/test_stats.py
Log:
fix removal of var in obrientransform, add regression test

Modified: trunk/scipy/stats/stats.py
===================================================================
--- trunk/scipy/stats/stats.py	2009-02-19 04:30:03 UTC (rev 5563)
+++ trunk/scipy/stats/stats.py	2009-02-19 04:43:39 UTC (rev 5564)
@@ -1232,17 +1232,17 @@
     for i in range(k):
         nargs.append(args[i].astype(float))
         n[i] = float(len(nargs[i]))
-        v[i] = var(nargs[i])
-        m[i] = mean(nargs[i],None)
+        v[i] = np.var(nargs[i], ddof=1)
+        m[i] = np.mean(nargs[i])
     for j in range(k):
-        for i in range(n[j]):
+        for i in range(n[j]):  # raises warning because n[j] is float
             t1 = (n[j]-1.5)*n[j]*(nargs[j][i]-m[j])**2
             t2 = 0.5*v[j]*(n[j]-1.0)
             t3 = (n[j]-1.0)*(n[j]-2.0)
             nargs[j][i] = (t1-t2) / float(t3)
     check = 1
     for j in range(k):
-        if v[j] - mean(nargs[j],None) > TINY:
+        if v[j] - np.mean(nargs[j]) > TINY:
             check = 0
     if check != 1:
         raise ValueError, 'Lack of convergence in obrientransform.'

Modified: trunk/scipy/stats/tests/test_stats.py
===================================================================
--- trunk/scipy/stats/tests/test_stats.py	2009-02-19 04:30:03 UTC (rev 5563)
+++ trunk/scipy/stats/tests/test_stats.py	2009-02-19 04:43:39 UTC (rev 5564)
@@ -1238,6 +1238,15 @@
     assert_equal(v, vc)
     assert_array_almost_equal(sk, skc, decimal=13) #not sure about precision
     assert_array_almost_equal(kurt, kurtc, decimal=13)
+    
+def test_obrientransform():
+    #this is a regression test to check np.var replacement
+    #I didn't separately verigy the numbers
+    x1 = np.arange(5)
+    result = np.array(
+      [[  5.41666667,   1.04166667,  -0.41666667,   1.04166667,  5.41666667],
+       [ 21.66666667,   4.16666667,  -1.66666667,   4.16666667, 21.66666667]])
+    assert_array_almost_equal(stats.obrientransform(x1, 2*x1), result, decimal=8)