[SciPy-dev] scipy.stats.sem is wrong

Roman Bertle bertle at smoerz.org
Wed Nov 15 05:35:39 CST 2006


Hello,

i think scipy.stats.sem is wrong. It gives the same result as
scipy.stats.stderr (using N-1 and not N), whereas scipy.stats.tsem
uses N and gives the correct result. I have attached a patch correcting
this.

Related to this, i wonder why there are so many related functions in
scipy.stats doing the same, but in a slightly different way. E.g. there
are nanstd, std, tstd, some use numpy.std, some not, some take an axis
argument, some not. And there is samplestd and samplevar, but sampleerr
is called sem instead. Shouldn't these functions be unified somehow?

Regards,

Roman
-------------------------
diff -rud python-scipy-0.5.1/Lib/stats/stats.py python-scipy-0.5.1-new/Lib/stats/stats.py
--- python-scipy-0.5.1/Lib/stats/stats.py	2006-08-29 11:58:37.000000000 +0200
+++ python-scipy-0.5.1-new/Lib/stats/stats.py	2006-11-15 12:18:23.000000000 +0100
@@ -1166,9 +1166,7 @@
 integer (the axis over which to operate)
 """
     a, axis = _chk_asarray(a, axis)
-    n = a.shape[axis]
-    s = samplestd(a,axis) / sqrt(n-1)
-    return s
+    return samplestd(a,axis) / float(sqrt(a.shape[axis]))
 
 
 def z(a, score):
diff -rud python-scipy-0.5.1/Lib/stats/tests/test_stats.py python-scipy-0.5.1-new/Lib/stats/tests/test_stats.py
--- python-scipy-0.5.1/Lib/stats/tests/test_stats.py	2006-08-29 11:58:37.000000000 +0200
+++ python-scipy-0.5.1-new/Lib/stats/tests/test_stats.py	2006-11-15 12:11:29.000000000 +0100
@@ -740,15 +740,16 @@
 ##        assert_approx_equal(y,0.775177399)
         y = scipy.stats.stderr(self.testcase)
         assert_approx_equal(y,0.6454972244)
+
     def check_sem(self):
         """
         this is not in R, so used
-        sqrt(var(testcase)*3/4)/sqrt(3)
+        sqrt(samplevar(testcase))/sqrt(4)
         """
         #y = scipy.stats.sem(self.shoes[0])
         #assert_approx_equal(y,0.775177399)
         y = scipy.stats.sem(self.testcase)
-        assert_approx_equal(y,0.6454972244)
+        assert_approx_equal(y,0.5590169944)
 
     def check_z(self):
         """
-------------------------


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